├── .gitignore ├── LICENSE ├── NORMA.Rproj ├── README.md ├── functions ├── annotations.R ├── helpDownloadHandlers.R ├── network.R ├── refreshing │ ├── convex_hulls_3D.R │ └── modularity.R ├── topology.R └── upload.R ├── global.R ├── server.R ├── ui.R ├── user_temp └── folder_create ├── views ├── about.R ├── annotations.R ├── help.R ├── network.R ├── topology.R ├── upload.R └── welcome.R └── www ├── Examples ├── BCAR3 │ ├── BCAR3.txt │ ├── BCAR3_GO_BP.txt │ ├── BCAR3_GO_MF.txt │ └── BCAR3_KEGG.txt ├── BioGrid_Chicken_Gallus │ ├── BioGrid_Chicken_Gallus_Pathways_KEGG_PATHWAY_FILTERED.txt │ └── Biogrid_no_self_loops.txt ├── Human_Coexpression │ ├── NORMA_Human_coexpression_Annotation_GO_BP.txt │ ├── NORMA_Human_coexpression_Annotation_GO_CC.txt │ ├── NORMA_Human_coexpression_Annotation_GO_MF.txt │ ├── NORMA_Human_coexpression_Annotation_KEGG.txt │ ├── NORMA_Human_coexpression_Expression_MCODE.txt │ └── NORMA_Human_coexpression_NETWORK.txt ├── IntAct_COVID19 │ ├── HomoSapiens_Gene_Ontology_GOTERM_BP_DIRECT_FILTERED.txt │ ├── HomoSapiens_Gene_Ontology_GOTERM_CC_DIRECT_FILTERED.txt │ ├── HomoSapiens_Gene_Ontology_GOTERM_MF_DIRECT_FILTERED.txt │ ├── HomoSapiens_Pathways_KEGG_PATHWAY_FILTERED.txt │ ├── HomoSapiens_Protein_Domains_INTERPRO_FILTERED.txt │ ├── HomoSapiens_Protein_Domains_SMART_FILTERED.txt │ └── Intact-data_COVID19_no_self_loops.txt ├── TAU │ ├── TAU_KEGG_Annotation_NORMA.txt │ ├── TAU_Louvain.txt │ ├── TAU_expressions.txt │ └── TAU_network_DEGs_NORMA.txt └── TP53 │ ├── string_expression_colors.txt │ ├── string_interactions.txt │ └── string_interactions_groups_comma_duplicate.txt ├── Figures ├── Banner.png ├── Community_detection_algorithms.png ├── Convex_Hulls.PNG ├── Convex_Hulls_3D.PNG ├── Expression_colors.png ├── Network_view_interactive.png ├── Pies.PNG ├── Strategy_1.png ├── Strategy_2.png ├── Strategy_3.png ├── Topology.PNG ├── Topology_comparisons.PNG ├── Upload-1.png ├── Upload-2.png ├── Upload-3.png └── venn.png ├── annot_table.css ├── annotation_cleaner.R ├── favicon.ico ├── intro.css ├── intro.js ├── introbutton.js └── norma.css /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | 5 | # Session Data files 6 | .RData 7 | 8 | # User-specific files 9 | .Ruserdata 10 | 11 | # Example code in package build process 12 | *-Ex.R 13 | 14 | # Output files from R CMD build 15 | /*.tar.gz 16 | 17 | # Output files from R CMD check 18 | /*.Rcheck/ 19 | 20 | # RStudio files 21 | .Rproj.user/ 22 | 23 | # produced vignettes 24 | vignettes/*.html 25 | vignettes/*.pdf 26 | 27 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 28 | .httr-oauth 29 | 30 | # knitr and R markdown default cache directories 31 | *_cache/ 32 | /cache/ 33 | 34 | # Temporary files created by R markdown 35 | *.utf8.md 36 | *.knit.md 37 | 38 | # R Environment Variables 39 | .Renviron 40 | 41 | user_temp/*.html 42 | user_temp/*.rda 43 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 g.pavlopoulos 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /NORMA.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | [![R-CMD-check](https://github.com/yourusername/NORMA/workflows/R-CMD-check/badge.svg)](https://github.com/yourusername/NORMA/actions) 4 | [![Shiny App](https://img.shields.io/badge/Shiny-online-brightgreen)](https://pavlopoulos-lab-services.org/shiny/app/norma) 5 | [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) 6 | 7 | # NORMA: The Network Makeup Artist 8 | 9 | > A web tool for interactive network annotation visualization and topological analysis. 10 | 11 | --- 12 | 13 | ## 📖 Table of Contents 14 | 15 | 1. [Overview](#overview) 16 | 2. [Key Features](#key-features) 17 | 3. [Installation](#installation) 18 | 4. [Usage](#usage) 19 | 5. [Input Formats](#input-formats) 20 | 6. [Examples & Demo Data](#examples--demo-data) 21 | 7. [Contact & Support](#contact--support) 22 | 8. [Publications](#publications) 23 | 9. [License](#license) 24 | 25 | --- 26 | 27 | ## 📝 Overview 28 | 29 | NORMA (Network Makeup Artist) is a Shiny-based web application that lets you: 30 | 31 | * **Visualize** multiple networks and their annotations (e.g., GO terms, pathway enrichments) 32 | * **Overlay** annotations as pie-chart nodes or convex-hull “venn” shapes 33 | * **Detect** communities automatically when no annotations are provided 34 | * **Refine** layouts for optimal group separation with common graph algorithms 35 | * **Highlight** and export publication-quality figures interactively 36 | * **Compare** network topology metrics across different datasets 37 | 38 | --- 39 | 40 | ## 🚀 Key Features 41 | 42 | * **Multi-network support**: Load and visualize several networks side by side. 43 | * **Annotation overlays**: 44 | 45 | * **Pie-chart nodes** for multi-category annotations 46 | * **Convex-hulls** for set-overlap style visualization 47 | * **Community detection**: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping. 48 | * **Flexible layouts**: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more. 49 | * **Interactive figure export**: Customize colors, sizes, labels; download as PNG or PDF. 50 | * **Topological analysis**: Compute degree, clustering coefficient, betweenness, etc., and compare across networks. 51 | 52 | --- 53 | 54 | ## 🛠 Installation 55 | 56 | 1. **Install R** (≥4.0) 57 | 2. **Install RStudio** (optional, but recommended) 58 | 3. **Clone this repo** 59 | 60 | ```bash 61 | git clone https://github.com/yourusername/NORMA.git 62 | cd NORMA 63 | ``` 64 | 4. **Install required packages** 65 | 66 | ```r 67 | # From your R console: 68 | install.packages(c( 69 | "shiny", "igraph", "visNetwork", "plotly", 70 | "data.table", "DT", "RColorBrewer" 71 | )) 72 | ``` 73 | 5. **Run the app** 74 | 75 | ```r 76 | # In RStudio or R console: 77 | shiny::runApp("path/to/NORMA") 78 | ``` 79 | 80 | --- 81 | 82 | ## 💻 Usage 83 | 84 | * **Online demo**: [Launch NORMA in your browser](https://pavlopoulos-lab-services.org/shiny/app/norma) 85 | * **Local**: Once the app is running, use the sidebar to upload: 86 | 87 | * **Network file** (edge list or adjacency) 88 | * **Annotation file** (tab-delimited with node → category) 89 | * Toggle between “Pie-chart nodes” and “Convex-hulls” in **Visualization**. 90 | * Explore **Layout**, **Annotation**, and **Analysis** tabs for customization. 91 | 92 | --- 93 | 94 | ## 📂 Input Formats 95 | 96 | * **Network**: 97 | 98 | * Edge list: `sourcetarget` 99 | * Adjacency matrix: CSV or TSV 100 | * **Annotations**: 101 | 102 | * Plain table: 103 | 104 | ```text 105 | node_idcategory1,category2,... 106 | ``` 107 | * See the **Help → Input File** tab in the app for detailed examples. 108 | 109 | --- 110 | 111 | ## 📊 Examples & Demo Data 112 | 113 | Download sample networks and annotation sets from the app’s **Help → Examples** tab or directly from our website. These include: 114 | 115 | * Human protein–protein interaction subnetworks 116 | * GO term enrichment outputs for test datasets 117 | * Synthetic networks demonstrating overlapping modules 118 | 119 | --- 120 | 121 | ## 📬 Contact & Support 122 | 123 | For questions, issues, or feature requests, please email: 124 | 125 | > **George A. Pavlopoulos** 126 | > [pavlopoulos@fleming.gr](mailto:pavlopoulos@fleming.gr) 127 | 128 | Or open an issue on GitHub: 129 | [https://github.com/yourusername/NORMA/issues](https://github.com/yourusername/NORMA/issues) 130 | 131 | --- 132 | 133 | ## 📚 Publications 134 | 135 | * **NORMA: The Network Makeup Artist** 136 | Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A. 137 | *Genomics, Proteomics & Bioinformatics*. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24. 138 | doi: [10.1016/j.gpb.2021.02.005](https://doi.org/10.1016/j.gpb.2021.02.005) 139 | PMID: [34171457](https://pubmed.ncbi.nlm.nih.gov/34171457/) 140 | 141 | * **The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies** 142 | Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A. 143 | *Bioinformatics Advances*. 2022 May 13;2(1)\:vbac036. 144 | doi: [10.1093/bioadv/vbac036](https://doi.org/10.1093/bioadv/vbac036) 145 | PMID: [36699373](https://pubmed.ncbi.nlm.nih.gov/36699373/) 146 | 147 | --- 148 | 149 | ## 📄 License 150 | 151 | This project is licensed under the **MIT License** – see the [LICENSE](LICENSE) file for details. 152 | -------------------------------------------------------------------------------- /functions/helpDownloadHandlers.R: -------------------------------------------------------------------------------- 1 | # Help pages - Download Example files #### 2 | output$dros_net <- downloadHandler( 3 | filename = function() { 4 | paste('Drosophila (TAU) Network file', '.txt', sep = '') 5 | }, 6 | content = function(file) { 7 | write.table(dros_net, file, row.names = F, sep = "\t", quote = F) 8 | } 9 | ) 10 | output$dros_annot <- downloadHandler( 11 | filename = function() { 12 | paste('Drosophila KEGG pathways', '.txt', sep = '') 13 | }, 14 | content = function(file) { 15 | write.table(dros_annot, file,row.names = F, col.names = F, sep = "\t", quote = F) 16 | } 17 | ) 18 | output$dros_louvain <- downloadHandler( 19 | filename = function() { 20 | paste('Drosophila Louvain automated annotation', '.txt', sep = '') 21 | }, 22 | content = function(file) { 23 | write.table(dros_louvain, file,row.names = F, col.names = F, sep = "\t", quote = F) 24 | } 25 | ) 26 | output$dros_express <- downloadHandler( 27 | filename = function() { 28 | paste('Drosophila Expressions file', '.txt', sep = '') 29 | }, 30 | content = function(file) { 31 | write.table(dros_express, file,row.names = F, col.names = F, sep = "\t", quote = F) 32 | } 33 | ) 34 | 35 | #-------------------------------------------# 36 | 37 | output$string_net_tp53 <- downloadHandler( 38 | filename = function() { 39 | paste('STRING TP53 Network file', '.txt', sep = '') 40 | }, 41 | content = function(file) { 42 | write.table(string_net_tp53, file, row.names = F, sep = "\t", quote = F) 43 | } 44 | ) 45 | output$string_annot <- downloadHandler( 46 | filename = function() { 47 | paste('STRING TP53 Annotation file', '.txt', sep = '') 48 | }, 49 | content = function(file) { 50 | write.table(string_annot, file, row.names = F,col.names = F, sep = "\t", quote = F) 51 | } 52 | ) 53 | output$string_expr <- downloadHandler( 54 | filename = function() { 55 | paste('STRING TP53 Expression file', '.txt', sep = '') 56 | }, 57 | content = function(file) { 58 | write.table(string_expr, file, row.names = F,col.names = F, sep = "\t", quote = F) 59 | } 60 | ) 61 | 62 | #-------------------------------------------# 63 | 64 | output$string_net_bcar3 <- downloadHandler( 65 | filename = function() { 66 | paste('STRING BCAR3 Network file', '.txt', sep = '') 67 | }, 68 | content = function(file) { 69 | write.table(string_net_bcar3, file, row.names = F, sep = "\t", quote = F) 70 | } 71 | ) 72 | output$string_bp <- downloadHandler( 73 | filename = function() { 74 | paste('STRING BCAR3 GO Biological Processes file', '.txt', sep = '') 75 | }, 76 | content = function(file) { 77 | write.table(string_bp, file, row.names = F,col.names = F, sep = "\t", quote = F) 78 | } 79 | ) 80 | output$string_mf <- downloadHandler( 81 | filename = function() { 82 | paste('STRING BCAR3 GO Molecular functions file', '.txt', sep = '') 83 | }, 84 | content = function(file) { 85 | write.table(string_mf, file, row.names = F,col.names = F, sep = "\t", quote = F) 86 | } 87 | ) 88 | output$string_kegg <- downloadHandler( 89 | filename = function() { 90 | paste('STRING BCAR3 GO KEGG file', '.txt', sep = '') 91 | }, 92 | content = function(file) { 93 | write.table(string_kegg, file, row.names = F,col.names = F, sep = "\t", quote = F) 94 | } 95 | ) 96 | 97 | #-------------------------------------------# 98 | 99 | output$co_express <- downloadHandler( 100 | filename = function() { 101 | paste('Human Gene Co-expression Network file', '.txt', sep = '') 102 | }, 103 | content = function(file) { 104 | write.table(co_express, file, row.names = F, sep = "\t", quote = F) 105 | } 106 | ) 107 | output$co_express_bp <- downloadHandler( 108 | filename = function() { 109 | paste('Human Gene Co-expression GO Biological Processes file', '.txt', sep = '') 110 | }, 111 | content = function(file) { 112 | write.table(co_express_bp, file,row.names = F,col.names = F, sep = "\t", quote = F) 113 | } 114 | ) 115 | output$co_express_mf <- downloadHandler( 116 | filename = function() { 117 | paste('Human Gene Co-expression GO Molecura functions file', '.txt', sep = '') 118 | }, 119 | content = function(file) { 120 | write.table(co_express_mf, file,row.names = F,col.names = F, sep = "\t", quote = F) 121 | } 122 | ) 123 | output$co_express_cc <- downloadHandler( 124 | filename = function() { 125 | paste('Human Gene Co-expression Cellular Componets file', '.txt', sep = '') 126 | }, 127 | content = function(file) { 128 | write.table(co_express_cc, file,row.names = F,col.names = F, sep = "\t", quote = F) 129 | } 130 | ) 131 | output$co_express_kegg <- downloadHandler( 132 | filename = function() { 133 | paste('Human Gene Co-expression KEGG pathways file', '.txt', sep = '') 134 | }, 135 | content = function(file) { 136 | write.table(co_express_kegg, file,row.names = F,col.names = F, sep = "\t", quote = F) 137 | } 138 | ) 139 | output$co_express_mcode <- downloadHandler( 140 | filename = function() { 141 | paste('Human Gene Co-expression MCODE node coloring file', '.txt', sep = '') 142 | }, 143 | content = function(file) { 144 | write.table(co_express_mcode, file,row.names = F,col.names = F, sep = "\t", quote = F) 145 | } 146 | ) 147 | #-----------------------------------------------------------------------------# 148 | 149 | output$covid_19_net <- downloadHandler( 150 | filename = function() { 151 | paste('COVID-19 Network file', '.txt', sep = '') 152 | }, 153 | content = function(file) { 154 | write.table(covid_19_net, file, row.names = F, quote = F, sep = "\t") 155 | } 156 | ) 157 | output$covid_19_interpro <- downloadHandler( 158 | filename = function() { 159 | paste('HomoSapiens Protein Domains - INTERPRO file', '.txt', sep = '') 160 | }, 161 | content = function(file) { 162 | write.table(covid_19_interpro, file, row.names = F, col.names= F, quote = F, sep = "\t") 163 | } 164 | ) 165 | output$covid_19_bp <- downloadHandler( 166 | filename = function() { 167 | paste('HomoSapiens GO Annotation - Biological Process file', '.txt', sep = '') 168 | }, 169 | content = function(file) { 170 | write.table(covid_19_bp, file, row.names = F, col.names= F, quote = F, sep = "\t") 171 | } 172 | ) 173 | output$covid_19_mf <- downloadHandler( 174 | filename = function() { 175 | paste('HomoSapiens GO Annotation - Molecular Function file', '.txt', sep = '') 176 | }, 177 | content = function(file) { 178 | write.table(covid_19_mf, file, row.names = F, col.names= F, quote = F, sep = "\t") 179 | } 180 | ) 181 | output$covid_19_cc <- downloadHandler( 182 | filename = function() { 183 | paste('HomoSapiens Protein Domains GO Annotation - Cellular Components file', '.txt', sep = '') 184 | }, 185 | content = function(file) { 186 | write.table(covid_19_cc, file, row.names = F, col.names= F, quote = F, sep = "\t") 187 | } 188 | ) 189 | output$covid_19_kegg <- downloadHandler( 190 | filename = function() { 191 | paste('HomoSapiens Protein Domains KEGG pathways file', '.txt', sep = '') 192 | }, 193 | content = function(file) { 194 | write.table(covid_19_kegg, file, row.names = F, col.names= F, quote = F, sep = "\t") 195 | } 196 | ) 197 | output$covid_19_smart <- downloadHandler( 198 | filename = function() { 199 | paste('HomoSapiens Protein Domains SMART file', '.txt', sep = '') 200 | }, 201 | content = function(file) { 202 | write.table(covid_19_smart, file, row.names = F, col.names= F, quote = F, sep = "\t") 203 | } 204 | ) 205 | 206 | #-----------------------------------------------------------------------------# 207 | 208 | output$Gallus_gallus_net <- downloadHandler( 209 | filename = function() { 210 | paste('Gallus gallus Network file', '.txt', sep = '') 211 | }, 212 | content = function(file) { 213 | write.table(Gallus_gallus_net, file,row.names = F, quote = F, sep = "\t") 214 | } 215 | ) 216 | output$Gallus_gallus_kegg <- downloadHandler( 217 | filename = function() { 218 | paste('BioGrid Chicken Gallus KEGG pathways file', '.txt', sep = '') 219 | }, 220 | content = function(file) { 221 | write.table(Gallus_gallus_kegg, file,row.names = F, col.names = F, quote = F, sep = "\t") 222 | } 223 | ) 224 | 225 | output$R_script <- downloadHandler( 226 | filename = function() { 227 | paste('Annotation_cleaner', '.R', sep = '') 228 | }, 229 | content = function(file) { 230 | write.table(R_script, file, row.names = F,col.names = F, sep = "\t", quote = F) 231 | } 232 | ) 233 | -------------------------------------------------------------------------------- /functions/network.R: -------------------------------------------------------------------------------- 1 | # main functions #### 2 | getStoredNetsChoices_just_network <- function() { 3 | snets <- StoredNets_just_network() 4 | if (nrow(snets) == 0) return(NULL) 5 | choices <- snets$id 6 | names(choices) <- snets$name 7 | return(choices) 8 | } 9 | 10 | fetchFirstSelectedStoredIgraph_just_network <- function() { 11 | dataset <- fetchFirstSelectedStoredDataset_just_network() 12 | if (is.null(dataset)) 13 | return(NULL) 14 | else 15 | return(convert_to_igraph(dataset)) 16 | } 17 | 18 | # Download-button for automated annotations 19 | file_name <- function() { 20 | automated_annotations <- input$automated_annotations 21 | 22 | if (automated_annotations == "Fast-Greedy\tcluster_fast_greedy(igraph)") { 23 | filename <- "Fast-Greedy_" 24 | } 25 | if (automated_annotations == "Louvain\tcluster_louvain(igraph)") { 26 | filename <- "Louvain_" 27 | } 28 | if (automated_annotations == "Label-Propagation\tcluster_label_prop(igraph)") { 29 | filename <- "Label-Propagation_" 30 | } 31 | if (automated_annotations == "Walktrap\tcluster_walktrap(igraph)") { 32 | filename <- "Walktrap_" 33 | } 34 | if (automated_annotations == "Betweenness\tcluster_edge_betweenness(igraph)") { 35 | filename <- "Betweenness_" 36 | } 37 | return(filename) 38 | } 39 | 40 | # sub-routines #### 41 | fetchFirstSelectedStoredDataset_just_network <- reactive({ 42 | ssn <- SelectedStoredNets_just_network() 43 | if (!is.null(ssn) && nrow(ssn) > 0) { 44 | return(fetchDataset_just_network(ssn[1,]$id)) 45 | } else { 46 | return(NULL) 47 | } 48 | }) 49 | 50 | StoredNets_just_network <- reactive({ 51 | return(reactiveVars$StoredNetworks_just_network) 52 | }) 53 | 54 | SelectedStoredNets_just_network <- function() { 55 | if (length(reactiveVars$SelectedStoredNetworksIds_just_network) > 0) { 56 | return(StoredNets_just_network()[which( 57 | reactiveVars$StoredNetworks_just_network$id %in% 58 | reactiveVars$SelectedStoredNetworksIds_just_network 59 | ),]) 60 | } 61 | else if (nrow(StoredNets_just_network()) == 0 || 62 | is.na(StoredNets_just_network()[1,])) 63 | return(NULL) 64 | else { 65 | updateCheckboxGroupInput( 66 | session, 67 | "uiLoadGraphOptionsOutput_just_network", 68 | "Selected network(s)", 69 | choices = getStoredNetsChoices_just_network(), 70 | selected = getStoredNetsChoices_just_network()[1] 71 | ) 72 | return(StoredNets_just_network()[1,]) 73 | } 74 | } 75 | 76 | fetchDataset_just_network <- function(nid) { 77 | retVal <- NULL 78 | if (length(nid) > 0) { 79 | retVal <- readRDS(paste0(USER_TEMP_FOLDER, "/", nid, ".rda")) 80 | attr(retVal, "id") <- nid 81 | } 82 | return(retVal) 83 | } 84 | 85 | convert_to_igraph <- function(dataset1){ 86 | weighted_tf <- FALSE 87 | if (attr(dataset1, "weighted")) { 88 | weighted_tf <- attr(dataset1, "weighted") 89 | } 90 | set.seed(123) 91 | igraph <- graph.data.frame(dataset1, directed = F, vertices = NULL) 92 | if (attr(dataset1, which = "weighted")) 93 | E(igraph)$weight <- dataset1$Weight 94 | return(igraph) 95 | } 96 | 97 | -------------------------------------------------------------------------------- /functions/refreshing/convex_hulls_3D.R: -------------------------------------------------------------------------------- 1 | convex_hull_3D <- function() { 2 | set.seed(123) 3 | 4 | g <- fetchFirstSelectedStoredIgraph_annotations_tab() 5 | if (is.null(g)) 6 | return() 7 | 8 | # dataset <- get.edgelist(g) 9 | dataset <- fetchFirstSelectedStoredDataset_annotations_tab() 10 | if (is.null(dataset)) 11 | return() 12 | 13 | original_dataset_weighted <- fetchFirstSelectedStoredDataset_annotations_tab() 14 | if (is.null(original_dataset_weighted)) 15 | return(NULL) 16 | 17 | annotation_graph <- fetchFirstSelectedStoredGroups2_annotations_tab() 18 | if (is.null(annotation_graph)) 19 | return() 20 | 21 | #---------------------------------------------------------------# 22 | my_network<- as.data.frame(get.edgelist(g)) 23 | my_network<- data.frame(Source = my_network$V1, Target = my_network$V2) 24 | 25 | groups <- as.data.frame(annotation_graph) 26 | 27 | groups<- data.frame(V1 = groups$Annotations, stri_split_fixed(groups$Nodes, ",", simplify = TRUE)) 28 | groups<-mutate_all(groups, funs(na_if(.,""))) 29 | number_of_groups<-dim(groups)[1] 30 | 31 | x <- list() 32 | for (i in 1:number_of_groups) { 33 | group_i<- groups[i,] 34 | group_i<- group_i[,-1] 35 | group_i <- group_i[!is.na(group_i)] 36 | x[[i]]<- (group_i) 37 | } 38 | 39 | GO <- list() 40 | for (i in 1:number_of_groups) { 41 | GO[[i]]<-rep(groups[i,1], length(x[[i]])) 42 | } 43 | 44 | column1<-my_network$Source 45 | column2<-my_network$Target 46 | node_names<-unique(union(column1, column2)) 47 | tt<-unlist(x) 48 | nodes_with_NA_groups<-setdiff(node_names,tt) 49 | 50 | members <- data_frame(id=unlist(x),group = unlist(GO)) 51 | members_with_NA_groups <- data_frame(id=unlist(x),group = unlist(GO)) 52 | #----------------------------------------------------------------# 53 | 54 | #-------------------------------------------------------------------------# 55 | 56 | new_nodes <- unique(union(dataset[,1], dataset[,2])) 57 | 58 | new_annot <- annotation_graph %>% 59 | mutate(V2 = strsplit(as.character(annotation_graph$Nodes), ",")) %>% 60 | unnest(V2) 61 | 62 | intersect_g_annot <- intersect(new_nodes, new_annot$V2) 63 | 64 | if(identical(intersect_g_annot, character(0))){ 65 | showModal(modalDialog( 66 | title = "Important message", 67 | "Please check if the selected annotation file corresponds to the selected network.", 68 | easyClose = T 69 | )) 70 | } 71 | #-------------------------------------------------------------------------# 72 | 73 | set.seed(123) 74 | lay <- layout_choices_3D(g, lay) 75 | 76 | #----------------------------------------------------------------# 77 | scene_scale_x_max <- max(lay[,1])*scaling_coordinates_convex_3D_X() 78 | scene_scale_x_min <- min(lay[,1])*scaling_coordinates_convex_3D_X() 79 | 80 | scene_scale_y_max <- max(lay[,2])*scaling_coordinates_convex_3D_Y() 81 | scene_scale_y_min <- min(lay[,2])*scaling_coordinates_convex_3D_Y() 82 | 83 | scene_scale_z_max <- max(lay[,3])*scaling_coordinates_convex_3D_Z() 84 | scene_scale_z_min <- min(lay[,3])*scaling_coordinates_convex_3D_Z() 85 | #----------------------------------------------------------------# 86 | # lay <- lay*scaling_coordinates_convex_3D() 87 | #-- Scaling coordinates --# 88 | coorx<- lay[,1]*scaling_coordinates_convex_3D_X() 89 | lay <- cbind(coorx,lay[,2:ncol(lay)]) 90 | 91 | coory<- lay[,2]*scaling_coordinates_convex_3D_Y() 92 | lay <- cbind(lay[,1], coory,lay[,3]) 93 | 94 | coorz<- lay[,3]*scaling_coordinates_convex_3D_Z() 95 | lay <- cbind(lay[,1:2], coorz) 96 | #-------------------------# 97 | 98 | colnames(lay) <- c("x", "y", "z") 99 | # node_names_3D <- unique(union(dataset[,1], dataset[,2])) 100 | 101 | 102 | #---------------------------------# 103 | 104 | node_names_3D <- names(V(g)) 105 | node_name_links_3D <- names(V(g)) 106 | #--------------------------------# 107 | 108 | 109 | if(length(node_names_3D) != nrow(lay)){ 110 | showModal(modalDialog( 111 | title = "Important message", 112 | "Please check if the selected annotation file corresponds to the selected network.", 113 | easyClose = T 114 | )) 115 | } 116 | else{ 117 | node_names_with_coords <- data.frame("Source" = node_names_3D, 118 | "x" = lay[,1], 119 | "y" = lay[,2], 120 | "z" = lay[,3]) 121 | } 122 | 123 | 124 | #--- hash table for names and coordinates ---# 125 | coordinates_hashmap <- new.env(hash = TRUE) 126 | for(i in 1:nrow(node_names_with_coords)){ 127 | coordinates_hashmap[[as.character(node_names_with_coords[i,1])]]<-c(node_names_with_coords[i,2], node_names_with_coords[i,3], node_names_with_coords[i,4]) 128 | } 129 | 130 | #---------------------------------------------------# 131 | 132 | nrowdat <- nrow(dataset) 133 | nrowannot <- nrow(annotation_graph) 134 | 135 | 136 | if(!(is.weighted(g))){ 137 | original_dataset_weighted <- cbind(original_dataset_weighted[,1:2],"Weight"=rep(0.5, nrow(original_dataset_weighted))) 138 | } else{ 139 | minx <- min(original_dataset_weighted[,3]) 140 | maxx <- max(original_dataset_weighted[,3]) 141 | 142 | scaling_weight_values<- c() 143 | for (i in 1:nrow(original_dataset_weighted)){ 144 | scaling_weight_values_i <- mapper(original_dataset_weighted[i,3], minx, maxx, 0.5, 20) 145 | scaling_weight_values <- c(scaling_weight_values, scaling_weight_values_i) 146 | } 147 | if(maxx > 50){ 148 | original_dataset_weighted <- cbind(original_dataset_weighted[,1:2],"Weight"=scaling_weight_values) 149 | } 150 | } 151 | 152 | if (length(s)==0) 153 | { 154 | s<-c(1:nrowannot) 155 | } 156 | 157 | if (length(s)) { 158 | s<-sort(s)#----------------------------------- 159 | x<- length(s) 160 | 161 | dataset1 <- get.edgelist(g) 162 | dataset1 <- data.frame("Source" = dataset[,1], "Target" = dataset[,2]) 163 | 164 | source <- matrix(ncol=3, nrow=nrow(dataset1)) 165 | target <- matrix(ncol=3, nrow=nrow(dataset1)) 166 | for(i in 1:nrow(dataset1)){ 167 | source[i,] <- coordinates_hashmap[[as.character(dataset1[i,1])]] 168 | target[i,] <- coordinates_hashmap[[as.character(dataset1[i,2])]] 169 | } 170 | 171 | edges_for_plotly <- data.frame("Source.x" = source[,1], "Source.y" = source[,2], "Source.z" = source[,3], 172 | "Target.x" = target[,1], "Target.y" = target[,2], "Target.z" = target[,3]) 173 | # x<- c() 174 | # for(i in 1:nrow(edges_for_plotly)){ 175 | # if(i == nrow(edges_for_plotly)){ 176 | # a <- paste(edges_for_plotly$Source.x[i], edges_for_plotly$Target.x[i], "null", sep = "," ) 177 | # }else{ 178 | # a <- paste(edges_for_plotly$Source.x[i], edges_for_plotly$Target.x[i], "null,", sep = "," ) 179 | # 180 | # } 181 | # x<- c(x, a) 182 | # } 183 | # 184 | # x <- as.vector(unlist(x)) 185 | # x <- paste(x, collapse=" ") 186 | # 187 | # y<- c() 188 | # for(i in 1:nrow(edges_for_plotly)){ 189 | # if(i == nrow(edges_for_plotly)){ 190 | # a = paste(edges_for_plotly$Source.y[i], edges_for_plotly$Target.y[i], "null", sep = "," ) 191 | # }else{ 192 | # a = paste(edges_for_plotly$Source.y[i], edges_for_plotly$Target.y[i], "null,", sep = "," ) 193 | # } 194 | # y<- c(y, a) 195 | # } 196 | # 197 | # y <- as.vector(unlist(y)) 198 | # y <- paste(y, collapse=" ") 199 | # 200 | # 201 | # z<- c() 202 | # for(i in 1:nrow(edges_for_plotly)){ 203 | # if(i == nrow(edges_for_plotly)){ 204 | # a = paste(edges_for_plotly$Source.z[i], edges_for_plotly$Target.z[i], "null", sep = "," ) 205 | # }else{ 206 | # a = paste(edges_for_plotly$Source.z[i], edges_for_plotly$Target.z[i], "null,", sep = "," ) 207 | # } 208 | # z<- c(z, a) 209 | # } 210 | # 211 | # z <- as.vector(unlist(z)) 212 | # z <- paste(z, collapse=" ") 213 | 214 | #--------------------------------------------------------------------# 215 | fileConn <- file(paste(USER_TEMP_FOLDER, "/convex_3D_", session$token,".html", sep=""), "w") 216 | #--------------------------------------------------------------------# 217 | 218 | cat(sprintf(" 219 | 220 | 221 | 222 | 223 | 224 |
225 | 226 | 528 | 529 | 530 | ", sep = ""), file = fileConn, append = T) 531 | 532 | 533 | 534 | } # if(length(s)) 535 | } -------------------------------------------------------------------------------- /functions/refreshing/modularity.R: -------------------------------------------------------------------------------- 1 | modularity<- function(method){ 2 | 3 | set.seed(123) 4 | 5 | clp <- automated_annotation_choices(net, automated_annotations) 6 | 7 | groups_all<- c() 8 | for (i in 1:length(clp)){ 9 | clp_i <- as.data.frame(clp[[i]]) 10 | ss<-paste(clp_i[,1], collapse="," ) 11 | groups_all[[i]]<-ss 12 | } 13 | 14 | prefix <- "Group-" 15 | suffix <- seq(1:length(clp)) 16 | 17 | max.length <- max(sapply(groups_all, length)) 18 | l <- lapply(groups_all, function(v) { c(v, rep(NA, max.length-length(v)))}) 19 | df<-as.data.frame(do.call(rbind, l)) 20 | groups_column_name<- paste(prefix, suffix, sep="") 21 | df<- cbind(groups_column_name, df) 22 | names(df) <- NULL 23 | 24 | return(df) 25 | } 26 | -------------------------------------------------------------------------------- /functions/topology.R: -------------------------------------------------------------------------------- 1 | # main functions #### 2 | getStoredNetsChoices_topology_tab <- function() { 3 | snets <- StoredNets_topology_tab() 4 | if (nrow(snets) == 0) 5 | return(NULL) 6 | choices <- snets$id 7 | names(choices) <- snets$name 8 | return(choices) 9 | } 10 | 11 | getDatasetName <- function(id) { 12 | sn <- StoredNets() 13 | idi <- which(sn$id == id) 14 | if (is.null(sn) || nrow(sn) == 0 || length(idi) == 0) 15 | return(NULL) 16 | return(sn[idi,]$name) 17 | } 18 | 19 | fetchDataset_topology_tab <- function(nid) { 20 | retVal <- NULL 21 | if (length(nid) > 0) { 22 | retVal <- readRDS(paste0(USER_TEMP_FOLDER, "/", nid, ".rda")) 23 | attr(retVal, "id") <- nid 24 | } 25 | return(retVal) 26 | } 27 | 28 | fetchAllSelectedStoredDataset_topology_tab <- function() { 29 | ssn <- SelectedStoredNets_topology_tab() 30 | ids <- c() 31 | if (!is.null(ssn) && nrow(ssn) > 0) { 32 | ret <- list() 33 | for (i in 1:nrow(ssn)) { 34 | ret[[i]] <- fetchDataset_topology_tab(ssn[i,]$id) 35 | ids <- c(ids, ssn[i,]$id) 36 | } 37 | names(ret) <- ids 38 | return(ret) 39 | } else { 40 | return(NULL) 41 | } 42 | } 43 | 44 | # Statistics 45 | stat_dataset <- function(dataset, datasetName) { 46 | res <- tryCatch({ 47 | columns <- c("Statistic", paste0("Value for ", datasetName)) 48 | if (is.null(dataset)) { 49 | dataset <- EmptyDataset(columns) 50 | } else { 51 | igraph <- convert_to_igraph(dataset) 52 | if (length(input$statistics) == 0) { 53 | dataset <- EmptyDataset(columns) 54 | } else { 55 | dataset <- netstats(igraph, input$statistics) 56 | colnames(dataset) <- columns 57 | } 58 | } 59 | return(dataset) 60 | }, warning = function(w) { 61 | 62 | }, error = function(e) { 63 | cat(paste0("ERROR while executing stat_dataset: ", e, "\n")) 64 | return(NULL) 65 | }, finally = { 66 | 67 | }) 68 | return(res) 69 | } 70 | 71 | stat_dataset2 <- function(dataset, datasetName) { 72 | res <- tryCatch({ 73 | columns <- c("Statistic", paste0("Value for ", datasetName)) 74 | if (is.null(dataset)) { 75 | dataset <- EmptyDataset(columns) 76 | } else { 77 | igraph <- convert_to_igraph(dataset) 78 | if (length(input$statistics2) == 0) { 79 | dataset <- EmptyDataset(columns) 80 | } else { 81 | dataset <- netstats(igraph, input$statistics2) 82 | colnames(dataset) <- columns 83 | } 84 | } 85 | return(dataset) 86 | }, warning = function(w) { 87 | 88 | }, error = function(e) { 89 | cat(paste0("ERROR while executing stat_dataset: ", e, "\n")) 90 | return(NULL) 91 | }, finally = { 92 | 93 | }) 94 | return(res) 95 | } 96 | 97 | # sub-routines #### 98 | SelectedStoredNets_topology_tab <- function() { 99 | if (length(reactiveVars$SelectedStoredNetworksIds_topology_tab) > 0) { 100 | return(StoredNets_topology_tab()[which( 101 | reactiveVars$StoredNetworks_topology_tab$id %in% 102 | reactiveVars$SelectedStoredNetworksIds_topology_tab 103 | ),]) 104 | } 105 | else if (nrow(StoredNets_topology_tab()) == 0 || 106 | is.na(StoredNets_topology_tab()[1,])) 107 | return(NULL) 108 | else { 109 | updateCheckboxGroupInput( 110 | session, 111 | "uiStoredGraphsOutputSelectTopolopgy", 112 | "Selected network(s)", 113 | choices = getStoredNetsChoices_topology_tab(), 114 | selected = getStoredNetsChoices_topology_tab()[1] 115 | ) 116 | return(StoredNets_topology_tab()[1,]) 117 | } 118 | } 119 | 120 | netstats <- function(igraph,statistics){ 121 | if(length(statistics)==0) 122 | return(NULL) 123 | results<-list() 124 | for(i in statistics){ 125 | tmp<-unlist(strsplit(i,"\t",fixed=T)) 126 | description<-tmp[1] 127 | command<-tmp[2] 128 | results[[description]]<-eval(parse(text=command)) 129 | } 130 | return(data.frame(cbind(names(results),as.character(results)))) 131 | } 132 | -------------------------------------------------------------------------------- /functions/upload.R: -------------------------------------------------------------------------------- 1 | # main functions #### 2 | addNetwork <- function(){ 3 | dataset <- loadNetworkFromFile() 4 | 5 | if (!is.null(dataset)) { 6 | if (nrow(dataset) < 10000) { 7 | nid <- UUIDgenerate(T) #time-base UUID is generated 8 | nn <- input$networkName 9 | cnt <- 1 #count 10 | while (nn %in% reactiveVars$StoredNetworks$name) { 11 | #reactiveVars: represents a single reactive variable. 12 | cnt <- cnt + 1 13 | nn <- 14 | paste(input$networkName, cnt) #paste: converts its arguments (via as.character) to character strings 15 | } 16 | df <- data.frame(id = nid, name = nn, stringsAsFactors = F) 17 | if (nrow(dataset) > 10000) { 18 | dataset <- dataset[1:10000,] 19 | } 20 | if (ncol(dataset) == 3) attr(dataset, which = 'weighted') <- T 21 | else attr(dataset, which = 'weighted') <- F 22 | 23 | reactiveVars$StoredNetworks <- 24 | rbind(reactiveVars$StoredNetworks, df) 25 | reactiveVars$StoredNetworks_just_network <- 26 | reactiveVars$StoredNetworks 27 | reactiveVars$StoredNetworks_annotations_tab <- 28 | reactiveVars$StoredNetworks 29 | reactiveVars$StoredNetworks_topology_tab <- 30 | reactiveVars$StoredNetworks 31 | 32 | saveRDS(dataset, paste0(USER_TEMP_FOLDER, "/", nid, ".rda")) 33 | if (length(reactiveVars$SelectedStoredNetworksIds) == 0) { 34 | reactiveVars$SelectedStoredNetworksIds <- c(nid) 35 | } 36 | } 37 | 38 | if (nrow(dataset) >= 10000) { 39 | dataset <- dataset[1:10000, ] 40 | shinyalert("Warning!", "Keeping the first 10,000 connections.", type = "error") 41 | } 42 | 43 | } else shinyalert("Error!", "Your input generated a NULL network.\n 44 | Please, follow the guidelines at the Help pages to upload a network in the required format.", type = "error") 45 | } 46 | 47 | remNetwork <- function(){ 48 | if (!is.null(input$availableNetworks)) { 49 | reactiveVars$StoredNetworks <- 50 | reactiveVars$StoredNetworks[-which(reactiveVars$StoredNetworks$id %in% 51 | input$availableNetworks),] 52 | nr <- nrow(reactiveVars$StoredNetworks) 53 | if (nr > 0) { 54 | reactiveVars$SelectedStoredNetworksIds <- 55 | reactiveVars$StoredNetworks[nr,]$id 56 | } 57 | } 58 | 59 | if (!is.null(input$availableNetworks)) { 60 | reactiveVars$StoredNetworks_just_network <- 61 | reactiveVars$StoredNetworks_just_network[-which(reactiveVars$StoredNetworks_just_network$id %in% 62 | input$availableNetworks),] 63 | nr <- nrow(reactiveVars$StoredNetworks_just_network) 64 | if (nr > 0) { 65 | reactiveVars$SelectedStoredNetworksIds_just_network <- 66 | reactiveVars$StoredNetworks_just_network[nr,]$id 67 | } 68 | } 69 | 70 | if (!is.null(input$availableNetworks)) { 71 | reactiveVars$StoredNetworks_annotations_tab <- 72 | reactiveVars$StoredNetworks_annotations_tab[-which( 73 | reactiveVars$StoredNetworks_annotations_tab$id %in% 74 | input$availableNetworks 75 | ),] 76 | nr <- nrow(reactiveVars$StoredNetworks_annotations_tab) 77 | if (nr > 0) { 78 | reactiveVars$SelectedStoredNetworksIds_annotations_tab <- 79 | reactiveVars$StoredNetworks_annotations_tab[nr,]$id 80 | } 81 | } 82 | 83 | if (!is.null(input$availableNetworks)) { 84 | reactiveVars$StoredNetworks_topology_tab <- 85 | reactiveVars$StoredNetworks_topology_tab[-which(reactiveVars$StoredNetworks_topology_tab$id %in% 86 | input$availableNetworks),] 87 | nr <- nrow(reactiveVars$StoredNetworks_topology_tab) 88 | if (nr > 0) { 89 | reactiveVars$SelectedStoredNetworksIds_topology_tab <- 90 | reactiveVars$StoredNetworks_topology_tab[nr,]$id 91 | } 92 | } 93 | } 94 | 95 | addAnnotations <- function(){ 96 | annotation <- loadAnnotations() 97 | if (!is.null(annotation)) { 98 | if (nrow(annotation) < 300) { 99 | nid <- UUIDgenerate(T) #time-base UUID is generated 100 | nn <- input$annotationName 101 | cnt <- 1 #count 102 | while (nn %in% reactiveVars$StoredAnnotations$name) { 103 | #reactiveVars: represents a single reactive variable. 104 | cnt <- cnt + 1 105 | nn <- 106 | paste(input$annotationName, cnt) #paste: converts its arguments (via as.character) to character strings 107 | } 108 | dtf <- data.frame(id = nid, 109 | name = nn, 110 | stringsAsFactors = F) 111 | if (nrow(annotation) > 10000) { 112 | annotation <- annotation[1:10000,] 113 | } 114 | reactiveVars$StoredAnnotations <- 115 | rbind(reactiveVars$StoredAnnotations, dtf) 116 | reactiveVars$StoredNetworks2_annotations_tab <- 117 | reactiveVars$StoredAnnotations 118 | 119 | saveRDS(annotation, paste0(USER_TEMP_FOLDER, "/", nid, ".rda")) 120 | if (length(reactiveVars$SelectedStoredAnnotationIds) == 0) { 121 | reactiveVars$SelectedStoredAnnotationIds <- c(nid) 122 | } 123 | } 124 | 125 | if (nrow(annotation) >= 300) { 126 | annotation <- annotation[1:300, ] 127 | shinyalert("Warning!", "Keeping the first 300 lines.", type = "error") 128 | } 129 | 130 | } else shinyalert("Error!", "Your input generated a NULL annotation table.\n 131 | Please, follow the guidelines at the Help pages to upload an annotation file in the required format.", type = "error") 132 | } 133 | 134 | remAnnotations <- function(){ 135 | if (!is.null(input$availableAnnotations)) { 136 | reactiveVars$StoredAnnotations <- 137 | reactiveVars$StoredAnnotations[-which(reactiveVars$StoredAnnotations$id %in% 138 | input$availableAnnotations),] 139 | nr <- nrow(reactiveVars$StoredAnnotations) 140 | if (nr > 0) 141 | reactiveVars$SelectedStoredAnnotationIds <- 142 | reactiveVars$StoredAnnotations[nr,]$id 143 | } 144 | 145 | 146 | if (!is.null(input$availableAnnotations)) { 147 | reactiveVars$StoredNetworks2_annotations_tab <- 148 | reactiveVars$StoredNetworks2_annotations_tab[-which( 149 | reactiveVars$StoredNetworks2_annotations_tab$id %in% 150 | input$availableAnnotations 151 | ),] 152 | nr <- nrow(reactiveVars$StoredNetworks2_annotations_tab) 153 | if (nr > 0) 154 | reactiveVars$SelectedStoredNetworksIds2_annotations_tab <- 155 | reactiveVars$StoredNetworks2_annotations_tab[nr,]$id 156 | } 157 | } 158 | 159 | addExpression <- function(){ 160 | expression <- loadExpressions() 161 | if (!is.null(expression)) { 162 | nid <- UUIDgenerate(T) #time-base UUID is generated 163 | nn <- input$expressionName 164 | cnt <- 1 #count 165 | while (nn %in% reactiveVars$StoredExpressions$name) { 166 | #reactiveVars: represents a single reactive variable. 167 | cnt <- cnt + 1 168 | nn <- 169 | paste(input$expressionName, cnt) #paste: converts its arguments (via as.character) to character strings 170 | } 171 | dtf <- data.frame(id = nid, 172 | name = nn, 173 | stringsAsFactors = F) 174 | if (nrow(expression) > 10000) { 175 | expressionName <- expressionName[1:10000,] 176 | shinyalert("Warning!", "Keeping the 10000 first rows.", type = "error") 177 | } 178 | reactiveVars$StoredExpressions <- 179 | rbind(reactiveVars$StoredExpressions, dtf) 180 | saveRDS(expression, paste0(USER_TEMP_FOLDER, "/", nid, ".rda")) 181 | if (length(reactiveVars$SelectedStoredExpressionIds) == 0) { 182 | reactiveVars$SelectedStoredExpressionIds <- c(nid) 183 | } 184 | } else shinyalert("Error!", "Your input generated a NULL expressions table.\n 185 | Please, follow the guidelines at the Help pages to upload an annotation file in the required format.", type = "error") 186 | } 187 | 188 | remExpression <- function(){ 189 | if (!is.null(input$availableExpressions)) { 190 | reactiveVars$StoredExpressions <- 191 | reactiveVars$StoredExpressions[-which(reactiveVars$StoredExpressions$id %in% 192 | input$availableExpressions),] 193 | nr <- nrow(reactiveVars$StoredExpressions) 194 | if (nr > 0) 195 | reactiveVars$SelectedStoredExpressionIds <- 196 | reactiveVars$StoredExpressions[nr,]$id 197 | } 198 | } 199 | 200 | getStoredNetsChoices <- function() { 201 | snets <- StoredNets() 202 | if (nrow(snets) == 0) 203 | return(NULL) 204 | choices <- snets$id 205 | names(choices) <- snets$name 206 | return(choices) 207 | } 208 | 209 | SelectedStoredNets <- function() { 210 | if (length(reactiveVars$SelectedStoredNetworksIds) > 0) { 211 | return(StoredNets()[which(reactiveVars$StoredNetworks$id %in% 212 | reactiveVars$SelectedStoredNetworksIds),]) 213 | } 214 | else if (nrow(StoredNets()) == 0 || 215 | is.na(StoredNets()[1,])) 216 | return(NULL) 217 | else return(StoredNets()[1,]) 218 | } 219 | 220 | fetchDataset <- function(nid) { 221 | retVal <- NULL 222 | if (length(nid) > 0) { 223 | retVal <- readRDS(paste0(USER_TEMP_FOLDER, "/", nid, ".rda")) 224 | attr(retVal, "id") <- nid 225 | } 226 | return(retVal) 227 | } 228 | 229 | getStoredAnnotChoices <- function() { 230 | sannots <- StoredAnnots() 231 | if (nrow(sannots) == 0) 232 | return(NULL) 233 | choices <- sannots$id 234 | names(choices) <- sannots$name 235 | return(choices) 236 | } 237 | 238 | # sub-routines #### 239 | loadNetworkFromFile <- function() { 240 | dataset1 <- NULL 241 | set.seed(123) 242 | 243 | switch( 244 | input$uiLoadGraphOptionsInput, 245 | oF = { 246 | if (!is.null(input$file1)) { 247 | tryCatch({ 248 | dataset1 <- read_data(input$file1$datapath) 249 | }, error = function(e) { 250 | print(paste("Upload tab error: ", e)) 251 | shinyalert("Error!", "Network format problem. Please ensure that columns are tab separated.", type = "error") 252 | }) 253 | } 254 | }, 255 | oR_String_interactions = { 256 | dataset1 <- string_net_bcar3 # "Examples/BCAR3/BCAR3.txt" 257 | dataset1 <- cbind(dataset1[,1:2], "Weight" = rep(1, nrow(dataset1))) 258 | }, 259 | oR_Drosophila = { 260 | n <- as.integer(input$oR_selected_size) 261 | dataset1 <- dros_net # "Examples/TAU/TAU_network_DEGs_NORMA.txt" 262 | dataset1 <- cbind(dataset1[,1:2], "Weight" = rep(1, nrow(dataset1))) 263 | } 264 | ) 265 | 266 | if (input$uiLoadGraphOptionsInput != "oF" && !is.null(dataset1)) { 267 | set.seed(123) 268 | if(ncol(dataset1) < 3) { 269 | dataset1 <- cbind(dataset1[,1:2], "Weight" = rep(1, nrow(dataset1))) 270 | } else { 271 | if (ncol(dataset1) == 2) { 272 | dataset1$V3 <- 1 273 | } else if (ncol(dataset1) > 3) { 274 | dataset1 <- dataset1[, 1:3] 275 | } else if (ncol(dataset1) != 3) 276 | return(NULL) 277 | } 278 | colnames(dataset1) <- c("Source", "Target", "Weight") 279 | } 280 | 281 | if (!is.null(dataset1)){ 282 | row_to_keep <- c() 283 | for(i in 1:nrow(dataset1)){ 284 | if(dataset1[i,1]==dataset1[i,2]){ 285 | row_to_keep <- c(row_to_keep, FALSE) 286 | } 287 | if(dataset1[i,1]!=dataset1[i,2]){ 288 | row_to_keep <- c(row_to_keep, TRUE) 289 | } 290 | } 291 | dataset1 = dataset1[row_to_keep,] 292 | } 293 | 294 | return(dataset1) 295 | } 296 | 297 | # Load annotations 298 | loadAnnotations <- function() { 299 | annotation1 <- NULL 300 | 301 | switch( 302 | input$uiLoadGraphOptionsInput_annotations, 303 | oF = { 304 | if (!is.null(input$file2)) { 305 | tryCatch({ 306 | annotation1 <- read_annotations(input$file2$datapath) 307 | }, error = function(e) { 308 | print(paste("Upload tab error: ", e)) 309 | shinyalert("Error!", "Annotations format problem. Please ensure that columns are tab separated.", type = "error") 310 | }) 311 | } 312 | }, 313 | oR_String_Annotation_BP = { 314 | annotation1 <- string_bp # "Examples/BCAR3/BCAR3_GO_BP.txt" 315 | }, 316 | oR_String_Annotation_MF = { 317 | annotation1 <- string_mf # "Examples/BCAR3/BCAR3_GO_MF.txt" 318 | }, 319 | oR_String_Annotation_KEGG = { 320 | annotation1 <- string_kegg # "Examples/BCAR3/BCAR3_KEGG.txt" 321 | }, 322 | oR_Drosophila_KEGG = { 323 | # n <- as.integer(input$oR_selected_size) 324 | annotation1 <- dros_annot # "Examples/TAU/TAU_KEGG_Annotation_NORMA.txt" 325 | }, 326 | oR_Drosophila_Luvain = { 327 | # n <- as.integer(input$oR_selected_size) 328 | annotation1 <- dros_louvain # "Examples/TAU/TAU_Louvain.txt" 329 | } 330 | ) 331 | 332 | if (!is.null(annotation1)) { 333 | colnames(annotation1) <- c("Annotations", "Nodes") 334 | } 335 | 336 | return(annotation1) 337 | } 338 | 339 | # Load expression files 340 | loadExpressions <- function() { 341 | expression1 <- NULL 342 | switch(input$uiLoadExpressionsInput, 343 | oF = { 344 | if (!is.null(input$file3)) { 345 | tryCatch({ 346 | expression1 <- read_expressions(input$file3$datapath) 347 | }, error = function(e) { 348 | print(paste("Upload tab error: ", e)) 349 | shinyalert("Error!", "Expressions format problem. Please ensure that columns are tab separated.", type = "error") 350 | }) 351 | } 352 | }, 353 | oR_Expression_file_Drosophila = { 354 | expression1 <- dros_express # "Examples/TAU/TAU_expressions.txt" 355 | } 356 | ) 357 | if (!is.null(expression1)) { 358 | colnames(expression1) <- c("ID", "Color") 359 | } 360 | return(expression1) 361 | } 362 | 363 | read_expressions <- function(datapath, type = c("txt"), header = F, sep = "\t", 364 | quote = "\"", weighted = F, na.strings = c("", "NA")){ 365 | expression1 <- read.table(datapath, header = header, sep = sep, 366 | quote = quote, comment.char="?") 367 | } 368 | 369 | read_data <- function(datapath, type = c("txt"), header = T, sep = "\t", quote = "\"", weighted = F){ 370 | dataset1 <- read.table(datapath, header = header, sep = sep, quote = quote) 371 | 372 | if (ncol(dataset1) == 2) dataset1$V3 <- 1 373 | else if (ncol(dataset1) > 3) dataset1 <- dataset1[, 1:3] 374 | else if (ncol(dataset1) != 3) return(NULL) 375 | 376 | colnames(dataset1) <- c("Source", "Target", "Weight") 377 | 378 | return(dataset1) 379 | } 380 | 381 | read_annotations <- function(datapath, type = c("txt"), header = F, sep = "\t", 382 | quote = "\"", weighted = F, na.strings = c("", "NA")){ 383 | annotation1 <- read.table(datapath, header = header, sep = sep, quote = quote) 384 | 385 | return(annotation1) 386 | } 387 | -------------------------------------------------------------------------------- /global.R: -------------------------------------------------------------------------------- 1 | # Load libraries or install dependencies #### 2 | if (!require(shinyBS)) install.packages('shinyBS') 3 | if (!require(bsplus)) install.packages('bsplus') 4 | if (!require(visNetwork)) install.packages("visNetwork") 5 | if (!require(shinyWidgets)) install.packages('shinyWidgets') 6 | if (!require(shinythemes)) install.packages('shinythemes') 7 | if (!require(shinyjs)) install.packages('shinyjs') 8 | if (!require(shinyalert)) install.packages('shinyalert') 9 | if (!require(shinycssloaders)) install.packages('shinycssloaders') 10 | if (!require(randomcoloR)) install.packages('randomcoloR') 11 | if (!require(DT)) install.packages('DT') 12 | if (!require(uuid))install.packages('uuid') 13 | if (!require(igraph)) install.packages('igraph') 14 | if (!require(stringi)) install.packages('stringi') 15 | if (!require(dplyr)) install.packages('dplyr') 16 | if (!require(tidyr)) install.packages('tidyr') 17 | if (!require(stringr)) install.packages('tidyr') 18 | if (!require(VennDiagram)) install.packages("VennDiagram") 19 | if (!require(lattice)) install.packages("lattice") 20 | if (!require(purrr)) install.packages('purrr') 21 | 22 | # Options #### 23 | options(shiny.usecairo = F) 24 | options(shiny.maxRequestSize = 30*1024^2) # 30 MB for uploaded networks 25 | # options(shiny.reactlog = TRUE) # debugging 26 | # options(shiny.error = browser) # debugging 27 | 28 | # Global variables #### 29 | PRINT_TIMES <- F # true, to benchmark some function speeds 30 | USER_TEMP_FOLDER <- 'user_temp' 31 | 32 | ui_options <- c(ui_table_font_sz = "80%") 33 | layouts_ui <- c( 34 | "Fruchterman-Reingold"="Fructerman\tlayout_nicely(igraph, dim=2)", 35 | # "Fruchterman-Reingold"="Fructerman\tlayout.fruchterman.reingold(igraph, dim=2)", 36 | "Random"="Random\tlayout.random(igraph, dim=2)", 37 | "Circle"="Circle\tlayout.circle(igraph)", 38 | "Kamada-Kawai"="Kamada-Kawai\tlayout.kamada.kawai(igraph, dim=2)", 39 | "Reingold-Tilford"="Reingold-Tilford\tlayout.reingold.tilford(igraph)", 40 | "Lgl"="Lgl\tlayout.lgl(igraph)", 41 | "Graphopt"="Graphopt\tlayout.graphopt(igraph)", 42 | "Gem"="Graphopt\tlayout.gem(igraph)", 43 | "Star"="Graphopt\tlayout_as_star(igraph)", 44 | "Grid"="Grid\tlayout.grid(igraph)" 45 | # "Auto"="Auto\tlayout.auto(igraph, dim=2)", 46 | # "SVD"="SVD\tlayout.svd(igraph, d=shortest.paths(igraph))" 47 | # "Nicely"="Nicely\tlayout_nicely(igraph, dim=2)", 48 | # "Tree"="Graphopt\tlayout_as_tree(igraph)", 49 | # "Spring"="Spring\tlayout.spring(igraph)", 50 | # "Fruchterman-Reingold Grid"="Fruchterman Grid\tlayout.fruchterman.reingold.grid(igraph)", 51 | # "Sphere"="Sphere\tlayout.sphere(igraph)", 52 | ) 53 | selected_layouts <- c( "Fructerman\tlayout_nicely(igraph, dim=2)" ) 54 | layouts_3D<-c( 55 | "Fruchterman-Reingold"="Fructerman\tlayout_with_fr(igraph, dim=3)", 56 | "Random"="Random\tlayout.random(igraph, dim=3)", 57 | "Kamada-Kawai"="Kamada-Kawai\tlayout.kamada.kawai(igraph, dim=3)", 58 | # "Reingold-Tilford"="Reingold-Tilford\tlayout.reingold.tilford(igraph, dim=3)", 59 | # "Lgl"="Lgl\tlayout.lgl(igraph, dim=3)", 60 | # "Graphopt"="Graphopt\tlayout.graphopt(igraph, dim=3)", 61 | # "Gem"="Graphopt\tlayout.gem(igraph, dim=3)", 62 | "Grid"="Grid\tlayout.grid(igraph, dim=3)" 63 | ) 64 | selected_layouts_3d <- c( "Fructerman\tlayout_with_fr(igraph, dim=3)" ) 65 | automated_annotations_ui <- c( 66 | # "Fast-Greedy"="Fast-Greedy\tcluster_fast_greedy(igraph)", 67 | "Louvain"="Louvain\tcluster_louvain(igraph)", 68 | "Label-Propagation"="Label-Propagation\tcluster_label_prop(igraph)", 69 | "Walktrap"="Walktrap\tcluster_walktrap(igraph)", 70 | "Betweenness"="Betweenness\tcluster_edge_betweenness(igraph)" 71 | ) 72 | selected_automated_annotations <- c( "Louvain\tcluster_louvain(igraph)" ) 73 | statistics <- c( 74 | "Number of Edges" = "Number of Edges\tecount(igraph)", 75 | "Number of Nodes" = "Number of Nodes\tvcount(igraph)", 76 | "Density" = "Density\tgraph.density(igraph)", 77 | "Average path length" = "Average path length\taverage.path.length(igraph)", 78 | "Clustering Coefficient" = "Clustering Coefficient\ttransitivity(igraph)", 79 | "Modularity" = "Modularity\tmodularity(igraph,membership(walktrap.community(igraph)))", 80 | "Average Eccentricity" = "Average Eccentricity\tmean(eccentricity(igraph))", 81 | "Average number of Neighbors" = "Average number of Neighbors\t(centr_eigen(igraph)$centralization)", 82 | "Centralization betweenness" = "Centralization.betweenness\tcentralization.betweenness(igraph)$centralization", 83 | # "Centralization closeness" = "Centralization.closeness\tcentralization.closeness(igraph)$centralization", 84 | "Centralization degree" = "Centralization.degree\tcentralization.degree(igraph)$centralization" 85 | ) 86 | selected_statistics <- c("Number of Edges" = "Number of Edges\tecount(igraph)") 87 | 88 | max_pixels_panel <- 5000 89 | 90 | # 300 Colors - Up to 100 are distinct 91 | qual_col_pals<-c("#1B9E77","#D95F02","#7570B3","#E7298A","#66A61E","#E6AB02","#A6761D","#666666","#7FC97F","#BEAED4", 92 | "#FDC086","#FFFF99","#386CB0","#F0027F","#BF5B17","#A6CEE3","#1F78B4","#B2DF8A","#33A02C","#FB9A99", 93 | "#E31A1C","#FDBF6F","#FF7F00","#CAB2D6","#a17bc9","#B15928","#FBB4AE","#B3CDE3","#CCEBC5","#a9a9a9", 94 | "#dcdcdc","#98fb98","#556b2f","#8b4513","#6b8e23","#2e8b57","#800000","#FDDAEC","#006400","#808000", 95 | "#6c3920","#778899","#3cb371","#bc8f8f","#b0737c","#008080","#b8860b","#bdb76b","#cd853f","#4682b4", 96 | "#d2691e","#9acd32","#20b2aa","#008b7b","#82007e","#32cd32","#8fbc8f","#0ba47e","#b03060","#d2b48c", 97 | "#66cdaa","#9932cc","#ff0000","#ffa500","#ffd700","#ffff00","#c71585","#0303ff","#7fff00","#00ff00", 98 | "#ba55d3","#00ff7f","#4169e1","#e9967a","#dc143c","#00ffff","#00bfff","#9370db","#0000ff","#a020f0", 99 | "#adff2f","#d8bfd8","#ff7f50","#ff00ff","#db7093","#f0e68c","#fa8072","#ffff54","#6495ed","#dda0dd", 100 | "#87ceeb","#ff1493","#afeeee","#ee82ee","#2f4f4f","#7fffd4","#ff69b4","#ffe4c4","#ffb6c1","#DECBE4", 101 | "#FED9A6","#FFFFCC","#E5D8BD","#191970","#F2F2F2","#B3E2CD","#FDCDAC","#CBD5E8","#F4CAE4","#E6F5C9", 102 | "#FFF2AE","#F1E2CC","#CCCCCC","#E41A1C","#377EB8","#4DAF4A","#984EA3","#FFFF33","#A65628","#F781BF", 103 | "#999999","#66C2A5","#FC8D62","#8DA0CB","#E78AC3","#A6D854","#FFD92F","#E5C494","#B3B3B3","#8DD3C7", 104 | "#FFFFB3","#BEBADA","#FB8072","#80B1D3","#FDB462","#B3DE69","#FCCDE5","#D9D9D9","#BC80BD","#095F02", 105 | "#E31A97","#A81AD2","#74ED33","#38F76B","#E607E1","#17D214","#E2E749","#5522DF","#1FF696","#1406E9", 106 | "#6A43DE","#C2F309","#E92D57","#5004DE","#9C4AE9","#2EF613","#EDAA2D","#2FB5EA","#47FAB2","#CC9221", 107 | "#5C4AFC","#E843D0","#FE3F64","#21DD3A","#1988D2","#BC11EF","#EEFB3D","#1B9E77","#D95F02","#7570B3", 108 | "#88e99a","#ca2dc5","#bce333","#643176","#34f50e","#b22839","#4be8f9","#6c3920","#bfcd8e","#1642cd", 109 | "#f4d403","#5310f0","#609111","#c697f4","#34466d","#b3d9fa","#155126","#fab5b5","#0ba47e","#ff0087", 110 | "#3d99ce","#bf711e","#fa718e","#798872","#fe5900","#b0737c","#E31A97","#A81AD2","#74ED33","#38F76B", 111 | "#DECBE4","#FED9A6","#FFFFCC","#E5D8BD","#FDDAEC","#F2F2F2","#B3E2CD","#FDCDAC","#CBD5E8","#F4CAE4", 112 | "#E6F5C9","#FFF2AE","#F1E2CC","#CCCCCC","#E41A1C","#377EB8","#4DAF4A","#984EA3","#FFFF33","#A65628", 113 | "#F781BF","#999999","#66C2A5","#FC8D62","#8DA0CB","#E78AC3","#A6D854","#FFD92F","#E5C494","#B3B3B3", 114 | "#8DD3C7","#FFFFB3","#BEBADA","#FB8072","#80B1D3","#FDB462","#B3DE69","#FCCDE5","#D9D9D9","#BC80BD", 115 | "#095F02","#E31A97","#A81AD2","#74ED33","#38F76B","#E607E1","#17D214","#E2E749","#5522DF","#1FF696", 116 | "#1406E9","#6A43DE","#C2F309","#E92D57","#5004DE","#9C4AE9","#2EF613","#EDAA2D","#2FB5EA","#47FAB2", 117 | "#CC9221","#5C4AFC","#E843D0","#FE3F64","#21DD3A","#1988D2","#BC11EF","#EEFB3D","#1B9E77","#D95F02", 118 | "#7570B3","#88e99a","#ca2dc5","#bce333","#643176","#34f50e","#b22839","#4be8f9","#483d8b","#bfcd8e", 119 | "#1642cd","#f4d403","#5310f0","#609111","#c697f4","#34466d","#b3d9fa","#155126","#fab5b5","#800080", 120 | "#ff0087","#3d99ce","#bf711e","#fa718e","#798872","#fe5900","#663399","#E31A97","#A81AD2","#74ED33") 121 | 122 | # Images for help pages and banner 123 | b64_1 <- base64enc::dataURI(file = "./www/Figures/Banner.png", mime = "image/png") 124 | b64_2 <- base64enc::dataURI(file = "./www/Figures/Upload-1.png", mime = "image/png") 125 | b64_3 <- base64enc::dataURI(file = "./www/Figures/Upload-2.png", mime = "image/png") 126 | b64_4 <- base64enc::dataURI(file = "./www/Figures/Upload-3.png", mime = "image/png") 127 | b64_5 <- base64enc::dataURI(file = "./www/Figures/Network_view_interactive.png", mime = "image/png") 128 | b64_6 <- base64enc::dataURI(file = "./www/Figures/Community_detection_algorithms.png", mime = "image/png") 129 | b64_7 <- base64enc::dataURI(file = "./www/Figures/Convex_Hulls.PNG", mime = "image/png") 130 | b64_8 <- base64enc::dataURI(file = "./www/Figures/Pies.PNG", mime = "image/png") 131 | b64_9 <- base64enc::dataURI(file = "./www/Figures/Expression_colors.png", mime = "image/png") 132 | b64_10 <- base64enc::dataURI(file = "./www/Figures/Topology.PNG", mime = "image/png") 133 | b64_11 <- base64enc::dataURI(file = "./www/Figures/Topology_comparisons.PNG", mime = "image/png") 134 | b64_12 <- base64enc::dataURI(file = "./www/Figures/venn.png", mime = "image/png") 135 | b64_3D_convex <- base64enc::dataURI(file = "./www/Figures/Convex_Hulls_3D.PNG", mime = "image/png") 136 | b64_strategy1 <- base64enc::dataURI(file = "./www/Figures/Strategy_1.png", mime = "image/png") 137 | b64_strategy2 <- base64enc::dataURI(file = "./www/Figures/Strategy_2.png", mime = "image/png") 138 | b64_strategy3 <- base64enc::dataURI(file = "./www/Figures/Strategy_3.png", mime = "image/png") 139 | 140 | 141 | 142 | # Help pages examples for download 143 | dros_net <- read.delim("./www/Examples/TAU/TAU_network_DEGs_NORMA.txt", header = T) 144 | dros_annot <- read.delim("./www/Examples/TAU/TAU_KEGG_Annotation_NORMA.txt", header = F) 145 | dros_louvain <- read.delim("./www/Examples/TAU/TAU_Louvain.txt", header = F) 146 | dros_express <- read.delim("./www/Examples/TAU/TAU_expressions.txt", header = F) 147 | string_net_tp53 <- read.delim("./www/Examples/TP53/string_interactions.txt", header = T) 148 | string_annot <- read.delim("./www/Examples/TP53/string_interactions_groups_comma_duplicate.txt", header = F) 149 | string_expr <- read.delim("./www/Examples/TP53/string_expression_colors.txt", header = F) 150 | string_net_bcar3 <- read.delim("./www/Examples/BCAR3/BCAR3.txt", header = T) 151 | string_bp <- read.delim("./www/Examples/BCAR3/BCAR3_GO_BP.txt", header = F) 152 | string_mf <- read.delim("./www/Examples/BCAR3/BCAR3_GO_MF.txt", header = F) 153 | string_kegg <- read.delim("./www/Examples/BCAR3/BCAR3_KEGG.txt", header = F) 154 | co_express <- read.delim("./www/Examples/Human_Coexpression/NORMA_Human_coexpression_NETWORK.txt", header = T) 155 | co_express_bp <- read.delim("./www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_GO_BP.txt", header = F) 156 | co_express_mf <- read.delim("./www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_GO_MF.txt", header = F) 157 | co_express_cc <- read.delim("./www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_GO_CC.txt", header = F) 158 | co_express_kegg <- read.delim("./www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_KEGG.txt", header = F) 159 | co_express_mcode <- read.delim("./www/Examples/Human_Coexpression/NORMA_Human_coexpression_Expression_MCODE.txt", header = F) 160 | covid_19_net <- read.delim("./www/Examples/IntAct_COVID19/Intact-data_COVID19_no_self_loops.txt", header = T) 161 | covid_19_interpro <- read.delim("./www/Examples/IntAct_COVID19/HomoSapiens_Protein_Domains_INTERPRO_FILTERED.txt", header = F) 162 | covid_19_bp <- read.delim("./www/Examples/IntAct_COVID19/HomoSapiens_Gene_Ontology_GOTERM_BP_DIRECT_FILTERED.txt", header = F) 163 | covid_19_mf <- read.delim("./www/Examples/IntAct_COVID19/HomoSapiens_Gene_Ontology_GOTERM_MF_DIRECT_FILTERED.txt", header = F) 164 | covid_19_cc <- read.delim("./www/Examples/IntAct_COVID19/HomoSapiens_Gene_Ontology_GOTERM_CC_DIRECT_FILTERED.txt", header = F) 165 | covid_19_kegg <- read.delim("./www/Examples/IntAct_COVID19/HomoSapiens_Pathways_KEGG_PATHWAY_FILTERED.txt", header = F) 166 | covid_19_smart <- read.delim("./www/Examples/IntAct_COVID19/HomoSapiens_Protein_Domains_SMART_FILTERED.txt", header = F) 167 | Gallus_gallus_net <- read.delim("./www/Examples/BioGrid_Chicken_Gallus/Biogrid_no_self_loops.txt", header = T) 168 | Gallus_gallus_kegg <- read.delim("./www/Examples/BioGrid_Chicken_Gallus/BioGrid_Chicken_Gallus_Pathways_KEGG_PATHWAY_FILTERED.txt", header = F) 169 | 170 | R_script <- read.delim("./www/annotation_cleaner.R", header = F) 171 | 172 | # General functions #### 173 | automated_annotation_choices <- function(igraph,automated_annotations_ui){ 174 | if(length(automated_annotations_ui)==0) return(NULL) 175 | results<-list() 176 | 177 | for(i in automated_annotations_ui){ 178 | tmp<-unlist(strsplit(i,"\t",fixed=T)) 179 | description<-tmp[1] 180 | command<-tmp[2] 181 | results[[description]] <- eval(parse(text=command)) 182 | } 183 | return(results[[description]]) 184 | } 185 | 186 | # Colors if there is NOT "NA" in dataset (nodes) 187 | group_pal_rows <- function(n){ 188 | 189 | qual_col_pals[1:300] 190 | 191 | if(n>=300){ 192 | qual_col_pals<-c(qual_col_pals, rep(c("grey50"), times = (n-300) )) 193 | nn<- qual_col_pals[1:n] 194 | nnames<-c(nn) 195 | } else { 196 | nn<- qual_col_pals[1:n] 197 | nnames<-c(nn) 198 | } 199 | } 200 | 201 | mapper <- function(value, istart, istop, ostart, ostop){ 202 | return (ostart + (ostop - ostart) * ((value - istart) / (istop - istart))) 203 | } 204 | 205 | # ui helper function 206 | ui_dataTable_panel <- function(datasetName, pagination = TRUE) { 207 | return(parse( 208 | text = paste0( 209 | "div(div(DT::dataTableOutput('", 210 | datasetName, 211 | "'), class='box-panel-padding'), class='box-panel')" 212 | ) 213 | )) 214 | } 215 | 216 | EmptyDataset <- function(columns) { 217 | dataset <- data.frame(V1 = integer()) 218 | lapply(columns[-1], function(x) 219 | dataset[, x] <<- integer()) 220 | colnames(dataset) <- columns 221 | return(dataset) 222 | } 223 | 224 | # # DO ONCE 225 | # css_colors <- group_pal_rows(300) 226 | # css_generated <- "" 227 | # for (i in 1: 300){ 228 | # css_generated <- paste(css_generated, ".x", i, "{background-color: ", css_colors[i],";}","table.dataTable tr.selected td.x",i,"{background-color: ",css_colors[i], " !important;}", sep="") 229 | # css_generated <- paste(css_generated," ", sep="\n") 230 | # } 231 | # print(css_generated) 232 | -------------------------------------------------------------------------------- /ui.R: -------------------------------------------------------------------------------- 1 | # libs and files #### 2 | source("./views/welcome.R", local=TRUE) 3 | source("./views/upload.R", local=TRUE) 4 | source("./views/network.R", local=TRUE) 5 | source("./views/annotations.R", local=TRUE) 6 | source("./views/topology.R", local=TRUE) 7 | source("./views/help.R", local=TRUE) 8 | source("./views/about.R", local=TRUE) 9 | 10 | # UI fixedPage #### 11 | fixedPage( 12 | theme = shinytheme("sandstone"), 13 | useShinyjs(), 14 | useShinyalert(), 15 | tags$head(tags$script(src = "intro.js")), 16 | tags$head(tags$script(src = "introbutton.js")), 17 | tags$head(tags$link(rel = "stylesheet", type = "text/css", href = "norma.css")), 18 | tags$head(tags$link(rel = "stylesheet", type = "text/css", href = "intro.css")), 19 | tags$head(tags$link(rel = "stylesheet", type = "text/css", href = "annot_table.css")), 20 | tags$head(tags$link(rel = "shortcut icon", href = "favicon.ico")), 21 | tags$img(src = b64_1), 22 | navbarPage("NORMA: The NetwORk Makeup Artist", 23 | tabPanel( "Welcome", welcomePage ), 24 | tabPanel( "Upload", icon = icon("upload"), uploadPage ), 25 | tabPanel( "Network", networkPage ), 26 | tabPanel( "Annotations", annotationsPage), 27 | tabPanel( "Topology", icon = icon("globe", lib = "glyphicon"), topologyPage ), 28 | tabPanel( "Help", icon = icon("question"), helpPage ), 29 | tabPanel( "About", icon = icon("users"), aboutPage ) 30 | ) 31 | ) 32 | -------------------------------------------------------------------------------- /user_temp/folder_create: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PavlopoulosLab/NORMA/8a43f009ca81ac4a2c27793c0d8b95f81109fcee/user_temp/folder_create -------------------------------------------------------------------------------- /views/about.R: -------------------------------------------------------------------------------- 1 | aboutPage <- div(id = "about_div", 2 | strong("The Team:"), 3 | tags$ul( 4 | tags$li("Mikaela Koutrouli - BSRC 'Alexander Fleming'"), 5 | tags$li("Evangelos Karatzas - BSRC 'Alexander Fleming'"), 6 | tags$li("Katerina Papanikolopoulou - BSRC 'Alexander Fleming'"), 7 | tags$li("Yorgos Sofianatos - BSRC 'Alexander Fleming'"), 8 | tags$li("Georgios A. Pavlopoulos - BSRC 'Alexander Fleming'") 9 | ), 10 | br(), 11 | strong("Code:"), 12 | helpText("Available at: https://github.com/PavlopoulosLab/NORMA"), 13 | br(), 14 | strong("Publications:"), 15 | br(), 16 | tags$a(target="_blank", href="https://www.biorxiv.org/content/10.1101/2022.03.02.482621v1.abstract", "The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies"), 17 | helpText("bioRxiv, 2022 March, doi: 10.1101/2022.03.02.482621"), 18 | tags$a(target="_blank", href="https://pubmed.ncbi.nlm.nih.gov/34171457", "NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization"), 19 | helpText("Genomics Proteomics Bioinformatics, 2021 Jun 22:S1672-0229(21)00130-3, doi: 10.1016/j.gpb.2021.02.005, Epub ahead of print, PMID: 34171457.") 20 | ) 21 | -------------------------------------------------------------------------------- /views/network.R: -------------------------------------------------------------------------------- 1 | networkPage <- div(id = "network_div", 2 | conditionalPanel( 3 | condition = "input.availableNetworks == 0", 4 | bsAlert("tabUploadMainAlert"), 5 | uiOutput("uiLoadGraphOptionsOutput_just_network") 6 | ), 7 | br(), br(), 8 | tabsetPanel( 9 | tabPanel( 10 | "Interactive Network", 11 | visNetworkOutput('tabVizIgraphSimple', width = 1000, height = 550), 12 | class = 'box-panel-padding', 13 | 14 | class = 'box-panel', 15 | ), 16 | 17 | tabPanel( 18 | "Automated Community Detection", 19 | br(), 20 | selectInput( 21 | "automated_annotations", 22 | "Community Detection Algorithms:", 23 | choices = automated_annotations_ui, 24 | selected = selected_automated_annotations, 25 | multiple = FALSE 26 | ), 27 | downloadButton("downloadData", "Export as annotation file", icon("download")), 28 | br(), 29 | br(), 30 | prettyCheckbox( 31 | inputId = "show_labels_algorithms_tab",outline = T,fill = T,bigger = T, 32 | label = "Show Labels", 33 | thick = T, 34 | shape = "curve", 35 | animation = "pulse", 36 | status = "info", 37 | inline = F, 38 | value = F 39 | ), 40 | plotOutput("modularity_plot", width = 1000, height = 600), 41 | eval(ui_dataTable_panel('Modularity_table')), 42 | br() 43 | ) 44 | ) #tabsetPanel 45 | ) 46 | -------------------------------------------------------------------------------- /views/topology.R: -------------------------------------------------------------------------------- 1 | topologyPage <- div(id = "topology_div", 2 | sidebarLayout( 3 | sidebarPanel( 4 | bsAlert("tabTopologySideAlert"), 5 | conditionalPanel(condition = "input.statisticsMethodsMainTabsetPanel == 'tableView'", 6 | uiOutput("uiStoredGraphsOutputSelectTopolopgy")), 7 | conditionalPanel( 8 | condition = "input.statisticsMethodsMainTabsetPanel == 'plotView'", 9 | uiOutput("uiStoredGraphsOutputMultipleSelectTopolopgy") 10 | ), 11 | ), 12 | conditionalPanel(condition = "input.availableNetworks == 0", 13 | mainPanel( 14 | bsAlert("tabTopologyMainAlert"), 15 | tabsetPanel( 16 | id = "statisticsMethodsMainTabsetPanel", 17 | tabPanel( 18 | "Summaries", 19 | value = "tableView", 20 | icon = icon("table"), 21 | div( 22 | div( 23 | checkboxGroupInput( 24 | "statistics2", 25 | "The statistics:", 26 | choices = statistics, 27 | selected = selected_statistics 28 | ), 29 | eval(ui_dataTable_panel("statres", FALSE)), 30 | class = 'box-panel-padding', 31 | class = 'box-panel' 32 | ), 33 | div( 34 | span( 35 | actionButton("btnStatSelectAll", "Select all", style = "float: right;"), 36 | class = "input-group-btn" 37 | ), 38 | span(actionButton("btnStatSelectNone", "Clear"), class = "input-group-btn"), 39 | class = "input-group" 40 | ) 41 | ) 42 | ), 43 | tabPanel( 44 | "Comparative Plots", 45 | value = "plotView", 46 | icon = icon("chart-bar"), 47 | div( 48 | div( 49 | radioButtons( 50 | "statistics", 51 | "The statistics:", 52 | choices = statistics, 53 | selected = selected_statistics 54 | ), 55 | uiOutput("statisticsMethodsPlotRender"), 56 | class = 'box-panel-padding' 57 | ), 58 | class = 'box-panel' 59 | ), 60 | tags$style( 61 | HTML( 62 | ".js-irs-6 .irs-bar {border-top-color: #2C8160; border-bottom-color: #2C8160;} .js-irs-6 .irs-bar-edge {border-color: #2C8160;} 63 | .js-irs-6 .irs-single, .js-irs-6 .irs-bar-edge, .js-irs-6 .irs-bar {background: #2C8160;}" 64 | ) 65 | ), 66 | 67 | sliderInput( 68 | "statisticsPlotPercentMagnify", 69 | "Adjust plot height (% taller)", 70 | min = 0, 71 | max = 100, 72 | value = 0 73 | ), 74 | span( 75 | actionButton("btnRefreshPalette", "Refresh palette", icon = icon("sync")) 76 | ) 77 | ) 78 | 79 | ) 80 | )) 81 | ) 82 | ) 83 | -------------------------------------------------------------------------------- /views/upload.R: -------------------------------------------------------------------------------- 1 | uploadPage <- div(id = "upload_div", 2 | sidebarLayout( 3 | 4 | # sidebarPanel #### 5 | sidebarPanel( 6 | actionButton("introButton", "Guide Tutorial"), 7 | br(), 8 | hr(), 9 | tags$div(class="network_div", 10 | tags$h3('1. Networks'), 11 | selectInput( 12 | "uiLoadGraphOptionsInput", 13 | "Choose Network(s)", 14 | c( 15 | "File upload" = "oF", 16 | "Example STRING BCAR3 Network" = "oR_String_interactions", 17 | "Example Drosophila TAU Network" = "oR_Drosophila" 18 | ) 19 | )%>% 20 | shinyInput_label_embed( 21 | shiny_iconlink() %>% 22 | bs_embed_popover( 23 | title = paste0("Please follow the steps below: 24 | - Load your network file in tab delimited format 25 | - Give it a name 26 | - Hit the ADD button") 27 | ) 28 | ), 29 | uiOutput("uiLoadGraphOptionsOutput"), 30 | # checkboxInput("weighted",label = "Weight", value =F), 31 | div( 32 | span( 33 | actionButton( 34 | "btnAddNetwork", 35 | "ADD", 36 | icon = icon("plus"), 37 | style = "color: #fff; background-color: #7F461B; border-color: #7F461B" 38 | ), 39 | class = "input-group-btn" 40 | ), 41 | tags$input( 42 | id = "networkName", 43 | type = "text", 44 | class = "form-control", 45 | placeholder = "Type network name ..", 46 | value = "Network name" 47 | ), 48 | class = "input-group" 49 | ), 50 | uiOutput("uiStoredGraphsOutputRadio") 51 | ), 52 | hr(), 53 | tags$div(class="annotations_div", 54 | tags$h3('2. Annotations'), 55 | ######2nd button-annotation 56 | selectInput( 57 | "uiLoadGraphOptionsInput_annotations", 58 | "Choose Annotation(s)", 59 | c( 60 | "File upload" = "oF", 61 | "Example BCAR3 STRING GO KEGG" = "oR_String_Annotation_KEGG", 62 | "Example BCAR3 STRING GO MF" = "oR_String_Annotation_MF", 63 | "Example BCAR3 STRING GO BP" = "oR_String_Annotation_BP", 64 | "Example TAU Drosophila KEGG" = "oR_Drosophila_KEGG", 65 | "Example TAU Drosophila Louvain" = "oR_Drosophila_Luvain" 66 | ) 67 | )%>% 68 | shinyInput_label_embed( 69 | shiny_iconlink() %>% 70 | bs_embed_popover( 71 | title = paste0("Please follow the steps below: 72 | - Load your annotation file in tab delimited format 73 | - Give it a name 74 | - Hit the ADD button") 75 | ) 76 | ), 77 | uiOutput("uiLoadGraphOptionsOutput_annotations"), 78 | div( 79 | span( 80 | actionButton( 81 | "btnAddNetwork2", 82 | "ADD", 83 | icon = icon("plus"), 84 | style = "color: #fff; background-color: #8D4A43; border-color: #8D4A43" 85 | ), 86 | class = "input-group-btn" 87 | ), 88 | tags$input( 89 | id = "annotationName", 90 | type = "text", 91 | class = "form-control", 92 | placeholder = "Type annotation name ..", 93 | value = "Annotation name" 94 | ), 95 | class = "input-group" 96 | ), 97 | uiOutput("uiStoredGraphsOutputRadio_annotations") 98 | ), 99 | hr(), 100 | tags$div(class="expressions_div", 101 | ######3rd button-expression 102 | tags$h3('3. Node-coloring'), 103 | selectInput( 104 | "uiLoadExpressionsInput", 105 | "Choose node - coloring file(s)", 106 | c("File upload" = "oF", 107 | # "Expression_file_STRING" = "oR_Expression_file_STRING", 108 | "Example TAU Drosophila node - coloring file" = "oR_Expression_file_Drosophila" 109 | ) 110 | )%>% 111 | shinyInput_label_embed( 112 | shiny_iconlink() %>% 113 | bs_embed_popover( 114 | title = paste0("Please follow the steps below: 115 | - Load your node - coloring file in tab delimited format 116 | - Give it a name 117 | - Hit the ADD button") 118 | ) 119 | ), 120 | uiOutput("uiLoadExpressionsOutput"), 121 | div( 122 | span( 123 | actionButton( 124 | "btnAddExpression", 125 | "ADD", 126 | icon = icon("plus"), 127 | style = "color: #fff; background-color: #B89778; border-color: #B89778" 128 | ), 129 | class = "input-group-btn" 130 | ), 131 | tags$input( 132 | id = "expressionName", 133 | type = "text", 134 | class = "form-control", 135 | placeholder = "Type expression name ..", 136 | value = "Node - coloring file name" 137 | ), 138 | class = "input-group" 139 | ), 140 | uiOutput("uiStoredGraphsOutputRadioEx") 141 | ) 142 | ), #sidebarPanel 143 | 144 | # mainPanel #### 145 | mainPanel( 146 | conditionalPanel( 147 | condition = "input.availableNetworks == 0", 148 | uiOutput("uiStoredGraphsOutputSelectUpload") 149 | ), 150 | 151 | conditionalPanel( 152 | condition = "input.availableAnnotations == 0", 153 | uiOutput("uiStoredGraphsOutputSelectUpload2") 154 | ), 155 | tabsetPanel( 156 | tabPanel( 157 | "Table View of Network(s)", 158 | icon = icon("table"), 159 | eval(ui_dataTable_panel('datasettab1')) 160 | ), 161 | tabPanel( 162 | "Table View of Annotation(s)", 163 | icon = icon("table"), 164 | eval(ui_dataTable_panel('datasettab2')) 165 | ) 166 | ) #tabsetPanel 167 | ) # mainPanel 168 | ) # sidebarLayout 169 | ) 170 | -------------------------------------------------------------------------------- /views/welcome.R: -------------------------------------------------------------------------------- 1 | welcomePage <- div(id = "welcome_div", 2 | h1("Welcome to NORMA, the NetwORk Makeup Artist"), 3 | strong("a tool that enables the visualization of annotation groups."), 4 | br(), 5 | br(), 6 | helpText( 7 | "NORMA is a handy tool for interactive network annotation, visualization and topological analysis, 8 | able to handle multiple networks and annotations simultaneously. Annotations and/or node groups can 9 | be precomputed or automatically calculated and users can combine several networks and groupings they 10 | are interested in. Annotated networks can be visualized using both pie-chart nodes and shaded convex 11 | hulls and can be shown using several layouts while users can isolate the groups of interest interactively. 12 | In addition, NORMA is suitable for direct comparison of topological features between one or more networks. 13 | In order for NORMA to run, two simple steps are required:" 14 | ), 15 | tags$ul( 16 | tags$li("1. Please load your network file(s), name it and hit the add button"), 17 | tags$li( 18 | "2. Please load your annotation file(s), name it and hit the add button" 19 | ) 20 | ), 21 | tags$ul( 22 | "Input file instructions as well as downloadable examples can be found in the HELP/EXAMPLES page." 23 | ) 24 | ) 25 | -------------------------------------------------------------------------------- /www/Examples/BCAR3/BCAR3.txt: -------------------------------------------------------------------------------- 1 | Source Target 2 | VCP NPLOC4 3 | BCAR1 PXN 4 | VCP DERL2 5 | NSFL1C VCP 6 | CDC42 WASL 7 | VCP DERL1 8 | NPLOC4 UFD1L 9 | SYVN1 VCP 10 | VCP UFD1L 11 | CDC42 WAS 12 | CDC42 PAK1 13 | CDC42 BAIAP2 14 | VCP FAF2 15 | CDC42 ARHGAP1 16 | VIMP VCP 17 | CDC42 PARD6A 18 | CDC42 TNK2 19 | CDC42 ITSN1 20 | CDC42 ARHGDIA 21 | CDC42 PARD6B 22 | SYVN1 DERL2 23 | CDC42 PAK2 24 | VIMP DERL1 25 | DERL1 DERL2 26 | WAS BAIAP2 27 | CDC42 PXN 28 | FAF2 DERL2 29 | SYVN1 DERL1 30 | UFD1L FAF2 31 | NPLOC4 FAF2 32 | BCAR1 BCAR3 33 | ITSN1 WASL 34 | BAIAP2 WASL 35 | BCAR1 TNK2 36 | BCAR1 CDC42 37 | PAK1 PXN 38 | PAK1 ARHGDIA 39 | FAF2 DERL1 40 | NEDD9 PXN 41 | PAK2 PAK1 42 | VIMP DERL2 43 | SYVN1 FAF2 44 | VIMP SYVN1 45 | CDC42 BCAR3 46 | UFD1L DERL1 47 | PAK2 PXN 48 | NSFL1C UFD1L 49 | NEDD9 BCAR3 50 | PARD6B PARD6A 51 | BAIAP2 PXN 52 | NSFL1C NPLOC4 53 | BCAR1 BAIAP2 54 | PAK2 PARD6A 55 | SYVN1 UFD1L 56 | WAS WASL 57 | TULP4 SPSB1 58 | SYVN1 NPLOC4 59 | VIMP FAF2 60 | UFD1L DERL2 61 | NPLOC4 DERL1 62 | NPLOC4 DERL2 63 | ITSN1 WAS 64 | VIMP NPLOC4 65 | TNK2 WAS 66 | NSFL1C FAF2 67 | TULP4 KCNE4 68 | BCAR3 TULP4 69 | BCAR3 KCNE4 70 | NSFL1C DERL2 71 | SAT1 BCAR3 72 | NSFL1C DERL1 73 | BCAR3 VCP 74 | PAK2 ARHGDIA 75 | KCNE4 TULP1 76 | BCAR3 TULP1 77 | PXN WASL 78 | VIMP UFD1L 79 | WAS ARHGAP1 80 | WAS PXN 81 | WAS PAK1 82 | BCAR3 SPSB1 83 | ARHGAP1 ARHGDIA 84 | BCAR1 PARD6A 85 | PAK1 WASL 86 | BCAR1 WASL 87 | ARHGDIA PXN 88 | BCAR1 WAS 89 | PAK2 WASL 90 | WAS PAK2 91 | ARHGAP1 PXN 92 | ARHGDIA WASL -------------------------------------------------------------------------------- /www/Examples/BCAR3/BCAR3_GO_BP.txt: -------------------------------------------------------------------------------- 1 | cellular process ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,FAF2,ITSN1,KCNE4,NEDD9,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PARD6B,PXN,SAT1,SPSB1,SYVN1,TNK2,TULP1,TULP4,UFD1L,VCP,VIMP,WAS,WASL 2 | biological regulation ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,FAF2,ITSN1,KCNE4,NEDD9,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PARD6B,PXN,SAT1,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 3 | regulation of biological process ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,ITSN1,KCNE4,NEDD9,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PARD6B,PXN,SAT1,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 4 | regulation of cellular process ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,ITSN1,NEDD9,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PARD6B,PXN,SAT1,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 5 | response to stimulus ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,FAF2,ITSN1,NEDD9,NPLOC4,PAK1,PAK2,PARD6A,PXN,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 6 | localization ARHGAP1,BAIAP2,BCAR1,CDC42,DERL1,DERL2,FAF2,ITSN1,KCNE4,NPLOC4,NSFL1C,PAK1,PAK2,PXN,SYVN1,TNK2,TULP1,TULP4,UFD1L,VCP,VIMP,WAS,WASL 7 | cellular response to stimulus ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,FAF2,ITSN1,NEDD9,NPLOC4,PAK1,PAK2,PARD6A,PXN,SYVN1,TNK2,UFD1L,VCP,VIMP,WAS,WASL 8 | signal transduction ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,ITSN1,NEDD9,PAK1,PAK2,PARD6A,PXN,SYVN1,TNK2,VCP,VIMP,WAS,WASL 9 | establishment of localization ARHGAP1,BAIAP2,CDC42,DERL1,DERL2,FAF2,ITSN1,KCNE4,NPLOC4,NSFL1C,PAK1,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 10 | positive regulation of biological process ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,ITSN1,NSFL1C,PAK1,PAK2,PARD6A,PXN,TNK2,TULP1,VCP,WAS,WASL 11 | regulation of response to stimulus ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL2,ITSN1,NPLOC4,PAK1,PAK2,PXN,SYVN1,UFD1L,VCP,VIMP,WAS,WASL 12 | transport ARHGAP1,BAIAP2,CDC42,DERL1,DERL2,FAF2,ITSN1,KCNE4,NPLOC4,PAK1,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 13 | positive regulation of cellular process ARHGAP1,ARHGDIA,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,ITSN1,NSFL1C,PAK1,PAK2,PXN,TNK2,TULP1,VCP,WAS,WASL 14 | cellular component organization BAIAP2,BCAR1,CDC42,DERL1,FAF2,ITSN1,NEDD9,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PARD6B,PXN,TULP1,VCP,WAS,WASL 15 | response to chemical BAIAP2,BCAR1,BCAR3,CDC42,DERL1,DERL2,FAF2,NPLOC4,PAK1,PAK2,PARD6A,PXN,SYVN1,UFD1L,VCP,VIMP,WAS 16 | cellular localization ARHGAP1,CDC42,DERL1,DERL2,FAF2,ITSN1,NPLOC4,NSFL1C,SYVN1,TULP1,TULP4,UFD1L,VCP,VIMP,WAS,WASL 17 | response to organic substance BAIAP2,BCAR1,CDC42,DERL1,DERL2,FAF2,NPLOC4,PAK1,PAK2,PARD6A,PXN,SYVN1,UFD1L,VCP,VIMP,WAS 18 | negative regulation of biological process ARHGAP1,ARHGDIA,CDC42,DERL2,ITSN1,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,SYVN1,TNK2,UFD1L,VIMP,WAS,WASL 19 | organonitrogen compound metabolic process CDC42,DERL1,DERL2,FAF2,NPLOC4,NSFL1C,PAK1,PAK2,SAT1,SPSB1,SYVN1,TNK2,TULP4,UFD1L,VCP,VIMP 20 | cellular protein metabolic process CDC42,DERL1,DERL2,FAF2,NPLOC4,NSFL1C,PAK1,PAK2,SPSB1,SYVN1,TNK2,TULP4,UFD1L,VCP,VIMP 21 | establishment of localization in cell ARHGAP1,CDC42,DERL1,DERL2,FAF2,ITSN1,NPLOC4,NSFL1C,SYVN1,UFD1L,VCP,VIMP,WAS,WASL 22 | cellular response to organic substance BAIAP2,BCAR1,CDC42,DERL1,DERL2,PAK1,PAK2,PARD6A,PXN,SYVN1,UFD1L,VCP,VIMP,WAS 23 | regulation of signal transduction ARHGAP1,ARHGDIA,BAIAP2,BCAR3,CDC42,ITSN1,NPLOC4,PAK1,PAK2,PXN,SYVN1,UFD1L,VCP,VIMP 24 | response to stress CDC42,DERL1,DERL2,FAF2,NPLOC4,PAK1,PAK2,PXN,SYVN1,TNK2,UFD1L,VCP,VIMP,WAS 25 | negative regulation of cellular process ARHGAP1,ARHGDIA,CDC42,DERL2,ITSN1,NPLOC4,PAK1,PAK2,PARD6A,SYVN1,UFD1L,VIMP,WAS,WASL 26 | protein localization ARHGAP1,BAIAP2,DERL1,DERL2,FAF2,NPLOC4,SYVN1,TULP1,TULP4,UFD1L,VCP,VIMP,WASL 27 | cell surface receptor signaling pathway ARHGDIA,BAIAP2,BCAR1,CDC42,ITSN1,NEDD9,PAK1,PAK2,PARD6A,PXN,TNK2,WAS,WASL 28 | regulation of cellular component organization ARHGDIA,BAIAP2,BCAR1,CDC42,DERL2,NSFL1C,PAK1,PXN,TNK2,TULP1,VCP,WAS,WASL 29 | regulation of localization ARHGAP1,BCAR1,DERL2,KCNE4,NSFL1C,PAK1,PARD6A,PARD6B,TNK2,TULP1,VIMP,WAS,WASL 30 | regulation of molecular function ARHGAP1,ARHGDIA,BCAR3,DERL1,FAF2,ITSN1,NSFL1C,PAK1,PAK2,TNK2,VCP,WAS,WASL 31 | response to organonitrogen compound BAIAP2,BCAR1,DERL1,DERL2,FAF2,NPLOC4,PAK1,PXN,SYVN1,UFD1L,VCP,VIMP 32 | intracellular transport ARHGAP1,CDC42,DERL1,DERL2,FAF2,NPLOC4,SYVN1,UFD1L,VCP,VIMP,WAS,WASL 33 | cellular protein modification process CDC42,DERL1,DERL2,PAK1,PAK2,SPSB1,SYVN1,TNK2,TULP4,UFD1L,VCP,VIMP 34 | organelle organization BAIAP2,BCAR1,CDC42,FAF2,NEDD9,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,WAS,WASL 35 | cellular protein localization DERL1,DERL2,FAF2,NPLOC4,SYVN1,TULP1,TULP4,UFD1L,VCP,VIMP,WASL 36 | vesicle-mediated transport ARHGAP1,BAIAP2,CDC42,FAF2,ITSN1,PAK1,TNK2,TULP1,VCP,WAS,WASL 37 | positive regulation of response to stimulus ARHGAP1,BAIAP2,BCAR1,BCAR3,CDC42,ITSN1,PAK1,PAK2,VCP,WAS,WASL 38 | regulation of catalytic activity ARHGAP1,ARHGDIA,FAF2,ITSN1,NSFL1C,PAK1,PAK2,TNK2,VCP,WAS,WASL 39 | cellular component assembly BAIAP2,CDC42,DERL1,NEDD9,NSFL1C,PARD6A,PARD6B,PXN,VCP,WAS,WASL 40 | enzyme linked receptor protein signaling pathway BAIAP2,BCAR1,CDC42,ITSN1,PAK1,PAK2,PARD6A,PXN,TNK2,WASL 41 | regulation of immune response BAIAP2,BCAR1,CDC42,NPLOC4,PAK1,PAK2,UFD1L,VIMP,WAS,WASL 42 | cytoskeleton organization BAIAP2,BCAR1,CDC42,NEDD9,NSFL1C,PAK1,PAK2,PARD6A,WAS,WASL 43 | organonitrogen compound catabolic process DERL1,DERL2,FAF2,NPLOC4,NSFL1C,SAT1,SYVN1,UFD1L,VCP,VIMP 44 | positive regulation of cellular component organization ARHGDIA,BAIAP2,CDC42,NSFL1C,PAK1,PXN,TULP1,VCP,WAS,WASL 45 | cellular response to stress DERL1,DERL2,FAF2,NPLOC4,PAK2,PXN,SYVN1,UFD1L,VCP,VIMP 46 | cellular catabolic process DERL1,DERL2,FAF2,NPLOC4,NSFL1C,SAT1,SYVN1,UFD1L,VCP,VIMP 47 | regulation of intracellular signal transduction ARHGAP1,ARHGDIA,CDC42,ITSN1,NPLOC4,PAK1,PAK2,SYVN1,UFD1L,VIMP 48 | multi-organism process BAIAP2,CDC42,DERL1,DERL2,ITSN1,PAK2,PARD6A,VCP,VIMP,WASL 49 | immune system process BAIAP2,BCAR1,CDC42,FAF2,PAK1,PAK2,TNK2,VCP,WAS,WASL 50 | proteasome-mediated ubiquitin-dependent protein catabolic process DERL1,DERL2,FAF2,NPLOC4,NSFL1C,SYVN1,UFD1L,VCP,VIMP 51 | transmembrane receptor protein tyrosine kinase signaling pathway BAIAP2,BCAR1,CDC42,ITSN1,PAK1,PAK2,PXN,TNK2,WASL 52 | import into cell ARHGAP1,BAIAP2,CDC42,ITSN1,PAK1,TNK2,TULP1,WAS,WASL 53 | protein transport ARHGAP1,DERL1,DERL2,FAF2,NPLOC4,SYVN1,UFD1L,VCP,VIMP 54 | regulation of cellular protein metabolic process BCAR3,DERL1,DERL2,NSFL1C,PAK1,PAK2,PARD6A,TNK2,VCP 55 | retrograde protein transport, ER to cytosol DERL1,DERL2,FAF2,NPLOC4,SYVN1,UFD1L,VCP,VIMP 56 | small GTPase mediated signal transduction ARHGAP1,BCAR3,CDC42,ITSN1,PAK1,PAK2,TNK2,WAS 57 | actin cytoskeleton organization BAIAP2,BCAR1,CDC42,NEDD9,PAK1,PAK2,WAS,WASL 58 | regulation of cytoskeleton organization ARHGDIA,BAIAP2,CDC42,NSFL1C,PAK1,PXN,WAS,WASL 59 | endocytosis BAIAP2,CDC42,ITSN1,PAK1,TNK2,TULP1,WAS,WASL 60 | protein modification by small protein conjugation or removal CDC42,DERL1,SPSB1,SYVN1,TULP4,UFD1L,VCP,VIMP 61 | generation of neurons ARHGDIA,BAIAP2,CDC42,PAK1,PAK2,PARD6B,TULP1,WASL 62 | regulation of apoptotic process ARHGDIA,BCAR1,ITSN1,PAK1,PAK2,SYVN1,VCP,VIMP 63 | regulation of phosphate metabolic process BCAR3,ITSN1,NSFL1C,PAK1,PAK2,PARD6A,TNK2,VCP 64 | regulation of transport ARHGAP1,DERL2,KCNE4,PAK1,TNK2,TULP1,VIMP,WASL 65 | regulation of protein modification process BCAR3,DERL1,NSFL1C,PAK1,PAK2,PARD6A,TNK2,VCP 66 | anatomical structure morphogenesis BAIAP2,BCAR3,CDC42,PAK1,PARD6B,SAT1,TULP1,WASL 67 | ubiquitin-dependent ERAD pathway DERL1,DERL2,FAF2,NPLOC4,SYVN1,VCP,VIMP 68 | response to topologically incorrect protein DERL1,DERL2,FAF2,SYVN1,UFD1L,VCP,VIMP 69 | positive regulation of cytoskeleton organization BAIAP2,CDC42,NSFL1C,PAK1,PXN,WAS,WASL 70 | immune response-activating cell surface receptor signaling pathway BAIAP2,BCAR1,CDC42,PAK1,PAK2,WAS,WASL 71 | regulation of actin cytoskeleton organization ARHGDIA,BAIAP2,CDC42,PAK1,PXN,WAS,WASL 72 | positive regulation of cellular component biogenesis BAIAP2,CDC42,PAK1,PXN,VCP,WAS,WASL 73 | neuron projection development BAIAP2,CDC42,PAK1,PAK2,PARD6B,TULP1,WASL 74 | protein ubiquitination CDC42,DERL1,SPSB1,SYVN1,TULP4,VCP,VIMP 75 | immune effector process BAIAP2,CDC42,FAF2,PAK1,VCP,WAS,WASL 76 | regulation of response to stress DERL2,NPLOC4,PAK1,PAK2,SYVN1,UFD1L,VIMP 77 | movement of cell or subcellular component BCAR1,CDC42,PAK2,PXN,TNK2,WAS,WASL 78 | regulation of phosphorylation BCAR3,ITSN1,PAK1,PAK2,PARD6A,TNK2,VCP 79 | positive regulation of signal transduction ARHGAP1,BAIAP2,BCAR3,ITSN1,PAK1,PAK2,VCP 80 | Fc receptor signaling pathway BAIAP2,CDC42,PAK1,PAK2,WAS,WASL 81 | cellular response to topologically incorrect protein DERL1,DERL2,SYVN1,UFD1L,VCP,VIMP 82 | response to unfolded protein DERL1,DERL2,FAF2,SYVN1,VCP,VIMP 83 | positive regulation of supramolecular fiber organization BAIAP2,CDC42,PAK1,PXN,WAS,WASL 84 | phagocytosis BAIAP2,CDC42,PAK1,TULP1,WAS,WASL 85 | actin filament organization BAIAP2,BCAR1,CDC42,NEDD9,WAS,WASL 86 | regulation of actin filament organization BAIAP2,CDC42,PAK1,PXN,WAS,WASL 87 | regulation of protein complex assembly BAIAP2,CDC42,PAK1,VCP,WAS,WASL 88 | viral process CDC42,DERL1,ITSN1,PAK2,PARD6A,VCP 89 | regulation of plasma membrane bounded cell projection organization ARHGDIA,BAIAP2,CDC42,PAK1,WAS,WASL 90 | regulation of growth BCAR1,CDC42,DERL2,NEDD9,PAK1,PAK2 91 | positive regulation of phosphorylation BCAR3,ITSN1,PAK1,PAK2,TNK2,VCP 92 | cellular response to endogenous stimulus BAIAP2,BCAR1,PAK1,PARD6A,PXN,VIMP 93 | positive regulation of protein modification process BCAR3,DERL1,PAK1,PAK2,TNK2,VCP 94 | regulation of hydrolase activity ARHGAP1,ARHGDIA,NSFL1C,PAK2,TNK2,VCP 95 | vascular endothelial growth factor receptor signaling pathway BAIAP2,BCAR1,CDC42,PAK2,PXN 96 | Fc-gamma receptor signaling pathway involved in phagocytosis BAIAP2,CDC42,PAK1,WAS,WASL 97 | dendrite development BAIAP2,CDC42,PAK2,TULP1,WASL 98 | endoplasmic reticulum unfolded protein response DERL1,DERL2,SYVN1,VCP,VIMP 99 | establishment or maintenance of cell polarity CDC42,NSFL1C,PAK1,PARD6A,PARD6B 100 | -------------------------------------------------------------------------------- /www/Examples/BCAR3/BCAR3_GO_MF.txt: -------------------------------------------------------------------------------- 1 | protein binding ARHGAP1,BAIAP2,BCAR1,BCAR3,CDC42,DERL1,FAF2,ITSN1,KCNE4,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PXN,SAT1,SYVN1,TNK2,TULP1,UFD1L,VCP,VIMP,WAS,WASL 2 | enzyme binding ARHGAP1,BCAR1,BCAR3,CDC42,DERL1,FAF2,ITSN1,NPLOC4,NSFL1C,PAK1,PAK2,PARD6A,PXN,SYVN1,TNK2,UFD1L,VCP,VIMP,WAS 3 | molecular function regulator ARHGAP1,ARHGDIA,BCAR3,FAF2,ITSN1,NSFL1C,PAK2,TNK2,VCP,WAS,WASL 4 | enzyme regulator activity ARHGAP1,ARHGDIA,FAF2,ITSN1,NSFL1C,PAK2,TNK2,VCP,WAS,WASL 5 | identical protein binding BAIAP2,CDC42,PAK1,PAK2,SAT1,TNK2,VCP,WAS 6 | protein kinase binding BCAR1,CDC42,PAK1,PAK2,PARD6A,PXN,WAS 7 | GTPase binding ARHGAP1,BCAR3,ITSN1,PAK1,PAK2,PARD6A,WAS 8 | protein domain specific binding ARHGAP1,BAIAP2,BCAR1,CDC42,TNK2,VCP,WAS 9 | ubiquitin protein ligase binding DERL1,FAF2,NPLOC4,PXN,TNK2,VCP 10 | Ras GTPase binding ARHGAP1,ITSN1,PAK1,PAK2,PARD6A,WAS 11 | ATPase binding DERL1,NSFL1C,SYVN1,UFD1L,VIMP 12 | Rho GTPase binding ITSN1,PAK1,PAK2,PARD6A,WAS 13 | GTPase regulator activity ARHGAP1,ARHGDIA,TNK2,WAS,WASL 14 | enzyme activator activity ARHGAP1,ARHGDIA,ITSN1,PAK2,VCP 15 | ubiquitin-specific protease binding DERL1,SYVN1,VCP,VIMP 16 | protein serine/threonine kinase activity CDC42,PAK1,PAK2,TNK2 17 | Rac GTPase binding PAK1,PAK2,WAS 18 | ubiquitin binding FAF2,NPLOC4,NSFL1C 19 | SH3 domain binding ARHGAP1,BCAR1,WAS 20 | protein binding, bridging ARHGAP1,BAIAP2,BCAR3 21 | -------------------------------------------------------------------------------- /www/Examples/BCAR3/BCAR3_KEGG.txt: -------------------------------------------------------------------------------- 1 | Protein processing in endoplasmic reticulum DERL1,DERL2,NPLOC4,NSFL1C,SYVN1,UFD1L,VCP,VIMP 2 | Regulation of actin cytoskeleton BAIAP2,BCAR1,CDC42,PAK1,PAK2,PXN,WAS,WASL 3 | Chemokine signaling pathway BCAR1,CDC42,PAK1,PXN,WAS,WASL 4 | Bacterial invasion of epithelial cells BCAR1,CDC42,PXN,WAS,WASL 5 | Tight junction CDC42,PARD6A,PARD6B,WAS,WASL 6 | Axon guidance CDC42,PAK1,PAK2,PARD6A,PARD6B 7 | Focal adhesion BCAR1,CDC42,PAK1,PAK2,PXN 8 | Endocytosis CDC42,PARD6A,PARD6B,WAS,WASL 9 | Adherens junction BAIAP2,CDC42,WAS,WASL 10 | Fc gamma R-mediated phagocytosis CDC42,PAK1,WAS,WASL 11 | Rap1 signaling pathway BCAR1,CDC42,PARD6A,PARD6B 12 | Human papillomavirus infection CDC42,PARD6A,PARD6B,PXN 13 | Pathogenic Escherichia coli infection CDC42,WAS,WASL 14 | Shigellosis CDC42,WAS,WASL 15 | Renal cell carcinoma CDC42,PAK1,PAK2 16 | Salmonella infection CDC42,WAS,WASL 17 | T cell receptor signaling pathway CDC42,PAK1,PAK2 18 | Leukocyte transendothelial migration BCAR1,CDC42,PXN 19 | Proteoglycans in cancer CDC42,PAK1,PXN 20 | Ras signaling pathway CDC42,PAK1,PAK2 21 | MAPK signaling pathway CDC42,PAK1,PAK2 22 | VEGF signaling pathway CDC42,PXN 23 | Epithelial cell signaling in Helicobacter pylori infection CDC42,PAK1 24 | ErbB signaling pathway PAK1,PAK2 25 | Choline metabolism in cancer WAS,WASL 26 | Neurotrophin signaling pathway ARHGDIA,CDC42 27 | Hippo signaling pathway PARD6A,PARD6B -------------------------------------------------------------------------------- /www/Examples/BioGrid_Chicken_Gallus/BioGrid_Chicken_Gallus_Pathways_KEGG_PATHWAY_FILTERED.txt: -------------------------------------------------------------------------------- 1 | ErbB signaling pathway Q00944,Q04929,P00523,P01109,Q90891,P13387,Q9W7C5,P05625,Q04982 2 | Carbon metabolism P00356,O57391,P00548,P07341,P51903,Q5ZLN1,Q5ZME2,P51913,P00940,P00508 3 | Biosynthesis of antibiotics P00356,O57391,P00548,P07341,O57535,P51903,Q5ZLN1,P00337,Q5ZME2,P51913,P00940,P00508,P00340,P38024 4 | Gap junction P00523,P09244,Q90891,P08070,P13387,P50147,P09207,P05625,P13863 5 | Ribosome Q98TF6,Q98TF8,P67883,P32429,P61355,P47826,Q5ZJ56,P47836,P50890,P18660,P22451 6 | Focal adhesion Q00944,Q04929,P00523,Q90623,P13387,P05094,P60706,P53478,P11799,P49024,P12003,Q04982,P62207,P05625 7 | Progesterone-mediated oocyte maturation Q04619,P07812,P18652,P11501,P50147,P05625,Q04982,P13863 8 | Vascular smooth muscle contraction Q8AYS8,P11799,Q90623,P05419,P63270,Q90891,P62207,P05625,Q04982 9 | Protein processing in endoplasmic reticulum Q04619,Q5ZKF5,Q90593,Q8JG64,O73885,P11501,P08110,Q5ZHY5,P81628,Q5ZK03,P08106 10 | Pyruvate metabolism P00548,P00337,Q5ZME2,P11029,P00340 11 | VEGF signaling pathway Q00944,P00523,P49024,Q90891,P05625,Q00649 12 | Insulin signaling pathway Q04929,P05419,Q90891,P11029,P62207,P05625,Q04982,O13016 13 | Tight junction P00523,P48463,P05094,P60706,P53478,Q01406 -------------------------------------------------------------------------------- /www/Examples/BioGrid_Chicken_Gallus/Biogrid_no_self_loops.txt: -------------------------------------------------------------------------------- 1 | Source Target 2 | P62760 P60706 3 | P62764 P60706 4 | O15392 P53352 5 | Q9IAY5 P49024 6 | Q9IAY5 P49024 7 | P49024 Q9IAY5 8 | Q13625 P46936 9 | O93512 O60542 10 | P41238 Q7T2T1 11 | O42414 Q9JI92 12 | O42414 Q9JI92 13 | P05556 Q00944 14 | P05556 P49024 15 | P27986 Q9DDT2 16 | P28497 P23297 17 | P49024 P12003 18 | P49024 Q00944 19 | Q4KWZ7 Q9DEA3 20 | Q9DEA3 Q4KWZ7 21 | P53478 Q9UUJ1 22 | P53478 P32390 23 | P53478 P78929 24 | P12003 P60010 25 | P79987 P56517 26 | P79987 P56519 27 | P79987 Q9W7I5 28 | P79987 Q3C1E9 29 | Q9W7I5 P79987 30 | P56517 P79987 31 | P56519 P79987 32 | Q5ZJY5 O93257 33 | Q5R1T0 P56517 34 | Q5R1T0 P56519 35 | Q5R1T0 P56517 36 | Q5R1T0 P56519 37 | Q5R1T0 P56520 38 | Q09472 P17678 39 | P23204 P17678 40 | P23204 P23824 41 | P23204 P23825 42 | Q92993 P70082 43 | Q92993 P0C1H3 44 | Q92993 P84247 45 | Q92993 P62801 46 | P56519 Q9HAZ2 47 | O18738 P31696 48 | Q8AYS7 Q1T7B8 49 | Q8AYS7 Q1T7C0 50 | Q8AYS7 Q1T7B7 51 | Q8AYS7 Q1T7C1 52 | Q8AYS7 Q1T7B9 53 | Q90ZF9 Q1T7B8 54 | Q90ZF9 Q1T7C0 55 | Q90ZF9 Q1T7B7 56 | Q90ZF9 Q1T7C1 57 | Q90ZF9 Q1T7B9 58 | Q76I90 Q76I89 59 | Q76I89 Q76I90 60 | Q8AYS8 P09572 61 | Q8AYS8 P11501 62 | Q8AYS8 Q90593 63 | Q8AYS8 P16053 64 | Q8AYS8 P08106 65 | Q8AYS8 O73885 66 | Q8AYS8 Q5ZHY5 67 | Q8AYS8 Q5ZL72 68 | Q8AYS8 P09207 69 | Q8AYS8 Q5ZLC5 70 | Q8AYS8 P05094 71 | Q8AYS8 P00508 72 | Q8AYS8 P54097 73 | Q8AYS8 P17153 74 | Q8AYS8 Q5ZMT0 75 | Q8AYS8 P28497 76 | Q8AYS8 P62207 77 | Q8AYS8 Q5ZKC9 78 | Q8AYS8 Q5F3W6 79 | Q8AYS8 P60878 80 | Q8AYS8 Q5ZM44 81 | Q8AYS8 P08250 82 | Q8AYS8 Q5ZMB2 83 | Q8AYS8 Q00649 84 | Q8AYS8 Q5ZKK4 85 | Q8AYS8 Q5ZIV5 86 | Q8AYS8 Q5ZMD1 87 | Q8AYS8 Q5ZLQ6 88 | Q8AYS8 P07090 89 | Q8AYS8 P81628 90 | Q8AYS8 P42324 91 | Q8AYS8 P62758 92 | Q8AYS8 P62764 93 | Q8AYS8 P08110 94 | Q8AYS8 O93510 95 | Q8AYS8 P13731 96 | Q8AYS8 Q5F425 97 | Q8AYS8 P18359 98 | Q8AYS8 P02789 99 | Q8AYS8 Q5ZL57 100 | Q8AYS8 P19121 101 | Q8AYS8 O57391 102 | Q8AYS8 Q9PTG6 103 | Q8AYS8 P63270 104 | Q8AYS8 P51913 105 | Q8AYS8 P05122 106 | Q8AYS8 Q5ZME2 107 | Q8AYS8 Q5ZHP5 108 | Q8AYS8 P48463 109 | Q8AYS8 P04354 110 | Q8AYS8 P50890 111 | Q8AYS8 P05419 112 | Q8AYS8 P80566 113 | Q8AYS8 P31395 114 | Q8AYS8 P00940 115 | Q8AYS8 Q5ZLN1 116 | Q8AYS8 Q5ZJF4 117 | Q8AYS8 P00340 118 | Q8AYS8 P09654 119 | Q8AYS8 O42163 120 | Q8AYS8 P16580 121 | Q8AYS8 P02112 122 | Q8AYS8 P80026 123 | Q8AYS8 Q5ZLG1 124 | Q8AYS8 O57535 125 | Q8AYS8 Q07212 126 | Q8AYS8 O13268 127 | Q8AYS8 P00337 128 | Q8AYS8 P00356 129 | Q8AYS8 P51903 130 | Q8AYS8 P07341 131 | Q8AYS8 P00548 132 | Q8AYS8 P14732 133 | Q8AYS8 P13648 134 | Q8AYS8 Q5F3W6 135 | Q8AYS8 P42324 136 | Q8AYS8 P60878 137 | Q8AYS8 P17153 138 | Q8AYS8 Q5ZL72 139 | Q8AYS8 Q5F425 140 | Q8AYS8 P80566 141 | Q8AYS8 Q01406 142 | Q8AYS8 P08106 143 | Q8AYS8 P31395 144 | Q8AYS8 Q90593 145 | Q8AYS8 Q04619 146 | Q8AYS8 P14731 147 | Q5F3W6 Q8AYS8 148 | P42324 Q8AYS8 149 | P60878 Q8AYS8 150 | P17153 Q8AYS8 151 | Q5ZL72 Q8AYS8 152 | Q5F425 Q8AYS8 153 | P80566 Q8AYS8 154 | Q01406 Q8AYS8 155 | P08106 Q8AYS8 156 | P31395 Q8AYS8 157 | Q90593 Q8AYS8 158 | Q04619 Q8AYS8 159 | P14731 Q8AYS8 160 | P84023 P49140 161 | P84023 P83038 162 | P38531 P04637 163 | P38531 P06876 164 | P38531 P01103 165 | F1N9Y5 P00548 166 | F1N9Y5 P09244 167 | F1N9Y5 O73885 168 | F1N9Y5 Q5ZL72 169 | F1N9Y5 P11501 170 | F1N9Y5 Q90705 171 | F1N9Y5 Q5ZLC5 172 | F1N9Y5 P51913 173 | F1N9Y5 Q5ZM98 174 | F1N9Y5 P38024 175 | F1N9Y5 P47826 176 | F1N9Y5 P08070 177 | F1N9Y5 Q90593 178 | F1N9Y5 P15771 179 | F1N9Y5 Q9IAY5 180 | F1N9Y5 P50890 181 | F1N9Y5 Q5ZJK8 182 | F1N9Y5 P51903 183 | F1N9Y5 P67883 184 | F1N9Y5 P00340 185 | F1N9Y5 Q6EE31 186 | F1N9Y5 P22451 187 | F1N9Y5 Q8UVD9 188 | F1N9Y5 Q5ZJU3 189 | F1N9Y5 O57535 190 | F1N9Y5 Q5ZLP8 191 | F1N9Y5 Q04619 192 | F1N9Y5 Q5ZIQ3 193 | F1N9Y5 P47836 194 | F1N9Y5 Q5ZKC9 195 | F1N9Y5 Q5ZK03 196 | F1N9Y5 Q8AYC9 197 | F1N9Y5 P00356 198 | F1N9Y5 Q5ZLN4 199 | F1N9Y5 Q5ZJ56 200 | F1N9Y5 P18660 201 | F1N9Y5 Q5ZMT0 202 | F1N9Y5 Q8JFP1 203 | F1N9Y5 P32429 204 | F1N9Y5 P16039 205 | F1N9Y5 P00337 206 | F1N9Y5 P08106 207 | F1N9Y5 Q5ZMS3 208 | F1N9Y5 P61355 209 | F1N9Y5 Q5ZJ54 210 | F1N9Y5 P63247 211 | F1N9Y5 Q5ZKA5 212 | F1N9Y5 P08629 213 | F1N9Y5 P16527 214 | F1N9Y5 Q5ZMN2 215 | F1N9Y5 Q5ZJZ5 216 | F1N9Y5 P18359 217 | F1N9Y5 Q5ZKF5 218 | F1N9Y5 Q5ZLN1 219 | F1N9Y5 Q9YGC1 220 | F1N9Y5 Q5ZLE6 221 | F1N9Y5 Q8UW59 222 | F1N9Y5 Q5ZKB9 223 | F1N9Y5 P13863 224 | F1N9Y5 Q90WU3 225 | F1N9Y5 Q5ZI72 226 | F1N9Y5 Q5ZIA5 227 | F1N9Y5 P11029 228 | F1N9Y5 Q98TF8 229 | F1N9Y5 Q5ZL42 230 | F1N9Y5 Q5ZKC1 231 | F1N9Y5 P17790 232 | F1N9Y5 Q5ZMN3 233 | F1N9Y5 Q98TF6 234 | F1N9Y5 Q5ZLC6 235 | F1N9Y5 P24367 236 | F1N9Y5 P11799 237 | F1N9Y5 Q5ZK62 238 | F1N9Y5 P26584 239 | F1N9Y5 P14315 240 | F1N9Y5 Q5ZKG5 241 | F1N9Y5 P42558 242 | F1N9Y5 P41239 243 | F1N9Y5 P05419 244 | F1N9Y5 P43347 245 | F1N9Y5 P63283 246 | F1N9Y5 Q5ZJN4 247 | F1N9Y5 Q5ZL57 248 | F1N9Y5 Q8JG64 249 | F1N9Y5 O42392 250 | F1N9Y5 Q5ZK01 251 | F1N9Y5 P19179 252 | F1N9Y5 O93256 253 | F1N9Y5 Q02391 254 | P28683 P62140 255 | Q6A078 P00698 256 | P68400 O13016 257 | P12931 O13016 258 | P07812 Q04619 259 | P07812 P08106 260 | P62207 Q90623 261 | Q90ZF9 Q76I89 262 | Q90ZF9 Q76I90 263 | Q90ZF9 Q76I89 264 | P00523 P19785 265 | P11501 Q5ZL72 266 | P11501 P08106 267 | Q04619 Q5ZL72 268 | Q04619 P08106 269 | P68399 P01109 270 | P67868 P01109 271 | Q12341 P02263 272 | Q12341 P62801 273 | Q5ZL72 P08106 274 | Q5ZL72 Q04619 275 | Q04619 P08106 276 | Q06592 P62801 277 | Q06592 P84247 278 | P39979 P62801 279 | Q3C1E9 P79987 280 | Q3C1E9 Q5R1S9 281 | Q3C1E9 P84247 282 | Q3C1E9 P62801 283 | P07812 Q15185 284 | P07812 P07900 285 | P07812 P34932 286 | P07812 P25685 287 | P07812 P31948 288 | P25293 P70082 289 | P25293 P0C1H3 290 | P25293 P84247 291 | P25293 P62801 292 | Q702N8 P68139 293 | A4UGR9 P68139 294 | P68139 P42639 295 | P42684 Q04929 296 | Q92831 P02263 297 | Q92831 P62801 298 | Q9DEA3 Q4KWZ7 299 | Q02842 Q5ZJL9 300 | Q15185 P11501 301 | P00523 P51913 302 | Q04982 Q5ZIK9 303 | Q04982 P48463 304 | Q04982 Q5ZM98 305 | Q04982 P67869 306 | Q04982 O73885 307 | Q04982 Q5ZMN3 308 | Q04982 P16039 309 | Q04982 P42558 310 | Q04982 Q6U7I1 311 | Q04982 P05625 312 | Q04982 Q5ZMD1 313 | Q04982 Q5ZLQ6 314 | Q04982 Q5ZMT0 315 | Q04982 Q5ZKC9 316 | Q04982 P50147 317 | Q04982 Q5F3W6 318 | Q04982 O57476 319 | Q04982 P11501 320 | Q04982 Q90828 321 | Q04982 Q90891 322 | Q04982 Q90593 323 | Q04982 P08110 324 | P18652 O95071 325 | O42414 P16092 326 | P16092 O42414 327 | P61088 Q9DEA3 328 | Q15819 Q9DEA3 329 | Q9W7C5 Q401C0 330 | Q401C0 Q9W7C5 331 | P11275 P13387 332 | Q7T0L4 Q9PU53 333 | Q07496 P32004 334 | -------------------------------------------------------------------------------- /www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_GO_BP.txt: -------------------------------------------------------------------------------- 1 | protein biosynthesis RPS15,RPS15,RPL37,RPS5,RPL35,FAU,RPS11,RPS21,RPL18,RPS13,RPL21,RPL36,RPL12,RPLP2,RPS19,RPL27,RPL31,MRPS12,LOC440055,RPS27,LOC388344,RPL27A,RPS10,RPS17,RPL28,LOC283412,RPL19,RPS16,RPS14,NARS,RPL7,RPS6,RPS2,U16,NACA,RPL18A,RPL13,RPL29,RPS15A,RPS20,RPS3A,RPS18,RPL14,MRPL34,RPL22,RPL34,RPS27A,EEF1D,RPL15,RPL9,RPL6,RPL26,RPL4,RPS4X,RPS24,RPS9,RPL13A,RPL17,EEF1A1,RPL5,RPL23,MDS1,RPS7,LOC402057,RPS25 2 | immune response HLA-DPB1,HLA-DPB1,TAPBP,IL2RG,HLA-DMA,HLA-DQA1,IL16,221651_x_at,IGLV3-10,ARL6IP2,HLA-B,CD164,HLA-DRA,HLA-DMB,TRIM22,HLA-DRB5,HLA-DRB1,IGL@,IGLC1,IGLV3-25,TRB@,HLA-DRB4,LTB,ARHGDIB,C6orf12,HLA-DQB1,HLA-DPA1,TRBV3-1,GPSM3,IGLC2,TRA@,214836_x_at,IGHV1-69,IGHA1,HLA-A,CD7,IGHG3,IGLJ3,IL7R,IL6ST,HLA-C,IGKC,IGHM 3 | signal transduction AKT1,AKT1,STAT1,IL2RG,CXCR4,OPHN1,CCL5,PGF,INPP5D,PRKAR1A,CD164,RPS27,HLA-DRB5,CD74,HLA-DRB1,PRKAR2A,CD53,HLA-DRB4,LTB,HSP90AA1,OGT,ROCK1,IFNGR1,PTGES3,HMGB1,GTF2I,GNB2L1,CAP1,SPN,NPM1,IQGAP1,PAFAH1B1,EIF3S3,RAC2,COPS2,PRKACB,PDE4C 4 | antigen presentation, endogenous antigen HLA-J,HLA-J,RPLP2,221651_x_at,IGLV3-10,IGHD,HLA-B,CD74,IGL@,IGLC1,HLA-E,IGLV3-25,C6orf12,IGLC2,214836_x_at,IGHV1-69,IGHA1,HLA-F,HLA-A,IGHG3,IGLJ3,HLA-G,HLA-C,IGKC,IGHM 5 | antigen processing, endogenous antigen via ... CAST,CAST,HLA-J,RPLP2,221651_x_at,IGLV3-10,IGHD,HLA-B,IGL@,IGLC1,HLA-E,IGLV3-25,C6orf12,IGLC2,214836_x_at,IGHV1-69,IGHA1,HLA-F,HLA-A,IGHG3,IGLJ3,HLA-G,HLA-C,IGKC,IGHM 6 | regulation of transcription, DNA-dependent NFE2L2,NFE2L2,STAT1,MGC2474,LYSMD4,ZMYND11,ZNF160,CDC5L,TRIM22,SFPQ,IFI16,HCLS1,ATRX,HMGB1,CSDE1,SCAND1,RPL6,LOC342346,SUB1 7 | electron transport MT1X,MT1X,MT1L,COX4I1,NCF1,SDHA,UQCRQ,UQCRC1,GPX4,UQCRFS1,NDUFV1,COX5B,NDUFS3,NDUFS8,COX5A,NDUFB4,CYC1,COX8A,RPA1 8 | protein amino acid phosphorylation AKT1,AKT1,RAVER2,GMFG,PRKAR1A,PRKD2,MYLK,PRKAR2A,ROCK1,TGFB1,PCM1,U16,LCK,CSNK1A1,HNRPDL,RPL4,PRKACB 9 | antigen processing, exogenous antigen via M... HLA-DPB1,HLA-DPB1,HLA-DMA,HLA-DQA1,HLA-DRA,HLA-DMB,HLA-DRB5,HLA-DRB1,HLA-DRB4,HLA-DQB1,HLA-DPA1 10 | antigen presentation, exogenous antigen HLA-DPB1,HLA-DPB1,HLA-DMA,HLA-DQA1,HLA-DRA,HLA-DMB,HLA-DRB5,HLA-DRB1,HLA-DRB4,HLA-DQB1,HLA-DPA1 11 | cell adhesion ITGAV,ITGAV,LAMC1,CCL5,FNBP4,ADRM1,CD164,TGFB1I1,SELL,DGCR6,COL6A1,PLEKHC1,CD2,ITGB2 12 | intracellular signaling cascade STAT1,STAT1,RAVER2,INPP5D,PRKAR1A,PRKD2,NCF1,PRKAR2A,WSB1,HCLS1,HMHA1,ROCK1,LCK 13 | transcription from RNA polymerase II promoter TARDBP,TARDBP,NFE2L2,STAT1,POLR2J,TGFB1I1,TCEA1,HMHA1,POLR2I,BTF3,COPS2,POLR2E 14 | cell motility CALD1,CALD1,CAPZA1,CCL5,TPM1,MSN,ACTR3,ARPC1B,ARHGDIB,ARPC3,ARPC5,PAFAH1B1 15 | detection of pest, pathogen or parasite HLA-DPB1,HLA-DPB1,HLA-DMA,HLA-J,HLA-DMB,HLA-DRB5,HLA-DRB1,HLA-DRB4,HLA-G 16 | nuclear mRNA splicing, via spliceosome HNRPM,HNRPM,SFRS10,HNRPH3,SFPQ,HIATL1,RPL35A,SF3B1,HNRPA2B1,HNRPA1 17 | mitochondrial electron transport, NADH to u... NDUFC1,NDUFC1,NDUFB6,NDUFB2,NDUFV1,NDUFS7,NDUFS3,NDUFS8,NDUFB4 18 | development CECR1,CECR1,CLPTM1,CD164,ARHGDIB,COL6A3,MYH11,ITGB2,DDX1 19 | phosphate transport COL6A3,COL6A3,COL1A1,COL6A1,COL4A2,COL4A1,COL3A1,COL1A2 20 | antigen presentation HLA-J,HLA-J,HLA-B,HLA-E,C6orf12,HLA-F,HLA-A,HLA-G,HLA-C 21 | transport G3BP,G3BP,SLC25A16,UCP2,SLC25A11,TMED5,SLC25A3,ATP2A3 22 | cell proliferation RPS21,RPS21,PGF,ZMYND11,RPS27,CD74,IFI16,MIF,ISG20 23 | anti-apoptosis AKT1,AKT1,FAIM3,SON,HMGB1,HSP90B1,NPM1,TPT1,PRDX2 24 | cell surface receptor linked signal transdu... CD3D,CD3D,CD2,CD79A,BIRC2,MIF,CSNK1A1,IL7R,IL6ST 25 | generation of precursor metabolites and energy ACO2,ACO2,ATPIF1,COX4I1,ECH1,UQCR,SLC25A3,COX8A 26 | protein complex assembly TAPBP,TAPBP,CAPZA1,GPAA1,LAMC1,TCEB2,CD3D,CD74 27 | mRNA processing SFPQ,SFPQ,SRP46,DHX15,HNRPR,SFRS11,SFRS5,RNPC2 28 | positive regulation of cell proliferation SSR1,SSR1,CAPNS1,PGF,RPL31,HCLS1,TGFB1,NAP1L1 29 | RNA splicing HNRPH3,HNRPH3,SFPQ,DHX15,PPP2CA,ZNF638,SFRS11 30 | transcription LYSMD4,LYSMD4,POLR2J,ZNF160,SFPQ,POLR1B,PCM1 31 | regulation of translational initiation EIF4G1,EIF4G1,EIF4A2,EIF4G2,EIF5,EIF3S3,DDX1 32 | pathogenesis HLA-DPB1,HLA-DPB1,HLA-DRB5,HLA-DRB1,HLA-DRB4 33 | proton transport ATP5J2,ATP5J2,ATP6V0D1,UCP2,ATP6V0B,ATP6V0C 34 | RNA processing HNRPU,HNRPU,RBPMS,DDX17,HNRPH1,HNRPDL,RNPC2 35 | regulation of transcription from RNA polyme... THRAP5,THRAP5,PRKAR1A,HMGB1,LOC342346,SUB1 36 | protein transport RAB1A,RAB1A,RAB6A,RAB6C,TLOC1,HSP90B1,COPB 37 | small GTPase mediated signal transduction RAP1B,RAP1B,RGS19,RAB1A,RAB6A,RAB6C,RPL29 38 | response to virus CCL5,CCL5,IRF7,TRIM22,IFI16,IFNGR1,ISG20 39 | inflammatory response CCL5,CCL5,IRF7,MEFV,ALOX5AP,TGFB1,ITGB2 40 | actin cytoskeleton organization and biogenesis ARHGDIB,ARHGDIB,PLEKHC1,DST,ROCK1,ARPC5 41 | protein folding PPIB,PPIB,HSP90AA1,HSP90B1,EIF3S3,KTN1 42 | induction of apoptosis CD2,CD2,PPP2CA,BCLAF1,LCK,RPS3A,SCAND1 43 | skeletal development CNOT2,CNOT2,COL1A1,TGFB1,COL1A2,MYH11 44 | regulation of progression through cell cycle STAT1,STAT1,PGF,ERH,PPP2CA,LCK,SCAND1 45 | negative regulation of cell proliferation CD164,CD164,TGFB1I1,TGFB1,CDKN1B,NPM1 46 | cellular defense response HLA-J,HLA-J,CCL5,NCF1,FAIM3,SPN,HLA-G 47 | translational elongation RPLP2,RPLP2,TUFM,EEF1B2,EEF1D,EEF1A1 48 | muscle development TAGLN,TAGLN,LYSMD4,SMTN,COL6A3,MBNL1 49 | ATP synthesis coupled proton transport ATP6V0B,ATP6V0B,ATP6V0C,ATP5D,ATP5G3 50 | proteolysis CAST,CAST,MASP1,YME1L1,MMP2,IGHG3 51 | microtubule-based movement 220725_x_at,220725_x_at,KNS2,KTN1 52 | metabolism ACO2,ACO2,ECH1,POPDC3,IGLC2,DIP2A 53 | apoptosis AD7C-NTP,AD7C-NTP,FIS1,ITGB2,CROP 54 | amino acid transport SLC38A2,SLC38A2,218041_x_at,RPL24 55 | response to unfolded protein HSP90AA1,HSP90AA1,HSP90B1,EIF3S3 56 | intracellular protein transport VDP,VDP,NAPA,CLTC,CD74,NPM1,COPE 57 | transcription initiation from RNA polymeras... THRAP5,THRAP5,IRF7,THRAP1,GTF2I 58 | response to oxidative stress CCL5,CCL5,GPX1,GPX4,CSDE1,PRDX2 59 | nucleobase, nucleoside, nucleotide and nucl... NDUFA10,NDUFA10,ERH,208246_x_at 60 | carbohydrate metabolism LOC91316,LOC91316,MAN2B1,AKR7A2 61 | protein modification SUMO2,SUMO2,RPN1,MAN2B1,RPS27A 62 | ubiquitin-dependent protein catabolism USP34,USP34,UBE4A,PSMB9,PSMB8 63 | defense response CD48,CD48,PTPRCAP,HLA-B,CD79A 64 | DNA replication MCM3AP,MCM3AP,NARS,NAP1L1,SET 65 | androgen receptor signaling pathway THRAP5,THRAP5,THRAP1,TGFB1I1 66 | protein targeting to mitochondrion TIMM8B,TIMM8B,TOMM20,TIMM13 67 | oxygen transport SLC38A2,SLC38A2,218041_x_at 68 | G-protein coupled receptor protein signalin... AKT1,AKT1,RGS19,CXCR4,FNBP4 69 | nervous system development OPHN1,OPHN1,MBNL1,PAFAH1B1 70 | mitochondrial transport UCP2,UCP2,HSP90AA1,EIF3S3 71 | embryo implantation LOC283412,LOC283412,RPL29 72 | DNA repair SFPQ,SFPQ,ATRX,HMGB1,RPA1 73 | protein refolding HSP90AA1,HSP90AA1,EIF3S3 74 | positive regulation of nitric oxide biosynt... HSP90AA1,HSP90AA1,EIF3S3 75 | lipid metabolism PAFAH1B1,PAFAH1B1,ATP8B1 76 | cell cycle arrest EIF4G2,EIF4G2,DST,CDKN1B 77 | cell cycle CUL4B,CUL4B,RPS27A,SEPT7 78 | protein ubiquitination UBE4A,UBE4A,PCNP,RPS27A 79 | protein targeting TOMM20,TOMM20,SRP9,COPB 80 | nucleosome assembly NAP1L1,NAP1L1,SET,H3F3A 81 | negative regulation of cell adhesion CD164,CD164,ARHGDIB,SPN 82 | cell-cell signaling CCL5,CCL5,PGF,LTB,ITGB2 83 | positive regulation of transcription TGFB1I1,TGFB1I1,RPS27A 84 | negative regulation of transcription IRF7,IRF7,SUMO1,BCLAF1 85 | hemopoiesis CD164,CD164,ZNF160,LCK 86 | cellular defense response (sensu Vertebrata) IGHA1,IGHA1,IGHG3,IGHM 87 | retrograde vesicle-mediated transport, Golg... TAPBP,TAPBP,COPE,COPB 88 | protein import into nucleus MCM3AP,MCM3AP,NDUFA13 89 | positive regulation of transcription, DNA-d... TGFB1I1,TGFB1I1,TGFB1 90 | negative regulation of cell growth PPP2CA,PPP2CA,NDUFA13 91 | integrin-mediated signaling pathway ITGAV,ITGAV,DST,ITGB2 92 | cotranslational protein targeting to membrane SSR1,SSR1,TLOC1,TRAM1 93 | Rho protein signal transduction ARHGDIB,ARHGDIB,ROCK1 94 | sensory perception of sound TIMM8B,TIMM8B,TIMM13 95 | regulation of translation PPP2CA,PPP2CA,EEF1A1 96 | regulation of transcription POLR2L,POLR2L,PPP2CA 97 | prostaglandin biosynthesis CD74,CD74,PTGES3,MIF 98 | mitosis TARDBP,TARDBP,CORO1A 99 | insulin receptor signaling pathway PHIP,PHIP,AKT1,MYH11 100 | DNA recombination ATRX,ATRX,HMGB1,RPA1 101 | tricarboxylic acid cycle ACO2,ACO2,SDHA,RPA1 102 | negative regulation of transcription, DNA-d... RPS14,RPS14,NDUFA13 103 | intra-Golgi vesicle-mediated transport NAPA,NAPA,COPE,COPB 104 | cell death EIF4G2,EIF4G2,TGFB1 105 | protein amino acid autophosphorylation RPS2,RPS2,U16,RPL4 106 | circulation RPL31,RPL31,COL3A1 107 | calcium ion transport ATP2A3,ATP2A3,TPT1 108 | axon guidance OPHN1,OPHN1,RPS27A 109 | ER-associated protein catabolism RPL27,RPL27,RPS27A 110 | regulation of actin filament polymerization ARPC3,ARPC3,ARPC5 111 | positive regulation of I-kappaB kinase/NF-k... BIRC2,BIRC2,EEF1D 112 | organ morphogenesis DGCR6,DGCR6,TGFB1 113 | negative regulation of transcription from R... IRF7,IRF7,ZMYND11 114 | mRNA splice site selection SRP46,SRP46,SFRS5 115 | erythrocyte differentiation RPS19,RPS19,HCLS1 116 | cytokinesis SEPT2,SEPT2,SEPT7 117 | chromosome segregation ARL8B,ARL8B,RIOK3 118 | cell-matrix adhesion ITGAV,ITGAV,ITGB2 119 | activation of NF-kappaB transcription factor U16,U16,NPM1,RPL4 120 | T cell activation CD3D,CD3D,CD2,CD7 121 | ubiquitin cycle TPT1,TPT1,UBE2D2 122 | regulation of cell adhesion NPTN,NPTN,PPP2CA 123 | cell growth TGFB1,TGFB1,DDX5 124 | angiogenesis CAST,CAST,ATPIF1 125 | translational initiation EIF5,EIF5,RPS3A 126 | transforming growth factor beta receptor si... FNTA,FNTA,TGFB1 127 | response to drug RAB6C,RAB6C,LCK 128 | regulation of apoptosis TPT1,TPT1,PRDX2 129 | chromosome organization and biogenesis (sen... ATRX,ATRX,H3F3A 130 | caspase activation STAT1,STAT1,LCK 131 | antimicrobial humoral response (sensu Verte... IL7R,IL7R,ITGB2 132 | I-kappaB kinase/NF-kappaB cascade PHIP,PHIP,STAT1 133 | transmembrane receptor protein tyrosine kin... CD7,CD7,COL1A2 134 | response to stress NPM1,NPM1,CROP 135 | response to metal ion MT1X,MT1X,MT1L 136 | calcium ion homeostasis CCL5,CCL5,TPT1 137 | regulation of macrophage activation CD74,CD74,MIF 138 | nucleocytoplasmic transport NPM1,NPM1,SET 139 | negative regulation of apoptosis CD74,CD74,MIF 140 | muscle contraction DES,DES,CALD1 141 | establishment and/or maintenance of cell po... CAP1,CAP1,SPN 142 | chemotaxis CCL5,CCL5,SPN 143 | Ras protein signal transduction G3BP,G3BP,LCK 144 | regulation of heart contraction DES,DES,TPM1 145 | activation of MAPKK activity U16,U16,RPL4 146 | JNK cascade U16,U16,RPL4 147 | cytoskeleton organization and biogenesis DES,DES,DST 148 | -------------------------------------------------------------------------------- /www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_GO_CC.txt: -------------------------------------------------------------------------------- 1 | integral to membrane SPCS2,SPCS2,ITGAV,CAST,REEP5,HLA-DPB1,SSR1,C11orf2,TAPBP,IL2RG,CXCR4,HLA-J,RPLP2,CD37,SLC25A16,221651_x_at,RPN1,IGLV3-10,FNBP4,UCP2,AD7C-NTP,ADRM1,IGHD,HLA-B,HLA-DMB,TLOC1,ATP6V0B,HLA-DRB5,SLC25A11,CD74,HLA-DRB1,IGL@,TMED5,IGLC1,HLA-E,SLC25A3,IGLV3-25,TRB@,ARL6IP5,HLA-DRB4,TRBC1,LAPTM5,CD2,C6orf12,IFNGR1,HLA-DQB1,FXYD5,POPDC3,ATP6V0C,TRBV3-1,IGLC2,214836_x_at,IGHV1-69,IGHA1,U16,HLA-F,HLA-A,CD7,CAV1,IGHG3,215176_x_at,IGLJ3,HLA-G,IL7R,ITGB2,IL6ST,RPL4,HLA-C,IGKC,IGHM,TRAM1,RPA1 2 | membrane HLA-DPB1,HLA-DPB1,SLC38A2,RAP1B,VDP,IL2RG,CXCR4,RAB1A,NPTN,RAB6A,HLA-DMA,HLA-DQA1,ADD3,SLC25A16,PGF,IL10RA,RAB6C,221651_x_at,MSN,IGLV3-10,RPL31,UCP2,IGHD,218041_x_at,HLA-DRA,HLA-DMB,YME1L1,SELL,ATP6V0B,HLA-DRB5,SLC25A11,HLA-DRB1,IGL@,IGLC1,SLC25A3,IGLV3-25,TRB@,HLA-DRB4,TRBC1,LTB,COL6A3,IFNGR1,HLA-DQB1,HLA-DPA1,CD79A,FXYD5,ATP6V0C,PPP2CA,TRBV3-1,IGLC2,ATP2A3,214836_x_at,IGHV1-69,IGHA1,IGHG3,215176_x_at,IGLJ3,IL7R,COPE,HLA-C,IGKC,IGHM,ATP5G3,RPA1,RPL24 3 | nucleus TARDBP,TARDBP,CNOT2,NFE2L2,ZFR,STAT1,SEPT2,MCM3AP,TINP1,LYSMD4,KPNB1,SFRS10,CBX3,THRAP5,G3BP,HNRPH3,IRF7,THRAP1,ZMYND11,POLR2J,ZNF160,MEFV,CDC5L,TRIM22,DDX17,IFI16,HCLS1,ATRX,HNRPH1,POLR1B,OGT,DHX15,ZNF611,MORF4L1,HNRPR,HMGB1,PPP2CA,CDKN1B,PCM1,BCLAF1,TIMM13,SRP9,RPS6,DDX5,ZNF638,RPL35A,SFRS11,PCNP,DDX50,ZNF552,RPS3A,NPM1,MBNL1,PAPOLA,AURKAIP1,FIBP,SH3BGRL,MATR3,RPS27A,SCAND1,DDX3X,SET,HNRPA2B1,RNPC2,SEPT7,H3F3A 4 | cytoplasm AKT1,AKT1,MT1E,FNTA,STAT1,MT1F,SEPT2,VDP,EIF4G1,KPNB1,DDX42,IRF7,MSN,ARL8B,CD3D,PRKAR2A,HCLS1,ARHGDIB,COL6A3,COL1A1,COL6A1,DST,217718_s_at,RPL36A,NARS,COL4A2,COL4A1,CDKN1B,NDUFA13,PCM1,ZNF638,NACA,EXOSC4,COL3A1,COL1A2,ARPC5,EIF5,NPM1,MBNL1,PAPOLA,SH3BGRL,TPT1,PRDX2,COPS2,COPE,XPO1,DDX3X,EEF1A1,HNRPA1 5 | ribosome RPL37,RPL37,RPS11,RPS21,RPL21,RPL36,RPL12,RPLP2,RPS19,RPL27,RPL31,LOC440055,LOC388344,RPL27A,RPL28,LOC283412,RPL19,RPS16,RPL36A,RPS6,RPS2,U16,RPL18A,RPL13,RPL29,RPS3A,RPS18,RPL14,RPL22,RPL34,RPS23,RPL15,RPL9,RPL6,RPL4,RPS4X,RPS24,RPL5,RPL23,MDS1,RPS7 6 | intracellular RPL37,RPL37,RAP1B,MGC2474,RPS21,RPL21,RPLP2,G3BP,GMFG,RPS19,RAB6C,PRKD2,RPL31,ZNF160,TGFB1I1,MEFV,GLTSCR2,MRPS12,CD74,RPL28,LOC283412,RPL19,ROCK1,SON,RPS6,RPS2,U16,RPL18A,RPL29,RPS18,RPL14,RPL22,RPL34,RPL15,RPL4,RPS4X,RPS24,RPL13A,RPL5,MDS1,RPS7 7 | integral to plasma membrane HNRPM,HNRPM,IL2RG,HLA-DQA1,CD48,CD37,CLPTM1,ADRM1,HLA-B,CD164,HLA-DRA,SELL,HLA-DRB5,SLC25A11,HLA-DRB1,SLC25A3,HLA-DRB4,LAPTM5,CD2,C6orf12,IFNGR1,HLA-DPA1,ATP2A3,IGHA1,HLA-A,CAV1,SPN,IGHG3,CD52,IL6ST,HLA-C,IGHM,ATP8B1 8 | cytosolic small ribosomal subunit (sensu Eu... RPS15,RPS15,RPS5,FAU,RPS11,RPS21,RPS13,RPS19,LOC440055,RPS27,RPS10,RPS17,RPS16,RPS14,RPS6,RPS2,RPS15A,RPS20,RPS3A,RPS18,RPS27A,RPS23,RPS24,RPS9,RPS7,LOC402057,RPS25 9 | cytosolic large ribosomal subunit (sensu Eu... RPL35,RPL35,RPL18,RPL21,RPL36,RPLP2,RPL27A,RPL28,LOC283412,RPL7,U16,RPL18A,RPL29,RPL14,RPL22,RPL34,RPL6,RPL4,RPL5,MDS1 10 | plasma membrane ARF1,ARF1,CD48,PTPRCAP,CD37,IL10RA,MSN,CD164,HLA-DRA,SELL,PRKAR2A,CD53,TRB@,TRBV3-1,TRA@,LCK,CD7,IL6ST 11 | mitochondrion ACO2,ACO2,ATPIF1,MSRB2,SDHA,UCP2,TUFM,LOC440055,GPX4,SLC25A3,PPP2CA,NDUFA13,FIBP,DBT,NDUFB4,CYC1,RPA1 12 | cytosol CAST,CAST,NCF1,NPEPPS,KNS2,PSMB9,PSMB8,HSP90AA1,OGT,PPP2CA,HSP90B1,EIF5,RPS3A,EIF3S3,SPG21,COPB 13 | membrane fraction RGS19,RGS19,ADRM1,HLA-B,PRKAR2A,LMOD1,COL6A3,IGHV1-69,IGHA1,U16,CD7,IGHG3,CD52,FIBP,RPL4,IGHM 14 | endoplasmic reticulum CAST,CAST,P4HB,SSR1,TAPBP,RPN1,PPIB,TLOC1,NAPA,HSP90B1,CAV1,KTN1,SET,TRAM1 15 | cytoskeleton CALD1,CALD1,RAVER2,ACTA2,TPM1,MSN,NPEPPS,ARHGDIB,LMOD1,ACTG2,ARPC3,ARPC5 16 | ribonucleoprotein complex HNRPM,HNRPM,SRP72,HNRPH3,HNRPU,HNRPK,HNRPR,HNRPA3P1,SIAHBP1,HNRPA1 17 | extracellular region CAST,CAST,P4HB,CNOT2,MASP1,IGL@,FBLN1,IFI30,COL4A1,MIF,IGHG3,IGKC 18 | MHC class I protein complex HLA-J,HLA-J,RPLP2,HLA-B,HLA-E,C6orf12,HLA-F,HLA-A,HLA-G,HLA-C 19 | heterogeneous nuclear ribonucleoprotein com... HNRPH3,HNRPH3,HNRPU,HNRPH1,HNRPR,HNRPDL,HNRPA2B1,HNRPA1 20 | mitochondrial inner membrane NDUFA7,NDUFA7,SLC25A16,UCP2,SLC25A11,SLC25A3,NDUFV1 21 | extracellular space CNOT2,CNOT2,IL16,AD7C-NTP,FBLN1,TGFB1,MMP2,SPN,TPT1 22 | nucleoplasm IFI16,IFI16,NDUFA13,ZNF638,XPO1,ISG20,RNPC2,HNRPA1 23 | collagen COL1A1,COL1A1,COL6A1,COL4A2,COL4A1,COL3A1,COL1A2 24 | nucleolus RPL35,RPL35,RPS19,IFI16,NCL,EXOSC4,NPM1,RPS7 25 | spliceosome complex HNRPM,HNRPM,HIATL1,SF3B1,HNRPA2B1,HNRPA1 26 | proton-transporting two-sector ATPase complex ATP6V0B,ATP6V0B,ATP6V0C,ATP5D,ATP5G3 27 | extracellular matrix (sensu Metazoa) LAMC1,LAMC1,FBLN1,DGCR6,COL6A3,TGFB1 28 | perinuclear region 217718_s_at,217718_s_at,HSP90B1,SET 29 | DNA-directed RNA polymerase II, core complex POLR2J,POLR2J,HCLS1,HMHA1,POLR2E 30 | actin cytoskeleton MARCKS,MARCKS,FNBP4,CORO1A,SMTN 31 | cAMP-dependent protein kinase complex PRKAR1A,PRKAR1A,PRKAR2A,PRKACB 32 | Arp2/3 protein complex ACTR3,ACTR3,ARPC1B,ARPC3,ARPC5 33 | lysosome HLA-DRA,HLA-DRA,LAPTM5,IFI30 34 | large ribosomal subunit RPL7,RPL7,RPL26,RPL13A,RPL17 35 | Golgi apparatus RGS19,RGS19,RAB6A,RAB6C,NAPA 36 | soluble fraction NCF1,NCF1,FBLN1,NARS,PPP2CA 37 | eukaryotic translation initiation factor 4F... EIF4G1,EIF4G1,EIF4A2,EIF4G2 38 | proton-transporting ATP synthase complex (s... ATP5J2,ATP5J2,ATP5D,ATP5G3 39 | microsome SPCS2,SPCS2,TAPBP,HSP90B1 40 | cytosolic ribosome (sensu Eukaryota) LOC388344,LOC388344,RPL13 41 | Golgi membrane TAPBP,TAPBP,VDP,CAV1,COPB 42 | transcription factor complex LOC342346,LOC342346,SUB1 43 | endoplasmic reticulum membrane TAPBP,TAPBP,HSP90B1,KTN1 44 | actin filament ACTA2,ACTA2,ACTG2,IQGAP1 45 | proteasome complex (sensu Eukaryota) PSMB3,PSMB3,PSMB9,PSMB8 46 | nuclear envelope PAFAH1B1,PAFAH1B1,XPO1 47 | endoplasmic reticulum lumen CAST,CAST,PPIB,HSP90B1 48 | stress fiber PLEKHC1,PLEKHC1,SEPT7 49 | small ribosomal subunit RPS5,RPS5,MRPS12,RPS2 50 | mitochondrial electron transport chain UQCRC1,UQCRC1,NDUFA13 51 | mitochondrial ribosome MRPS12,MRPS12,MRPL34 52 | mitochondrial inner membrane presequence tr... TIMM8B,TIMM8B,TIMM13 53 | mediator complex THRAP5,THRAP5,THRAP1 54 | collagen type VI COL6A3,COL6A3,COL6A1 55 | ER-Golgi intermediate compartment P4HB,P4HB,TMED5,KTN1 56 | respiratory chain complex III (sensu Eukary... UQCRQ,UQCRQ,UQCRFS1 57 | eukaryotic translation elongation factor 1 ... EEF1B2,EEF1B2,EEF1D 58 | cytoplasmic membrane-bound vesicle ARHGDIB,ARHGDIB,DST 59 | microtubule associated complex MEFV,MEFV,PAFAH1B1 60 | ubiquitin ligase complex RNF11,RNF11,UBE4A 61 | protein complex PSMB9,PSMB9,PSMB8 62 | proteasome core complex (sensu Eukaryota) PSMB9,PSMB9,PSMB8 63 | nuclear pore KPNB1,KPNB1,RGPD5 64 | integrin complex ITGAV,ITGAV,ITGB2 65 | signal recognition particle (sensu Eukaryota) SRP72,SRP72,SRP9 66 | cell surface P4HB,P4HB,ATPIF1 67 | myosin MYH9,MYH9,MYH11 68 | mitochondrial envelope UCRC,UCRC,COX5B 69 | centrosome NPM1,NPM1,CEP27 70 | basement membrane LAMC1,LAMC1,DST 71 | mitochondrial matrix MDH2,MDH2,ETFB 72 | COPI vesicle coat COPE,COPE,COPB 73 | pericentriolar material PCM1,PCM1,LCK 74 | intermediate filament DES,DES,RPL38 75 | lipid raft LCK,LCK,CAV1 76 | -------------------------------------------------------------------------------- /www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_GO_MF.txt: -------------------------------------------------------------------------------- 1 | protein binding TARDBP,TARDBP,ITGAV,CAST,RPS15,PHIP,NFE2L2,OAZ1,STAT1,SEPT2,TXNL2,ORC6L,IL2RG,RGS19,EIF4G1,RPS13,C1orf160,RAB6A,HLA-DMA,ZNHIT1,GPAA1,CUL4B,HLA-J,KPNB1,ARF1,IL16,CD48,CBX3,G3BP,SUMO2,ACTA2,TCEB2,EIF3S6,MT1H,RPS19,INPP5D,RAB6C,RNF11,PRKAR1A,NCF1,ZMYND11,HNRPK,SUMO1,TGFB1I1,CDC5L,KNS2,RBPMS,CAB39,SFPQ,CD3D,NAPA,ACTR3,CLTC,TTC3,EIF4A2,IFI16,ARL6IP5,EEF1B2,HCLS1,PSMB8,HMHA1,HSP90AA1,HNRPH1,SRP46,EIF4G2,FIS1,PLEKHC1,CD2,OGT,TAF7,217718_s_at,NARS,C6orf12,TGFB1,CDKN1B,NDUFA13,GPSM3,BCLAF1,HSP90B1,SERBP1,GTF2I,RPS6,U16,BIRC2,RPL35A,HLA-A,RPS15A,EXOSC4,RPS20,RPL38,ACTG2,CAV1,ACTR2,SKP1A,ACTR10,MIF,PCNP,RPS3A,RPL14,HLA-G,IL7R,AURKAIP1,FIBP,EIF3S3,HNRPDL,RPS27A,RAC2,ITGB2,COPS2,XPO1,SIAHBP1,POLR2E,NAP1L1,RPL4,SFRS5,HNRPA2B1,EEF1A1,UBE2D2,SEPT7,COPB,ATP5G3,RPL5,RPS7,RPA1,HNRPA1,RPL24 2 | RNA binding TARDBP,TARDBP,RPS5,HNRPM,LOC56902,EIF4G1,RPL18,RPL21,SFRS10,RPLP2,G3BP,HNRPH3,HNRPU,DDX42,RPS19,HNRPK,RBPMS,LOC440055,RPS27,LOC388344,SFPQ,DDX17,RPL27A,RPS10,RPS17,EIF4A2,RPL28,LOC283412,RPS14,HNRPH1,SRP46,EIF4G2,HNRPR,NCL,RPL7,HSP90B1,SRP9,HNRPA3P1,RPS2,U16,DDX5,ZNF638,RPL18A,RPL13,RPL29,SFRS11,DDX50,NPM1,RPS18,RPL14,PAPOLA,RPL22,MATR3,HNRPDL,RPL34,SCAND1,RPL9,RPL6,SIAHBP1,RPL4,RPS4X,SFRS5,SFRS3,HNRPA2B1,RPS9,RNPC2,RPL5,MDS1,LOC402057,HNRPA1 3 | structural constituent of ribosome RPS15,RPS15,RPL37,RPS5,RPL35,FAU,RPS11,RPS21,RPL18,RPS13,RPL21,RPL36,RPL12,RPLP2,RPS19,RPL27,RPL31,MRPS12,LOC440055,RPS27,LOC388344,RPL27A,RPS10,RPS17,RPL28,LOC283412,RPL19,RPS16,RPS14,RPL7,RPS6,RPS2,U16,RPL18A,RPL13,RPL29,RPS15A,RPS20,RPS3A,RPS18,RPL14,MRPL34,RPL22,RPL34,RPS27A,RPS23,RPL15,RPL9,RPL6,RPL26,RPL4,RPS4X,RPS24,RPS9,RPL13A,RPL17,RPL5,RPL23,MDS1,RPS7,LOC402057,RPS25 4 | nucleotide binding TARDBP,TARDBP,HNRPM,RAP1B,MCM3AP,RAB1A,RAB6A,RAVER2,SFRS10,G3BP,HNRPH3,ACTA2,DDX42,RAB6C,PRKD2,RBPMS,YME1L1,SFPQ,DDX17,EIF4A2,HSP90AA1,HNRPH1,SRP46,NARS,HNRPR,NCL,PCM1,HSP90B1,HNRPA3P1,U16,DDX5,ACTG2,SFRS11,DDX50,CSNK1A1,EIF3S3,MATR3,HNRPDL,DDX3X,SIAHBP1,RPL4,SFRS5,HNRPA2B1,EEF1A1,RNPC2,SEPT7,PRKACB,HNRPA1 5 | nucleic acid binding TARDBP,TARDBP,ZFR,HNRPM,LOC56902,MGC2474,RPS11,SFRS10,G3BP,HNRPH3,ZNF9,DDX42,HNRPK,ZNF160,MRPS12,SFPQ,DDX17,R3HCC1,EIF4A2,IFI16,HNRPH1,SRP46,NARS,ZNF611,SON,HNRPR,DDX5,SFRS11,DDX50,ZNF552,NPM1,MBNL1,MATR3,HNRPDL,DDX3X,SIAHBP1,SFRS5 6 | ATP binding NDUFA10,NDUFA10,AKT1,RAVER2,ACTA2,DDX42,PRKD2,MYH9,220725_x_at,YME1L1,DDX17,EIF4A2,HSP90AA1,208246_x_at,DHX15,NARS,ROCK1,NDUFA13,PCM1,HSP90B1,ATP2A3,RPS2,U16,DDX5,LCK,MYH11,ACTG2,DDX50,CSNK1A1,EIF3S3,DDX3X,RPL4,PRKACB 7 | receptor activity ITGAV,ITGAV,HNRPM,IL2RG,CXCR4,THRAP5,PTPRCAP,RPL27,IL10RA,THRAP1,TLOC1,HLA-DRB5,HLA-DRB1,HLA-DRB4,CD2,IFNGR1,TRBV3-1,IGHA1,U16,CD7,IGHG3,IL7R,IL6ST,RPL4,EEF1A1,IGHM,TRAM1 8 | MHC class I receptor activity HLA-J,HLA-J,RPLP2,221651_x_at,IGLV3-10,IGHD,HLA-B,IGL@,IGLC1,HLA-E,IGLV3-25,C6orf12,IGLC2,214836_x_at,IGHV1-69,IGHA1,HLA-F,HLA-A,IGHG3,IGLJ3,HLA-G,HLA-C,IGKC,IGHM 9 | zinc ion binding CAST,CAST,ZFR,MT1E,MT1F,KPNB1,MSRB2,TIMM8B,ZNF9,DDX42,RNF11,PRKD2,SDHA,ZMYND11,ZNF160,MEFV,RPS27,TTC3,ZNF611,TIMM13,POLR2I,MMP2,ZNF552,MBNL1,MATR3 10 | binding SRP72,SRP72,VDP,CAPZA1,TTC19,KPNB1,SLC25A16,MSN,UCP2,KNS2,CAB39,RGPD5,NAPA,SLC25A11,TTC3,SLC25A3,ALOX5AP,HIATL1,OGT,CHCHD2,SF3B1,COPS2,COPE,COPB 11 | DNA binding MCM3AP,MCM3AP,HNRPU,RNF11,IRF7,SDHA,POLR2L,POLR2J,CDC5L,SFPQ,POLR1B,SON,HMGB1,PCM1,BCLAF1,CSDE1,RPL6,LOC342346,SUB1,LOC58486,H3F3A 12 | NADH dehydrogenase (ubiquinone) activity NDUFC1,NDUFC1,NDUFA10,NDUFA7,NDUFB6,NDUFB2,NDUFA2,NDUFV1,NDUFA3,NDUFA13,NDUFS7,NDUFS3,NDUFS8,NDUFB4,NDUFAB1 13 | MHC class II receptor activity HLA-DPB1,HLA-DPB1,HLA-DMA,HLA-DQA1,HLA-DRA,HLA-DMB,HLA-DRB5,HLA-DRB1,HLA-DRB4,HLA-DQB1,HLA-DPA1,HLA-C 14 | electron carrier activity P4HB,P4HB,MT1X,MT1L,NCF1,UQCR,CYBA,FLJ14346,NDUFS3,NDUFS8,COX5A,ETFB,KTN1,AKR7A2,CYC1 15 | GTPase activity SEPT2,SEPT2,RAB6A,ARF1,RAB6C,NCF1,ARL6IP2,ARF5,ARL8B,RPL29,EIF5,RAC2,EEF1A1 16 | antigen binding IGL@,IGL@,IGLC1,IGLV3-25,IGLC2,IGHV1-69,IGHA1,IGHG3,IGLJ3,IL7R,IGKC,IGHM 17 | transferase activity FNTA,FNTA,PRKD2,POLR2J,POLR1B,COL6A3,NARS,RPS2,U16,CSNK1A1,RPL4,PRKACB 18 | transcription factor activity TARDBP,TARDBP,NFE2L2,STAT1,LYSMD4,MSRB2,TRIM22,HCLS1,GTF2I,SCAND1,MDS1 19 | metal ion binding MT1X,MT1X,ZFR,MT1M,MT1L,PRKD2,ZNF160,TTC3,ZNF611,ZNF552,MATR3,NDUFS8 20 | structural molecule activity DES,DES,FNBP4,CORO1A,NPEPPS,CLTC,COL6A3,RPL38,CAV1,MATR3,SEPT7 21 | GTP binding RAP1B,RAP1B,RAB1A,RAB6A,RAB6C,NCF1,ARL6IP2,ARL8B,EEF1A1,SEPT7 22 | extracellular matrix structural constituent LAMC1,LAMC1,FBLN1,COL1A1,COL6A1,COL4A2,COL4A1,COL3A1,COL1A2 23 | structural constituent of cytoskeleton DES,DES,ADD3,ACTA2,TPM1,MSN,ARPC1B,DST,ACTG2,ARPC3,ARPC5 24 | hydrolase activity DDX42,DDX42,PPP1CA,DDX17,EIF4A2,PPP2CA,DDX5,DDX50,DDX3X 25 | unfolded protein binding TAPBP,TAPBP,PPIB,HSP90AA1,PTGES3,HSP90B1,NPM1,EIF3S3 26 | transporter activity G3BP,G3BP,UCP2,ATP6V0B,SLC25A11,SLC25A3,ATP5D,ATP5G3 27 | kinase activity GUK1,GUK1,MYLK,PRKAR2A,WSB1,208246_x_at,ROCK1,CDKN1B 28 | iron ion binding ACO2,ACO2,MT1X,MT1L,PPP1CA,NDUFV1,PPP2CA,NDUFS8,CYC1 29 | DNA-directed RNA polymerase activity POLR2L,POLR2L,POLR2J,HMHA1,POLR1B,PCM1,POLR2I,POLR2E 30 | ATP-dependent helicase activity DDX42,DDX42,DDX17,EIF4A2,DHX15,DDX5,DDX50,DDX3X,DDX1 31 | protein serine/threonine kinase activity AKT1,AKT1,PRKD2,ROCK1,RPS2,U16,CSNK1A1,RPL4,PRKACB 32 | calcium ion binding MASP1,MASP1,SPARCL1,STAT1,FBLN1,HSP90B1,IGHG3,TPT1 33 | actin binding CNN1,CNN1,CALD1,CAPZA1,GMFG,SMTN,MEFV,NPEPPS,FXYD5 34 | protein homodimerization activity ATPIF1,ATPIF1,HSP90AA1,U16,NPM1,EIF3S3,RPL4 35 | signal transducer activity STAT1,STAT1,RGS19,BIRC2,HNRPDL,EEF1D,COPS2 36 | oxidoreductase activity NDUFA10,NDUFA10,GPX1,MDH2,GPX4,IGLC2,PRDX2 37 | transcription coactivator activity TGFB1I1,TGFB1I1,TAF7,NPM1,LOC342346,SUB1 38 | translation initiation factor activity EIF4G1,EIF4G1,EIF4A2,EIF4G2,EIF5,EIF3S3 39 | protein-tyrosine kinase activity RAVER2,RAVER2,PCM1,U16,LCK,HNRPDL,RPL4 40 | catalytic activity KIAA1840,KIAA1840,LOC91316,DIP2A,PDE4C 41 | hydrogen-transporting ATPase activity, rota... ATP6V0B,ATP6V0B,ATP6V0C,ATP5D,ATP5G3 42 | hydrogen-transporting ATP synthase activity... ATP6V0B,ATP6V0B,ATP6V0C,ATP5D,ATP5G3 43 | hematopoietin/interferon-class (D200-domain... STAT1,STAT1,IL2RG,IL10RA,IFNGR1,IL7R 44 | oxidoreductase activity, acting on NADH or ... NDUFV1,NDUFV1,NDUFS7,NDUFS3,NDUFS8 45 | single-stranded DNA binding HNRPDL,HNRPDL,LOC342346,SUB1,RPA1 46 | amino acid-polyamine transporter activity SLC38A2,SLC38A2,218041_x_at,RPL24 47 | receptor binding CCL5,CCL5,ARPP-19,MSN,LTB,GNB2L1 48 | calmodulin binding CALD1,CALD1,MARCKS,ATPIF1,IQGAP1 49 | cytochrome-c oxidase activity COX4I1,COX4I1,COX5B,COX5A,COX8A 50 | ubiquinol-cytochrome-c reductase activity UCRC,UCRC,UQCRQ,UQCRC1,UQCRFS1 51 | protein transporter activity VDP,VDP,KPNB1,TLOC1,AP2S1,COPE 52 | translation elongation factor activity TUFM,TUFM,EEF1B2,EEF1D,EEF1A1 53 | peptide antigen binding TAPBP,TAPBP,TRB@,TRBV3-1,TRA@ 54 | microtubule motor activity 220725_x_at,220725_x_at,KNS2 55 | phosphotransferase activity, alcohol group ... NDUFA10,NDUFA10,208246_x_at 56 | oxygen transporter activity SLC38A2,SLC38A2,218041_x_at 57 | RNA helicase activity DDX17,DDX17,DHX15,DDX5,DDX1 58 | growth factor activity CECR1,CECR1,GMFG,PGF,TGFB1 59 | RNA splicing factor activity, transesterifi... SFRS10,SFRS10,HIATL1,SF3B1 60 | heparin binding LOC283412,LOC283412,RPL29 61 | double-stranded DNA binding IFI16,IFI16,ZNF638,HNRPDL 62 | RNA polymerase II transcription mediator ac... CNOT2,CNOT2,THRAP5,THRAP1 63 | nitric-oxide synthase regulator activity HSP90AA1,HSP90AA1,EIF3S3 64 | isomerase activity P4HB,P4HB,ECH1,PPIB,KTN1 65 | TPR domain binding HSP90AA1,HSP90AA1,EIF3S3 66 | ubiquitin-protein ligase activity UBE4A,UBE4A,TPT1,UBE2D2 67 | protein domain specific binding YWHAZ,YWHAZ,217718_s_at 68 | cAMP-dependent protein kinase regulator act... PRKAR1A,PRKAR1A,PRKAR2A 69 | transcriptional repressor activity IRF7,IRF7,IFI16,BCLAF1 70 | protein kinase binding U16,U16,LCK,ITGB2,RPL4 71 | general RNA polymerase II transcription fac... TCEA1,TCEA1,TAF7,GTF2I 72 | MHC protein binding TRB@,TRB@,TRBV3-1,TRA@ 73 | ATP-dependent RNA helicase activity G3BP,G3BP,RPL35A,DDX3X 74 | protein heterodimerization activity CD3D,CD3D,PPP2CA,NPM1 75 | peptidase activity MASP1,MASP1,ZNF9,CLPP 76 | identical protein binding AKT1,AKT1,CD74,SCAND1 77 | vitamin D receptor binding THRAP5,THRAP5,THRAP1 78 | thyroid hormone receptor binding THRAP5,THRAP5,THRAP1 79 | serine-type endopeptidase inhibitor activity NFE2L2,NFE2L2,COL6A3 80 | sequence-specific DNA binding NFE2L2,NFE2L2,LYSMD4 81 | protein dimerization activity NFE2L2,NFE2L2,POLR2J 82 | motor activity MYH9,MYH9,KNS2,MYH11 83 | copper ion binding MT1E,MT1E,MT1F,DDX42 84 | cadmium ion binding MT1E,MT1E,MT1F,DDX42 85 | transmembrane receptor activity CD3D,CD3D,CD79A,SPN 86 | translation factor activity, nucleic acid b... EIF3S3,EIF3S3,EEF1D 87 | transcriptional activator activity THRAP5,THRAP5,TGFB1 88 | 3'-5'-exoribonuclease activity EXOSC4,EXOSC4,ISG20 89 | tropomyosin binding CALD1,CALD1,LMOD1 90 | transcription factor binding YWHAZ,YWHAZ,HMGB1 91 | threonine endopeptidase activity PSMB9,PSMB9,PSMB8 92 | serine-type endopeptidase activity MASP1,MASP1,IGHG3 93 | peroxidase activity CSDE1,CSDE1,PRDX2 94 | enzyme activator activity GMFG,GMFG,ALOX5AP 95 | antioxidant activity RPL27,RPL27,PRDX2 96 | actin filament binding MARCKS,MARCKS,DST 97 | acetylglucosaminyltransferase activity COL6A3,COL6A3,OGT 98 | ATPase binding ATPIF1,ATPIF1,LCK 99 | transcription regulator activity RPL7,RPL7,RPS27A 100 | sugar binding MASP1,MASP1,SELL 101 | ligase activity NARS,NARS,UBE2D2 102 | cytokine binding CD74,CD74,IFNGR1 103 | aminopeptidase activity CAST,CAST,NPEPPS 104 | protein phosphatase inhibitor activity PSMB9,PSMB9,SET 105 | succinate dehydrogenase activity SDHA,SDHA,RPA1 106 | structural constituent of muscle TPM1,TPM1,SMTN 107 | protein disulfide oxidoreductase activity P4HB,P4HB,KTN1 108 | protein disulfide isomerase activity P4HB,P4HB,KTN1 109 | ornithine decarboxylase inhibitor activity OAZ2,OAZ2,OAZ1 110 | glutathione peroxidase activity GPX1,GPX1,GPX4 111 | double-stranded RNA binding SON,SON,MBNL1 112 | CD4 receptor binding LCK,LCK,SPG21 113 | MAP kinase kinase kinase activity U16,U16,RPL4 114 | protein C-terminus binding DST,DST,LCK 115 | -------------------------------------------------------------------------------- /www/Examples/Human_Coexpression/NORMA_Human_coexpression_Annotation_KEGG.txt: -------------------------------------------------------------------------------- 1 | Ribosome RPS5,RPS5,RPL35,FAU,RPL18,RPL21,RPL36,RPL12,RPLP2,RPS19,RPL27,RPL10A,LOC440055,RPS27,LOC388344,RPL27A,RPS10,RPS17,RPL28,LOC283412,RPL23A,RPL36A,RPL7,RPS2,U16,RPL35A,RPL18A,RPL13,RPL29,RPS15A,RPS3A,RPL14,RPL22,RPL34,RPS27A,RPL9,RPL6,RPL4,RPS4X,RPS9,RPL13A,RPL17,RPL5,MDS1,LOC402057 2 | Oxidative phosphorylation NDUFC1,NDUFC1,ATP5J2,NDUFA10,NDUFA7,COX4I1,ATP6V0D1,NDUFB6,UCRC,SDHA,ATP6V0B,UQCRC1,NDUFB2,UQCRFS1,NDUFA2,NDUFV1,ATP6V0C,NDUFA3,NDUFA13,NDUFS7,COX5B,ATP5D,NDUFS3,NDUFS8,COX5A,NDUFB4,NDUFAB1,ATP5G3,CYC1,COX8A,RPA1 3 | Antigen processing and presentation HLA-DPB1,HLA-DPB1,TAPBP,HLA-DMA,HLA-DQA1,HLA-J,HLA-B,HLA-DRA,HLA-DMB,HLA-DRB5,CD74,HLA-DRB1,HLA-E,HLA-DRB4,HSP90AA1,C6orf12,HLA-DQB1,HLA-DPA1,IFI30,HLA-A,HLA-G,EIF3S3,HLA-C 4 | Cell adhesion molecules (CAMs) ITGAV,ITGAV,HLA-DPB1,HLA-DMA,HLA-DQA1,HLA-J,HLA-B,HLA-DRA,HLA-DMB,SELL,HLA-DRB5,HLA-DRB1,HLA-E,HLA-DRB4,CD2,C6orf12,HLA-DQB1,HLA-DPA1,HLA-A,SPN,HLA-G,ITGB2,HLA-C 5 | Type I diabetes mellitus HLA-DPB1,HLA-DPB1,HLA-DMA,HLA-DQA1,HLA-J,HLA-B,HLA-DRA,HLA-DMB,HLA-DRB5,HLA-DRB1,HLA-E,HLA-DRB4,C6orf12,HLA-DQB1,HLA-DPA1,HLA-A,HLA-G,HLA-C 6 | Focal adhesion ITGAV,ITGAV,AKT1,RAP1B,LAMC1,PGF,MYLK,COL6A3,COL1A1,COL6A1,ROCK1,COL4A2,COL4A1,BIRC2,COL3A1,COL1A2,CAV1,RAC2 7 | Natural killer cell mediated cytotoxicity HLA-J,HLA-J,CD48,HLA-B,HLA-E,C6orf12,IFNGR1,HLA-A,LCK,HLA-G,RAC2,ITGB2,HLA-C 8 | Regulation of actin cytoskeleton ITGAV,ITGAV,MSN,MYH9,MYLK,ARPC1B,ROCK1,ARPC3,ARPC5,IQGAP1,RAC2,ITGB2 9 | Cell Communication DES,DES,LAMC1,COL6A3,COL1A1,COL6A1,COL4A2,COL4A1,COL3A1,COL1A2,RPL38 10 | Pyrimidine metabolism POLR2L,POLR2L,POLR2J,HMHA1,POLR1B,208246_x_at,POLR2I,RPS15A,POLR2E 11 | ECM-receptor interaction ITGAV,ITGAV,LAMC1,COL6A3,COL1A1,COL6A1,COL4A2,COL4A1,COL3A1,COL1A2 12 | Purine metabolism GUK1,GUK1,POLR2L,POLR2J,HMHA1,POLR1B,POLR2I,RPS15A,POLR2E,PDE4C 13 | Hematopoietic cell lineage CD37,CD37,HLA-DRA,CD3D,HLA-DRB5,HLA-DRB1,HLA-DRB4,CD2,CD7,IL7R 14 | Cytokine-cytokine receptor interaction IL2RG,IL2RG,CXCR4,CCL5,IL10RA,LTB,IFNGR1,TGFB1,IL7R,IL6ST 15 | Leukocyte transendothelial migration RAP1B,RAP1B,CXCR4,NCF1,MSN,CYBA,ROCK1,MMP2,RAC2,ITGB2 16 | Jak-STAT signaling pathway AKT1,AKT1,STAT1,IL2RG,RAVER2,IL10RA,IFNGR1,IL7R,IL6ST 17 | Cell cycle ORC6L,ORC6L,YWHAZ,217718_s_at,TGFB1,CDKN1B,SKP1A 18 | RNA polymerase POLR2L,POLR2L,POLR2J,HMHA1,POLR1B,POLR2I,POLR2E 19 | Apoptosis AKT1,AKT1,PRKAR1A,ENDOG,PRKAR2A,BIRC2,PRKACB 20 | Cholera - Infection SEC61A1,SEC61A1,ATP6V0D1,ATP6V0B,ATP6V0C 21 | Pathogenic Escherichia coli infection - EPEC HCLS1,HCLS1,YWHAZ,ROCK1,NCL,RPL38,ARPC5 22 | Pathogenic Escherichia coli infection - EHEC HCLS1,HCLS1,YWHAZ,ROCK1,NCL,RPL38,ARPC5 23 | Epithelial cell signaling in Helicobacter pylori infection ATP6V0D1,ATP6V0D1,CCL5,ATP6V0B,ATP6V0C 24 | Wnt signaling pathway ROCK1,ROCK1,SKP1A,CSNK1A1,RAC2,PRKACB 25 | Pancreatic cancer AKT1,AKT1,STAT1,RAVER2,PGF,TGFB1,RAC2 26 | MAPK signaling pathway AKT1,AKT1,RAP1B,TGFB1,RAC2,PRKACB 27 | Insulin signaling pathway AKT1,AKT1,PRKAR1A,PRKAR2A,PRKACB 28 | Protein export SEC61A1,SEC61A1,SRP72,SRP9 29 | Ubiquitin mediated proteolysis TCEB2,TCEB2,SKP1A,UBE2D2 30 | Citrate cycle (TCA cycle) ACO2,ACO2,SDHA,MDH2,RPA1 31 | TGF-beta signaling pathway ROCK1,ROCK1,TGFB1,SKP1A 32 | Calcium signaling pathway MYLK,MYLK,ATP2A3,PRKACB 33 | Hedgehog signaling pathway CSNK1A1,CSNK1A1,PRKACB 34 | Chronic myeloid leukemia AKT1,AKT1,TGFB1,CDKN1B 35 | Axon guidance CXCR4,CXCR4,ROCK1,RAC2 36 | Toll-like receptor signaling pathway AKT1,AKT1,STAT1,CCL5 37 | Tight junction AKT1,AKT1,MYH9,HCLS1 38 | Glycan structures - degradation POPDC3,POPDC3,MAN2B1 39 | Colorectal cancer AKT1,AKT1,TGFB1,RAC2 40 | B cell receptor signaling pathway AKT1,AKT1,CD79A,RAC2 41 | Prion disease NFE2L2,NFE2L2,LAMC1 42 | T cell receptor signaling pathway AKT1,AKT1,CD3D,LCK 43 | Long-term potentiation RAP1B,RAP1B,PRKACB 44 | Adherens junction IQGAP1,IQGAP1,RAC2 45 | Glycan structures - biosynthesis 2 COL6A3,COL6A3,OGT 46 | GnRH signaling pathway MMP2,MMP2,PRKACB 47 | Adipocytokine signaling pathway AKT1,AKT1,RAVER2 48 | Basal transcription factors TAF7,TAF7,GTF2I 49 | VEGF signaling pathway AKT1,AKT1,RAC2 50 | Reductive carboxylate cycle (CO2 fixation) ACO2,ACO2,MDH2 51 | Glyoxylate and dicarboxylate metabolism ACO2,ACO2,MDH2 52 | Glutathione metabolism GPX1,GPX1,GPX4 53 | Fc epsilon RI signaling pathway AKT1,AKT1,RAC2 54 | Arachidonic acid metabolism GPX1,GPX1,GPX4 55 | mTOR signaling pathway AKT1,AKT1,PGF 56 | Tyrosine metabolism ECH1,ECH1,MIF 57 | -------------------------------------------------------------------------------- /www/Examples/Human_Coexpression/NORMA_Human_coexpression_Expression_MCODE.txt: -------------------------------------------------------------------------------- 1 | 207730_x_at green 2 | 214836_x_at green 3 | 215176_x_at green 4 | 215182_x_at green 5 | 216342_x_at green 6 | 216524_x_at green 7 | 217281_x_at green 8 | 220725_x_at green 9 | 221651_x_at green 10 | ACTA2 green 11 | ACTR2 green 12 | ACTR3 green 13 | AD7C-NTP green 14 | AP2S1 green 15 | ARF5 green 16 | ARHGDIB green 17 | ARL6IP2 green 18 | ARPC3 green 19 | ATP8B1 green 20 | ATRX green 21 | AURKAIP1 green 22 | BIRC2 green 23 | C6orf12 green 24 | CAV1 green 25 | CD52 green 26 | CD74 green 27 | CDC5L green 28 | CEP27 green 29 | CHCHD2 green 30 | COL1A1 green 31 | COL1A2 green 32 | COL3A1 green 33 | COL6A1 green 34 | COPE green 35 | COX5A green 36 | COX5B green 37 | COX8A green 38 | CROP green 39 | CTA-246H3.1 green 40 | CYBA green 41 | DBT green 42 | DDT green 43 | DDX3X green 44 | DDX5 green 45 | EIF3S3 green 46 | EIF3S6 green 47 | EIF4G2 green 48 | FAU green 49 | FBLN1 green 50 | FBXW12 green 51 | FLJ11021 green 52 | FLJ12151 green 53 | FLJ20294 green 54 | FLJ42393 green 55 | GNB2L1 green 56 | H3F3A green 57 | HIATL1 green 58 | HLA-A green 59 | HLA-B green 60 | HLA-C green 61 | HLA-DMA green 62 | HLA-DPA1 green 63 | HLA-DQB1 green 64 | HLA-DRB1 green 65 | HLA-DRB4 green 66 | HLA-DRB5 green 67 | HLA-E green 68 | HLA-F green 69 | HLA-G green 70 | HLA-J green 71 | HNRPDL green 72 | HNRPH3 green 73 | IFI30 green 74 | IGHA1 green 75 | IGHG3 green 76 | IGHM green 77 | IGHV1-69 green 78 | IGKC green 79 | IGKV1-5 green 80 | IGKV1D-13 green 81 | IGKV1OR15-118 green 82 | IGKV1OR2-108 green 83 | IGL@ green 84 | IGLC1 green 85 | IGLC2 green 86 | IGLJ3 green 87 | IGLV3-25 green 88 | IQGAP1 green 89 | KNS2 green 90 | LAPTM5 green 91 | LCK green 92 | LMOD1 green 93 | LOC152719 green 94 | LOC388344 green 95 | LOC440055 green 96 | LOC91316 green 97 | MAN2B1 green 98 | MATR3 green 99 | MBNL1 green 100 | MCM3AP green 101 | MDS1 green 102 | MGEA5 green 103 | MORF4L1 green 104 | MRPL34 green 105 | MT1E green 106 | MT1F green 107 | MT1G green 108 | MT1H green 109 | MT1L green 110 | MT1M green 111 | MT1X green 112 | MT2A green 113 | MYH11 green 114 | NACA green 115 | NAP1L1 green 116 | NARS green 117 | NDUFA2 green 118 | NDUFA3 green 119 | NDUFAB1 green 120 | NDUFB11 green 121 | NDUFB2 green 122 | NDUFB4 green 123 | NDUFS3 green 124 | NDUFS7 green 125 | NPM1 green 126 | PAPOLA green 127 | PCNP green 128 | PDE4C green 129 | PFAAP5 green 130 | PGF green 131 | PNRC2 green 132 | POLR2J green 133 | PRG1 green 134 | PRR11 green 135 | PTGES3 green 136 | RAC2 green 137 | RIOK3 green 138 | ROCK1 green 139 | RPL11 green 140 | RPL13 green 141 | RPL13A green 142 | RPL17 green 143 | RPL18 green 144 | RPL21 green 145 | RPL22 green 146 | RPL23 green 147 | RPL24 green 148 | RPL27 green 149 | RPL27A green 150 | RPL28 green 151 | RPL29 green 152 | RPL30 green 153 | RPL34 green 154 | RPL35A green 155 | RPL36 green 156 | RPL36A green 157 | RPL38 green 158 | RPL4 green 159 | RPL5 green 160 | RPL6 green 161 | RPL7 green 162 | RPL9 green 163 | RPLP2 green 164 | RPS14 green 165 | RPS17 green 166 | RPS18 green 167 | RPS19 green 168 | RPS2 green 169 | RPS23 green 170 | RPS24 green 171 | RPS25 green 172 | RPS27A green 173 | RPS3A green 174 | RPS4X green 175 | RPS5 green 176 | RPS6 green 177 | RPS7 green 178 | RPS9 green 179 | SEPT2 green 180 | SERBP1 green 181 | SFRS11 green 182 | SH3BGRL green 183 | SKP1A green 184 | SLC35E1 green 185 | SON green 186 | SUMO2 green 187 | TAF7 green 188 | TLOC1 green 189 | TRA@ green 190 | TRB@ green 191 | TUG1 green 192 | U16 green 193 | UQCR green 194 | UQCRC1 green 195 | UQCRFS1 green 196 | USP34 green 197 | XPO1 green 198 | YTHDC1 green 199 | ZNF160 green 200 | ZNF611 green 201 | ZNF638 green 202 | ZNHIT1 green 203 | 208246_x_at yellow 204 | 211637_x_at yellow 205 | 211645_x_at yellow 206 | ATP5G3 yellow 207 | ATP6V0B yellow 208 | ATP6V0D1 yellow 209 | BCLAF1 yellow 210 | CAPZA1 yellow 211 | COL6A3 yellow 212 | CXCR4 yellow 213 | HLA-DPB1 yellow 214 | HNRPH1 yellow 215 | IFI16 yellow 216 | LOC342346 yellow 217 | LOC56902 yellow 218 | LOC58486 yellow 219 | LOC645745 yellow 220 | MEFV yellow 221 | MRPS12 yellow 222 | NDUFS8 yellow 223 | PTRF yellow 224 | RPL31 yellow 225 | RPL35 yellow 226 | RPS11 yellow 227 | TAGLN yellow 228 | TGFB1 yellow 229 | TRBC1 yellow 230 | 208120_x_at red 231 | 208238_x_at red 232 | 211639_x_at red 233 | 211641_x_at red 234 | 211650_x_at red 235 | 211908_x_at red 236 | 212498_at red 237 | 216412_x_at red 238 | 216858_x_at red 239 | 217052_x_at red 240 | 217258_x_at red 241 | 217679_x_at red 242 | 217718_s_at red 243 | 218041_x_at red 244 | AASDHPPT red 245 | ACO2 red 246 | ACTG2 red 247 | ACTR10 red 248 | ADD3 red 249 | ADRM1 red 250 | AKR7A2 red 251 | AKT1 red 252 | ALOX5AP red 253 | ARF1 red 254 | ARL6IP5 red 255 | ARL8B red 256 | ARPC1B red 257 | ARPC5 red 258 | ARPP-19 red 259 | ATP2A3 red 260 | ATP5D red 261 | ATP5J2 red 262 | ATP6AP2 red 263 | ATP6V0C red 264 | ATPIF1 red 265 | BTF3 red 266 | C11orf2 red 267 | C11orf58 red 268 | C12orf10 red 269 | C12orf38 red 270 | C16orf24 red 271 | C17orf62 red 272 | C1orf160 red 273 | C1orf63 red 274 | C21orf33 red 275 | C3orf60 red 276 | CAB39 red 277 | CALD1 red 278 | CAP1 red 279 | CAPNS1 red 280 | CAST red 281 | CBX3 red 282 | CCL5 red 283 | CCNL1 red 284 | CD164 red 285 | CD2 red 286 | CD37 red 287 | CD3D red 288 | CD48 red 289 | CD53 red 290 | CD7 red 291 | CD79A red 292 | CDKN1B red 293 | CECR1 red 294 | CHMP2A red 295 | CLPP red 296 | CLPTM1 red 297 | CLTC red 298 | CNN1 red 299 | CNOT2 red 300 | COL4A1 red 301 | COL4A2 red 302 | COPB red 303 | COPS2 red 304 | COQ9 red 305 | CORO1A red 306 | COX4I1 red 307 | CSDE1 red 308 | CSNK1A1 red 309 | CUL4B red 310 | CXorf9 red 311 | CYC1 red 312 | DDX1 red 313 | DDX17 red 314 | DDX42 red 315 | DDX50 red 316 | DES red 317 | DEXI red 318 | DGCR6 red 319 | DHX15 red 320 | DIP2A red 321 | DKFZP566N034 red 322 | DST red 323 | DYNLT3 red 324 | ECH1 red 325 | EEF1A1 red 326 | EEF1B2 red 327 | EEF1D red 328 | EIF4A2 red 329 | EIF4G1 red 330 | EIF5 red 331 | ENDOG red 332 | ERH red 333 | ETFB red 334 | EXOSC4 red 335 | FAIM3 red 336 | FAM96B red 337 | FIBP red 338 | FIS1 red 339 | FLJ10154 red 340 | FLJ14346 red 341 | FNBP4 red 342 | FNTA red 343 | FXYD5 red 344 | G3BP red 345 | GBL red 346 | GLTSCR2 red 347 | GMFG red 348 | GOLGA8A red 349 | GOLGA8B red 350 | GPAA1 red 351 | GPSM3 red 352 | GPX1 red 353 | GPX4 red 354 | GTF2I red 355 | GUK1 red 356 | HCLS1 red 357 | HLA-DMB red 358 | HLA-DQA1 red 359 | HLA-DRA red 360 | HMGB1 red 361 | HMHA1 red 362 | HNRPA1 red 363 | HNRPA2B1 red 364 | HNRPA3P1 red 365 | HNRPK red 366 | HNRPM red 367 | HNRPR red 368 | HNRPU red 369 | HSP90AA1 red 370 | HSP90B1 red 371 | IFNGR1 red 372 | IGHD red 373 | IGLV3-10 red 374 | IL10RA red 375 | IL16 red 376 | IL2RG red 377 | IL6ST red 378 | IL7R red 379 | INPP5D red 380 | IRF7 red 381 | ISG20 red 382 | ITGAV red 383 | ITGB2 red 384 | KIAA0907 red 385 | KIAA1840 red 386 | KIDINS220 red 387 | KPNB1 red 388 | KTN1 red 389 | LAMC1 red 390 | LOC283412 red 391 | LOC402057 red 392 | LRRFIP1 red 393 | LTB red 394 | LYSMD4 red 395 | MARCKS red 396 | MASP1 red 397 | MDH2 red 398 | MGC2474 red 399 | MIF red 400 | MMP2 red 401 | MRP63 red 402 | MSN red 403 | MSRB2 red 404 | MYH9 red 405 | MYLK red 406 | NAPA red 407 | NBPF1 red 408 | NBPF12 red 409 | NCF1 red 410 | NCL red 411 | NDUFA10 red 412 | NDUFA13 red 413 | NDUFA7 red 414 | NDUFB6 red 415 | NDUFC1 red 416 | NDUFV1 red 417 | NFE2L2 red 418 | NPEPPS red 419 | NPTN red 420 | OAZ1 red 421 | OAZ2 red 422 | OGT red 423 | OPHN1 red 424 | ORC6L red 425 | OSBPL8 red 426 | P4HB red 427 | PAFAH1B1 red 428 | PCM1 red 429 | PDCD10 red 430 | PGLS red 431 | PHIP red 432 | PLEKHC1 red 433 | POLR1B red 434 | POLR2E red 435 | POLR2I red 436 | POLR2L red 437 | POPDC3 red 438 | PPIB red 439 | PPP1CA red 440 | PPP2CA red 441 | PRDX2 red 442 | PRKACB red 443 | PRKAR1A red 444 | PRKAR2A red 445 | PRKD2 red 446 | PSMB3 red 447 | PSMB8 red 448 | PSMB9 red 449 | PTPRCAP red 450 | PUM2 red 451 | R3HCC1 red 452 | RAB1A red 453 | RAB6A red 454 | RAB6C red 455 | RAP1B red 456 | RAVER2 red 457 | RBPMS red 458 | REEP5 red 459 | RGPD5 red 460 | RGS19 red 461 | RNF11 red 462 | RNPC2 red 463 | RPA1 red 464 | RPL10A red 465 | RPL12 red 466 | RPL14 red 467 | RPL15 red 468 | RPL18A red 469 | RPL19 red 470 | RPL23A red 471 | RPL26 red 472 | RPL32 red 473 | RPL37 red 474 | RPL39 red 475 | RPL41 red 476 | RPN1 red 477 | RPS10 red 478 | RPS13 red 479 | RPS15 red 480 | RPS15A red 481 | RPS16 red 482 | RPS20 red 483 | RPS21 red 484 | RPS27 red 485 | SCAND1 red 486 | SDHA red 487 | SEC61A1 red 488 | SELL red 489 | SEPT7 red 490 | SET red 491 | SF3B1 red 492 | SFPQ red 493 | SFRS10 red 494 | SFRS3 red 495 | SFRS5 red 496 | SIAHBP1 red 497 | SLC25A11 red 498 | SLC25A16 red 499 | SLC25A3 red 500 | SLC38A2 red 501 | SMTN red 502 | SPARCL1 red 503 | SPCS2 red 504 | SPG21 red 505 | SPN red 506 | SRP46 red 507 | SRP72 red 508 | SRP9 red 509 | SSR1 red 510 | STAT1 red 511 | SUB1 red 512 | SUMO1 red 513 | TAPBP red 514 | TARDBP red 515 | TCEA1 red 516 | TCEB2 red 517 | TGFB1I1 red 518 | THRAP1 red 519 | THRAP5 red 520 | TIMM13 red 521 | TIMM8B red 522 | TINP1 red 523 | TMED5 red 524 | TMEM123 red 525 | TMEM66 red 526 | TMEM93 red 527 | TOMM20 red 528 | TPM1 red 529 | TPT1 red 530 | TRAM1 red 531 | TRBV3-1 red 532 | TRIM22 red 533 | TTC19 red 534 | TTC3 red 535 | TUFM red 536 | TXNL2 red 537 | UBE2D2 red 538 | UBE4A red 539 | UCP2 red 540 | UCRC red 541 | UQCRQ red 542 | USP47 red 543 | VDP red 544 | WAC red 545 | WDR45 red 546 | WIPI2 red 547 | WSB1 red 548 | YIPF3 red 549 | YME1L1 red 550 | YWHAZ red 551 | ZC3H11A red 552 | ZFR red 553 | ZMYND11 red 554 | ZNF403 red 555 | ZNF552 red 556 | ZNF9 red 557 | hfl-B5 red 558 | -------------------------------------------------------------------------------- /www/Examples/IntAct_COVID19/HomoSapiens_Gene_Ontology_GOTERM_BP_DIRECT_FILTERED.txt: -------------------------------------------------------------------------------- 1 | negative regulation of anoikis P06731,Q07817,P05556,Q07820,P10415 2 | T cell receptor signaling pathway P35998,P48556,Q13200,P25787,Q99460,P62195,Q9UNM6,O14818,Q15008,P51665,P60900,O00231,P62191 3 | regulation of cellular response to heat Q99615,P08107,K7ELV2,P62258,Q9UL15,O95816,P0DMV8,P78406,Q92793,P52948 4 | RNA secondary structure unwinding Q9NR30,Q8TDD1,Q9BUQ8,Q9UHI6,O00148,P38919,Q13838 5 | SRP-dependent cotranslational protein targeting to membrane P60866,P08708,P61254,P62269,P39019,P42677,P61927,P62753,Q9Y3U8,P46782 6 | positive regulation of establishment of protein localization to telomere P40227,P17987,P48643,Q99832 7 | Fc-epsilon receptor signaling pathway P35998,P48556,Q13200,P25787,Q99460,P62195,P0DP23,Q9UNM6,O14818,Q15008,P51665,P60900,O00231,P62191 8 | mRNA transport Q09161,O14980,Q9Y5S9,Q53F19,P09651,Q96A72,Q9UN86 9 | negative regulation of transcription elongation from RNA polymerase II promoter Q8WX92,Q9H3P2,P18615,O94762 10 | nuclear export Q09161,Q9H814,P52298,P09651 11 | response to hydrogen peroxide O00629,Q13443,P22460,P42224,Q9P289,P09601,P10415 12 | intracellular protein transport Q9UM54,Q9H173,Q9ULJ7,Q14974,O00203,P35606,O14964,Q96JC1,P53621,O95373,Q9UBF2,Q9H270,O15397,O14980,O43592,P53618 13 | rRNA processing P60866,Q9NR30,P39019,P62753,P61927,P57678,O43818,P08708,P61254,Q9NU22,P62269,P42677,P38919,P46782,Q9Y3U8 14 | release of cytochrome c from mitochondria Q07817,Q16548,Q3ZCQ8,O00429,P10415 15 | positive regulation of translation P11940,Q9BRP8,Q14011,Q6PKG0,P98179,P38919,Q13838 16 | focal adhesion assembly P12814,Q08043,P35609,Q14155,P10415 17 | calcium activated phosphatidylserine scrambling A1A5B4,Q32M45,Q4KMQ2 18 | gene silencing by RNA P30876,Q09161,Q7KZF4,P11940,K7ELV2,P52298,O15397,P78406,P52948,P24928 19 | negative regulation of programmed cell death P02768,Q96EY1,O76024,P62195 20 | protein folding in endoplasmic reticulum Q8N766,Q8IXB1,Q86YB8,P11021 21 | positive regulation of viral genome replication P62937,P11940,Q6PKG0,Q9P035,P78563 22 | protein complex assembly P52907,O14745,Q9BSJ2,O43292,Q9Y375,Q9NU22,P30153,Q92793,P06493,O00505 23 | mitochondrion organization P06576,P35232,Q5VV67,O00429,Q96EY1,P09874,Q9Y276,Q99623 24 | T cell differentiation in thymus P61769,Q96EY1,P62753,P35222,P10415 25 | intra-Golgi vesicle-mediated transport P53621,Q9UBF2,P35606,P39880,P53618 26 | protein homotetramerization Q9H773,Q96GX9,O00429,P34897,Q14500,P35609,P14735 27 | calcium activated galactosylceramide scrambling A1A5B4,Q32M45,Q4KMQ2 28 | calcium activated phosphatidylcholine scrambling A1A5B4,Q32M45,Q4KMQ2 29 | viral entry into host cell P08107,P27487,P05556,P15151,P0DMV8,Q9BYF1,P15144,O00505,P14735 30 | DNA duplex unwinding Q13283,P12956,P13010,Q9Y265,P25205,O94762 31 | platelet degranulation P0DP23,P12814,P05155,P02768,O15439,P15692,O43707,P00747,P35609 32 | regulation of nucleic acid-templated transcription P12814,P35637,O43707,P35609 33 | cell proliferation O15503,P68036,Q14160,Q13561,P08581,P13010,Q16576,P06493,Q15303,P25100,Q07817,P09603,Q9BXP5,Q6PKG0,O95071,P42677,Q7L590,P12004,Q10589,P10415 34 | osteoblast differentiation P35998,Q9NR30,Q7KZF4,P06576,P35232,P12109,Q00839,J3QSV6,P38159 35 | intrinsic apoptotic signaling pathway in response to DNA damage Q07817,Q16548,Q92843,Q07820,P09601,P10415 36 | regulation of DNA recombination P52294,P52292,Q96FV9 37 | positive regulation of histone H3-K4 methylation P26358,P35222,Q9H3P2,P18615 38 | transport P53007,Q9Y6R1,P02768,Q9UBX3,P52948,Q15818,Q9UN86,Q9NZJ7,Q15311,P46379,P33527,P38606,Q13283,Q00325,Q02978,Q9Y3A6,Q13224,Q9H936,P48065 39 | positive regulation of intrinsic apoptotic signaling pathway O14745,Q07817,O00429,P63244,P10415 40 | 7-methylguanosine mRNA capping P30876,Q09161,P52298,Q53F19,P24928 41 | SREBP signaling pathway O15503,Q9Y5U4,Q12770 42 | IRES-dependent viral translational initiation P26599,Q14152,O00303 43 | extrinsic apoptotic signaling pathway in absence of ligand Q07817,Q16548,Q92843,Q07820,P10415 44 | ribosomal small subunit assembly P08708,P39019,P42677,P46782 45 | ubiquitin-dependent protein catabolic process P35998,P68036,P46379,Q9UNM6,P25787,O14818,Q9NXK8,O95071,P60900,O00231,P63279,Q9NVW2 46 | regulation of translational initiation Q09161,P52298,O75822,Q14152,O00303 47 | establishment of integrated proviral latency P62937,P12956,P13010 48 | response to endoplasmic reticulum stress Q8IXB1,Q13438,P57088,Q9Y4L1,P16615,O76024,Q9BS26 49 | chaperone-mediated protein folding Q96AY3,P68400,O14656,Q9Y680,Q00688 50 | gastrulation P37173,P63244,P62753,P09622 51 | fibrinolysis P07355,P00750,P05155,P00747 52 | negative regulation of mRNA splicing,via spliceosome O00422,P26599,Q9UKV3,P38159 53 | RNA processing Q13310,Q8TDD1,Q9UHI6,P98179,Q96FV9,Q00839,P78563,Q86U42 54 | negative regulation of apoptotic process Q9NVI7,P31689,P02768,Q96GX9,Q92843,Q96EY1,P62753,Q86W42,P06493,Q07820,Q15303,P06731,Q07817,Q16548,P46379,Q9Y466,P11021,P15692,Q5JVF3,Q99623,P10415,P63104 55 | negative regulation of intrinsic apoptotic signaling pathway Q07817,Q92843,Q07820,P10415 56 | protein targeting P27348,Q13438,P62258,Q96RT1,P63104 57 | regulation of smooth muscle cell proliferation P12956,P13010,P35222 58 | positive regulation of RNA polymerase II transcriptional preinitiation complex assembly P35998,P62191,P62195 59 | response to hypoxia P22460,P00750,P37173,P27487,O00469,Q12770,P15692,Q92793,P09601,O43707,P05026 60 | response to drug Q9UM54,Q5JWF2,P42224,P13010,P06493,Q92820,P35222,P61769,P37173,P33527,O14980,P40939,O15439,P28300,P05023,P10415 61 | membrane repolarization during cardiac muscle cell action potential P62258,P05023,P05026 62 | endoplasmic reticulum mannose trimming Q13438,Q9BZQ6,Q9NYU1 63 | positive regulation of potassium ion transport P33176,P35609,Q12959 64 | positive regulation of cellular component movement P39019,P15692,O43707 65 | response to unfolded protein P34932,Q96CS3,P31689,O95757,Q9BS26 66 | cellular protein modification process P00750,P68036,P38435,O00469,Q86YB8,P22314,P28300,P63279 67 | protein peptidyl-prolyl isomerization Q6UX04,P62937,Q96AY3,Q9Y680,Q00688 68 | muscle contraction Q9NYL9,P0DP23,P19105,Q08043,P60660,Q14500,P50402,Q86U42,O14950 69 | type I interferon signaling pathway P42224,P52630,P04439,P05161,Q10589,Q14653 70 | positive regulation of protein ubiquitination Q9NV92,P68036,Q13155,Q96EY1,P11021,O76024 71 | gluconeogenesis P04406,P53007,O75746,Q9UBX3,Q02978 72 | mitotic nuclear envelope disassembly K7ELV2,P78406,P06493,P50402,P52948 73 | positive regulation of mesenchymal cell proliferation P37173,P42224,P15692,P35222 74 | protein targeting to plasma membrane P07355,P19105,Q92953,P35613,O14950 75 | positive regulation of protein targeting to mitochondrion P19784,P48556,Q8TAD8,P68036,Q9H270,P55786,Q9Y265 76 | nuclear pore complex assembly P57088,Q9NQC3,P52948 77 | positive regulation of DNA-templated transcription,elongation Q13769,Q96FV9,Q13838 78 | endoplasmic reticulum unfolded protein response O76061,P11021,Q9BZQ6,Q9NYU1,O76024 79 | ER-associated misfolded protein catabolic process Q99470,Q9NYU1,O14656 80 | relaxation of cardiac muscle P05023,P16615,P05026 81 | proteasome assembly P48556,Q9UNM6,O00231 82 | regulation of cardiac muscle cell contraction Q14524,P05023,P63165 83 | lysine catabolic process Q9UDR5,Q9BQT8,P09622 84 | potassium ion import Q14500,P48050,P05023,P05026 85 | proteolysis involved in cellular protein catabolic process P25787,O14818,P11021,P60900,P14735 86 | substantia nigra development P0DP23,P27348,O15027,P62258,P11021 87 | establishment or maintenance of epithelial cell apical/basal polarity Q7KZI7,Q96RT1,Q12959 88 | microtubule cytoskeleton organization Q9P0L2,P04406,Q96N67,Q7KZI7,P06493,P27448 89 | positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway P27348,P62258,P10415,P63104 90 | -------------------------------------------------------------------------------- /www/Examples/IntAct_COVID19/HomoSapiens_Gene_Ontology_GOTERM_CC_DIRECT_FILTERED.txt: -------------------------------------------------------------------------------- 1 | membrane P04406,Q13200,O00203,P62753,Q9NXS2,P09601,Q16630,J3QSV6,P61769,P53621,Q9BSJ2,O43292,P62269,O00148,O95071,P53396,Q2PZI1,P50402,Q00839,Q8IXH7,Q8TEQ8,O14656,P10415,P05556,Q13561,Q13155,P39019,Q8TDD1,Q13011,O60884,Q9BZQ6,Q07820,P29122,Q13352,Q4KMQ2,Q9NZJ7,Q9P2E5,O60684,P11940,Q07817,P62258,P61254,Q9NU22,P38159,Q8NC51,Q9UM54,P35998,Q96A65,Q14974,O43633,P12956,P09874,P16615,P35222,P62195,P30876,Q02224,Q7KZF4,P27348,Q15311,P35232,Q9Y673,Q6PKG0,Q12789,P11021,Q5JWF2,O94826,P35613,Q14152,P07195,Q6DN90,P06576,P50395,P09603,P33527,O75400,Q9Y3U8,P53618,P07355,O14745,P31689,Q9H488,Q99519,Q9UL15,P39656,P30153,Q9Y6E2,Q99460,Q96S66,P11586,P27487,O75592,Q9H307,O00303,Q9Y265,P05023,P09651,P05026,P51570,Q96CW5,Q9UHI6,P04439,Q99470,Q7Z2K6,Q96S52,P26599,P20700,P47756,Q00325,P15692,P51665,P61158,P62191,P19338,Q15365,P27105,P06493,P33176,Q8IXB1,O95373,P46379,O15439,Q14739,P52292,O00429,P38919,O43765,P46782,Q99623,Q16891,P60866,Q9NR30,Q9C0B5,P60660,P13010,P57678,P25205,P08708,Q6P2E9,P62937,Q99615,Q8NEW0,O60762,P38435,P12109,Q9UNM6,O14980,P25705,Q7KZI7,Q9Y4L1,O43852,O00231,Q08431,P49069,Q6NXT4,Q10589 2 | nucleoplasm P48556,Q13200,Q13769,Q5H9R7,Q3ZCQ8,P53778,P62753,Q16630,Q9NTJ3,P0DP23,Q9BSJ2,P62269,O00148,O95071,P53396,Q7L590,Q00839,Q8IXH7,Q96J01,Q86WX3,Q13151,Q9BRP8,P39019,P39880,Q6NZY4,Q86W42,Q07820,O60885,Q13352,O60684,Q6IEG0,Q9UKV3,P52630,P67809,Q15008,Q9H936,P38159,Q9UM54,P35998,Q00403,Q9Y580,Q14974,P26358,Q14160,P12956,Q92793,P09622,Q96FV9,Q15303,P09874,P35222,P62195,P78563,P30876,P35232,Q6PKG0,Q12789,Q96MM7,Q92900,P63279,O94762,P63104,Q8WX92,Q86VM9,Q9BUQ8,Q92994,Q8N5P1,Q9H3P2,Q9NVW2,P63165,Q14653,Q13838,Q9NQG5,O43818,Q9BXP5,Q9H814,O95347,Q9Y466,O75400,O43592,Q9UER7,P61326,Q09161,P42224,Q99460,Q16576,P18615,Q6PJT7,Q9NWV8,Q5VV67,Q9H307,Q9Y265,P09651,O00629,P52294,Q9BQ95,O95619,P62140,P52298,Q8N0Z6,P49756,Q9UHI6,Q96RT1,P14735,P24928,P26599,P20700,O14818,P35637,Q9Y5S9,Q8NI27,P51665,Q96HW7,P60900,P62191,P19338,Q15365,P19784,Q7Z4H7,P25787,P67870,P06493,Q9ULX6,P68400,O00422,O95373,P08107,P83916,P46379,Q8NEM0,P52292,O75934,P98179,P38919,P12004,P05161,P46782,Q86U42,P60866,Q6I9Y2,Q9UKS6,Q9NR30,Q8TAD8,P13010,P57678,O00505,P52948,P25205,P08708,Q6P2E9,Q99615,Q14011,Q9UNM6,O15397,O14980,P0DMV8,P42677,P08621,Q86U32,O00231 3 | pseudopodium P12814,Q08043,P55085,O43707,P35609 4 | brush border P12814,P19105,Q08043,P47756,P60660,O00429,O43707,P61158,O14950 5 | nuclear matrix O95619,P20700,O75400,O43592,P60900,Q9ULX6,Q96FV9,Q9Y265,Q99623,Q13838 6 | zona pellucida receptor complex P49368,P17987,P48643,Q99832 7 | extracellular matrix P07355,P60866,P40227,P04406,P15924,P60660,P39019,P29122,P08708,P06576,P00750,P12109,P62269,P40939,P25705,P11021,Q00839,Q08431,P46782 8 | cytosolic small ribosomal subunit P60866,P08708,P62269,P39019,P42677,P62753,P46782 9 | actin filament P12814,Q08043,Q9H270,P47756,Q7KZI7,Q96EY1,P13797,P35609 10 | cytosolic proteasome complex P35998,P62191,P14735,P62195 11 | sarcolemma P07355,Q14315,P05556,P12109,Q14524,P35613,P05023,P05026,Q12959 12 | vesicle P07355,P0DP23,P27105,P33176,P50395,O14745,Q8NEW0,P04406,Q13561,Q9ULV4,P60660 13 | platelet alpha granule lumen P12814,P05155,P02768,P15692,O43707,P00747,P35609 14 | perinuclear region of cytoplasm P07355,Q9UM54,P27105,O14745,P04406,P31689,P42224,Q9UL15,O76061,P62753,P09601,P16615,P35222,P33176,Q9NV92,P08107,O00429,O43707,Q5JWF2,P05556,Q99569,P25205,Q8NEW0,P09603,P22460,P35637,P0DMV8,P63244,Q9P289,Q8NC51,Q12959 15 | spliceosomal complex P49756,O00148,O75934,P08621,Q9NW13,Q9UKA9,O75940,P09651,Q13838 16 | endoplasmic reticulum quality control compartment Q13438,Q96DZ1,Q9BZQ6,Q9NYU1 17 | membrane raft P07355,P27105,O14745,P22460,P37173,P27487,P05556,P35613,P31431,P35052,Q9BYF1,P07195,Q10589,Q12959 18 | Z disc Q14315,P12814,P19105,P22460,Q08043,P47756,Q14524,O43707,P35222,P35609,O14950 19 | COPI vesicle coat P53621,Q9UBF2,P35606,P53618 20 | small ribosomal subunit P60866,P62269,P63244,P62753,P46782 21 | mitochondrial nucleoid P06576,Q9NVI7,Q7L8L6,P40939,P34897,Q96EY1 22 | cell surface P07355,P05556,Q96PE1,Q14524,P08581,P04439,Q9BYF1,P29122,P14735,Q4KMQ2,Q13443,P06576,P00750,P35232,P27487,P15151,P31431,P11021,P15692,Q13224,Q00839,P00747,Q10589,P34741,Q9BS26,Q99623 23 | CRD-mediated mRNA stability complex P67809,O75534,Q00839 24 | endoplasmic reticulum-Golgi intermediate compartment O95070,P11021,Q9Y3A6,P15144,Q9NYU1,Q9BS26,P53618 25 | microtubule P40227,Q5SW79,Q96CW5,Q7Z4H7,P17987,Q13561,Q14152,Q99832,P49368,P33176,Q02224,Q9BSJ2,P48643,O00429,O60333,P50402,Q12959 26 | endocytic vesicle Q9UM54,P33176,Q9H270,P27487,P35247,P51148 27 | cytoplasmic stress granule P11940,Q14011,Q13310,Q13283,P67809 28 | proteasome regulatory particle,lid subcomplex P48556,Q9UNM6,O00231 29 | proteasome core complex,alpha-subunit complex P25787,O14818,P60900 30 | nuclear proteasome complex P35998,P62191,P62195 31 | mitochondrial matrix Q96EY1,P34897,O75439,Q07820,Q15303,P09622,Q8IZ52,Q9UDR5,Q07817,P06576,P11310,Q5JRX3,Q9BW92,Q10713,P25705,P13804,Q6L8Q7 32 | cytoplasmic mRNA processing body P35998,Q6P2E9,P25787,Q9Y5A9,P60900,Q9HCE1,Q92900 33 | lysosomal membrane P07355,Q9UM54,Q8IWA5,O75348,Q99519,O00203,P22314,Q96JC1,P51148,B7Z2Y1,P12109,P27487,Q9H270,P38606,P15144 34 | intracellular membrane-bounded organelle P35998,P04406,O14745,Q99519,P39656,Q96EY1,Q96S66,O14964,Q9NV92,P46379,O00429,O95070,Q9Y265,P05023,Q8N0Z8,P25205,P51148,Q9UDR5,Q6P2E9,O60762,Q9H814,P67809,O14980,Q15365,P53618 35 | mitochondrial outer membrane Q07817,Q16548,O94826,Q92843,O00429,Q86UT6,Q07820,Q99623,P10415,Q8N0X7 36 | integral component of endoplasmic reticulum membrane Q9NZ01,O00124,Q14739,P11021,P57088,Q9P035,Q9NQC3,O76024 37 | desmosome P15924,Q99569,P22314,Q9H307 38 | centrosome Q6NXT6,O14745,Q5SW79,Q96CW5,Q8TF76,Q7Z4H7,P17987,Q13561,P06493,P35222,P25205,Q9NQG5,P0DP23,Q07817,Q9H814,Q9BSJ2,P48643,Q8IWR1,Q9P289,P12004 39 | fascia adherens P12814,P15924,P35222 40 | cytoplasmic ribonucleoprotein granule P11940,P62753,Q00839,P19338 41 | caveola P22460,P37173,Q14524,P09601,P05023,P05026 42 | endoplasmic reticulum chaperone complex Q8IXB1,P11021,Q9Y4L1 43 | AP-3 adaptor complex Q9H270,O00203,Q96JC1 44 | DNA-directed RNA polymerase II,holoenzyme Q9NQG5,Q9UM54,O94762 45 | nuclear euchromatin P16402,P35222,P24928,P38159 46 | PcG protein complex P19784,Q9BSM1,P67870,P68400 47 | ruffle P07355,P12814,Q5JWF2,Q9UM54,O14745,P05556,Q14155 48 | ribosome P60866,P08708,Q86WX3,Q92552,P62269,P39019,P42677,P61927,P62753,Q9Y3U8 49 | transport vesicle Q5JWF2,P53621,Q9UBF2,Q9H8W4,P35606,Q15818,P53618 50 | cell-cell junction P07355,Q9NYL9,P12814,Q99569,Q14160,Q9H307,O43707,P61158,P35222,Q12959 51 | RNA cap binding complex Q09161,Q53F19 52 | Scrib-APC-beta-catenin complex Q14160,P35222 53 | proteasome storage granule Q13200,Q99460 54 | -------------------------------------------------------------------------------- /www/Examples/IntAct_COVID19/HomoSapiens_Gene_Ontology_GOTERM_MF_DIRECT_FILTERED.txt: -------------------------------------------------------------------------------- 1 | poly(A) RNA binding P62753,J3QSV6,Q16630,Q13283,P62269,O00148,Q02978,O43707,Q00839,Q86WX3,Q13151,P68036,Q9BRP8,P17987,P39019,Q8TDD1,Q6NZY4,P11940,Q9UKV3,P62258,P56270,P16402,P67809,P61254,P63244,Q8NC51,P38159,P40227,Q9Y580,Q14974,P12956,P09874,Q00688,P78563,P30876,Q7KZF4,Q6PKG0,P63279,Q92900,P63104,Q7L8L6,Q8N5P1,Q9BUQ8,Q86VM9,Q14152,P63165,Q9UN86,Q13838,Q8WTT2,O43818,P50395,Q9BXP5,O75400,P61326,Q96A72,Q9Y3U8,P07355,Q09161,Q9Y5A9,P31948,P18615,Q6PJT7,Q9H307,Q5VV67,Q8NCA5,P09651,P15924,Q13310,P20290,P52298,P22314,P49756,P04439,P24928,P26599,P35637,Q9Y5S9,Q9NW13,P19338,P62191,Q15365,P04003,O75534,Q9ULX6,Q9HCE1,Q53F19,O00422,P52292,Q14739,P98179,P38919,Q9UKA9,P46782,Q86U42,Q16891,P60866,Q8TAD8,Q9NR30,P13010,P08708,P62937,P49368,Q14011,P25705,Q7KZI7,P42677,P08621,Q9NQC3,Q86U32,O75940,Q10589 2 | protein binding Q9P021,Q13200,Q96GX9,Q13769,Q5H9R7,Q3ZCQ8,Q99988,Q86VR2,P62753,Q9NTJ3,P0DP23,P61769,Q9BSJ2,O43292,P62269,Q8TBB1,P59998,P50402,Q8IXH7,Q00839,P34741,Q99569,Q13561,Q07820,P55198,Q13352,Q4KMQ2,Q9NZJ7,Q96GG9,Q9H3K2,Q07817,Q9UKV3,P52630,P62258,Q86YB8,Q8NC51,P35998,P40227,Q00403,P26358,Q96PE1,P35606,Q92793,Q96FV9,Q15303,P09874,P35609,Q9Y680,Q00688,P78563,Q13443,Q15311,P27348,Q6PKG0,Q12789,P11021,Q92900,P63104,Q9ULJ7,Q8WX92,Q7L8L6,P35613,Q9BUQ8,Q9UBX3,Q9P035,P25100,Q13838,Q9NQG5,P06576,Q9Y5U4,Q13438,Q9BXP5,O60333,P55085,Q13224,Q9NS75,P53618,Q09161,O14745,Q9P0K1,Q9UL15,Q9Y5A9,P31948,P30153,Q9H773,Q6PJT7,O75592,Q8NCA5,Q9Y3A6,P57088,O00303,P05023,P09651,P05026,Q9NZ01,P52294,Q9BQ95,Q96CW5,O95619,Q13310,P20290,P52298,Q8N0Z6,P49756,P14735,P24928,P37173,Q9H270,Q9Y5S9,P51665,O00192,P60900,Q96HW7,P00747,P19338,Q15365,Q12959,P27105,Q9BSM1,P25787,P04003,Q9UQB3,Q14CM0,P81408,P67870,Q9HCE1,P68400,Q8IXB1,P33176,O00422,P00750,Q96IZ7,P08107,P46379,P83916,Q8NEM0,Q96DZ1,P48643,O00429,P52292,P05161,O43765,P46782,Q99623,Q9UKS6,Q9NR30,O75348,P52948,P51148,Q8N0X7,P49368,Q99615,P05155,O15397,P0DMV8,P08621,Q6ZTQ3,Q9NQC3,O43852,Q10589,O76024,P25440,P04406,Q9ULV4,Q14524,Q96EY1,P53778,P35247,P09601,Q16630,Q5BJF2,Q9H845,O15027,Q13283,P15151,Q9NXK8,O00148,O95071,O95070,P53396,Q7L590,O43707,O14656,P10415,Q05639,Q86WX3,P68036,Q9BRP8,Q9Y6R1,P05556,O75822,P17987,Q13155,P39019,Q00765,Q13011,Q15293,P48668,O60884,Q6NZY4,O60885,O60684,P11940,P61254,P56270,P67809,Q9NU22,Q15008,P63244,Q96HR9,P31150,P48065,P38159,Q9BS26,Q9H173,Q9UM54,P34932,Q96A65,Q14974,O43633,Q96IV0,P12956,Q14160,Q96PV6,P16615,P35222,Q99832,P62195,P12814,P30876,P19105,Q9H078,Q02224,P52907,Q7KZF4,P35232,Q9Y375,O95816,Q14257,P63279,Q5JWF2,O94826,Q8N5P1,Q86VM9,Q14152,P07195,Q9H3P2,P63165,Q9UN86,Q14155,Q6DN90,Q14653,Q96NW7,P09603,P50395,Q9H814,O95347,P40939,P31431,O75400,Q8IWR1,Q9UER7,P61326,Q96A72,P07355,P31689,P42224,K7ELV2,P39656,Q16576,Q9BYF1,P11586,P18615,P27487,Q9NWV8,Q7Z5G4,Q9H8W4,P13804,Q9Y6M9,Q8N8U2,Q9Y265,Q96SF7,O00629,Q5SW79,P15924,P62140,P22459,P22314,Q9UHI6,Q99471,Q9UH99,P04439,Q96RT1,O14950,Q96S52,P22460,P26599,O14818,P20700,P35637,Q12770,Q8NI27,Q9H4F8,Q86UT6,P15692,Q9P289,P61158,P62191,Q9Y276,P19784,Q8IV08,Q96CS3,O15503,P08581,Q92843,O75534,P06493,Q9ULX6,P61916,Q53F19,O14964,O95373,Q9NV92,Q16548,Q96F46,O00124,Q14739,P28300,O75934,P98179,P48050,P38919,P12004,Q86U42,Q16891,P60866,Q8IWF2,Q6I9Y2,Q8TAD8,Q08043,Q8TF76,P02768,P60660,P13010,P34897,P57678,Q9NYU1,O00505,P27448,P25205,Q14315,Q6P2E9,P62937,O60762,Q14011,Q92552,O14980,P25705,Q7KZI7,P42677,Q96K17,Q5JVF3,O00231,Q86U32,O75940,P49069 3 | protein domain specific binding Q14974,O43633,Q14524,Q9UHI6,P67870,P35609,O14964,P0DP23,P27348,Q9H270,P62258,O14980,P11021,P05023,P00747,P63104 4 | ion channel binding P0DP23,P12814,P27348,Q08043,P62258,Q14524,O43707,P35222,P63165,P35609,Q12959 5 | Hsp70 protein binding Q8IXB1,P31689,P46379,P31948,Q96EY1,P06493 6 | glycoprotein binding Q8IWF2,P61769,P00750,Q13438,Q96DZ1,P11021,Q9BYF1,P14735 7 | TBP-class protein binding P35998,Q00403,Q92994,P62191,P62195 8 | estrogen receptor binding P35637,Q8TDD1,P09874,P12004,P35222,Q99623 9 | misfolded protein binding Q8IXB1,P46379,P11021,O14656 10 | protein transporter activity O00629,P52294,O60684,O95373,Q14974,O15397,P52292,O00505 11 | BH3 domain binding Q07817,Q07820,P10415 12 | actin filament binding Q14315,P12814,Q9UM54,P47756,Q9ULV4,P59998,O43707,P61158,P13797,Q8NHY3,P35609 13 | poly(A) binding P11940,Q6PJT7,Q13310,P38919 14 | identical protein binding P04406,P42224,Q96GX9,P67870,P09874,Q99832,P35609,P61769,Q9H773,P11310,P27487,Q8NEM0,O95816,O00429,O00148,Q7L590,P12004,P10415,P63104,P02768,Q13561,Q9UH99,P34897,P07195,Q13838,Q14653,P06731,Q07817,O14818,P52630,P35637,P15692,Q9P289,P19338,P38159 15 | Ran GTPase binding O95373,Q14974,O15397,O14980,O43592 16 | integrin binding Q13443,P12814,Q08043,Q9P0K1,P05556,O43707,Q96RT1,Q08431,P35609 17 | proteasome-activating ATPase activity P35998,P62191,P62195 18 | dolichyl-phosphate-mannose-protein mannosyltransferase activity O60762,Q9Y673,Q99470 19 | cytoskeletal protein binding P07355,Q14315,Q9UKS6,O14656,P35609,Q12959 20 | oxidoreductase activity,acting on the CH-CH group of donors Q9NZ01,Q9H845,P11310,Q14739 21 | virus receptor activity P08107,P27487,P05556,P15151,P0DMV8,Q9BYF1,P15144,P14735 22 | protein N-terminus binding P19784,Q96A65,P27348,Q9UER7,O43707,P09874,P68400,Q99623 23 | protein homodimerization activity P27105,P42224,Q92843,O76061,P09601,Q15303,P35609,P12814,Q16548,P83916,P27487,P15151,O00429,O43707,Q96SF7,P10415,Q08043,P39019,Q07820,P14735,Q14653,Q4KMQ2,P06731,Q07817,P09603,P63244,P15692,P51665,Q9UER7,Q9P289,Q10589,Q6UY11 24 | NAD binding P04406,P40939,P07195,P09622,P09874 25 | protein kinase binding Q05639,Q13151,P62140,Q14524,Q9UL15,P39019,Q96EY1,P62753,P09874,P35222,Q14155,P0DP23,Q07817,P22460,P62269,Q9UER7,P05023,P63104,Q12959 26 | rRNA binding Q9NR30,Q7L8L6,P62269,P61927,P46782 27 | histone deacetylase binding P35232,P08107,P62258,P0DMV8,P52292,Q9UHI6,Q9Y466,Q9ULX6,P09874 28 | telomeric DNA binding P12956,P13010,P19338,Q92900 29 | RNA cap binding Q09161,Q6PKG0,P52298 30 | chromatin binding P25440,P26358,Q8N0Z6,Q9ULI0,P67870,P34897,Q92793,P06493,O60885,Q9H3P2,P18615,P30876,Q8WTT2,P83916,P67809,Q92900,P12004,Q6PML9,P38159 31 | cation transmembrane transporter activity Q8NEW0,Q6NXT4,Q6PML9 32 | phospholipid scramblase activity A1A5B4,Q32M45,Q4KMQ2 33 | peptidyl-prolyl cis-trans isomerase activity Q6UX04,P62937,Q96AY3,Q9Y680,Q00688 -------------------------------------------------------------------------------- /www/Examples/IntAct_COVID19/HomoSapiens_Pathways_KEGG_PATHWAY_FILTERED.txt: -------------------------------------------------------------------------------- 1 | Viral carcinogenesis Q00403,Q08043,Q14160,P04439,Q96EY1,Q92793,P06493,P35609,Q14653,P12814,P27348,Q7KZF4,P62258,O43707,P62191,P63104,Q12959 2 | Influenza A P52294,P42224,P78406,Q92793,P53778,P52948,Q13838,Q14653,P08107,P52630,P0DMV8,O14980,P52292,Q86UT6,P00747,Q86U42 3 | Herpes simplex infection P19784,P42224,P62140,P67870,P04439,Q92793,P06493,P68400,P24928,Q14653,P52630,Q9UER7,Q86U32 4 | Proximal tubule bicarbonate reclamation Q9Y6R1,Q9UBX3,P05023,P05026 5 | -------------------------------------------------------------------------------- /www/Examples/IntAct_COVID19/HomoSapiens_Protein_Domains_INTERPRO_FILTERED.txt: -------------------------------------------------------------------------------- 1 | P-loop containing nucleoside triphosphate hydrolase Q9UM54,P35998,Q9NVI7,Q9ULI0,Q5T9A4,Q9HCE1,Q9NTJ3,P11586,P62195,Q02224,P33176,Q9H078,P38606,O00429,O15439,O00148,Q00839,Q9Y265,P38919,Q92900,Q96MM7,O14656,O94762,Q05639,Q5JWF2,Q9NR30,Q8TDD1,Q9UHI6,Q9BUQ8,Q13838,P51148,P25205,P06576,P33527,O95347,Q9NU22,P25705,O60333,P62191,Q9Y276,Q12959 2 | EF-hand-like domain Q08043,P42224,P60660,Q15293,Q07820,P35609,Q9Y680,O14950,P0DP23,P12814,P19105,P52630,O75746,Q9H4F8,Q96AY3,O43707,O43852,Q14257,P13797 3 | Apoptosis regulator,Bcl-2,BH4 motif,conserved site Q07817,Q92843,P10415 4 | ATPase,F1/V1/A1 complex,alpha/beta subunit,C-terminal P06576,P38606,P25705 5 | Apoptosis regulator,Bcl-2 protein,BH4 Q07817,Q92843,P10415 6 | DNA/RNA helicase,DEAD/DEAH box type,N-terminal Q9NR30,Q8TDD1,Q9BUQ8,Q9UHI6,O00148,P38919,Q13838,O94762 7 | Filamin/ABP280 repeat-like Q14315,O75592,Q7Z4H8,Q6UW63 8 | Chaperone DnaJ P31689,Q96EY1,O60884 9 | Calponin homology domain Q14315,P12814,Q08043,O43707,P13797,Q8NHY3,P35609,Q14155 10 | RNA recognition motif domain,eukaryote P11940,Q14011,Q13310,P19338,P38159 11 | ATPase,AAA-type,conserved site P35998,Q9ULI0,P62191,Q9Y276,P62195 12 | Peptidase M16,zinc-binding site Q10713,O75439,P14735 13 | Kinase associated domain 1 (KA1) Q9P0L2,Q7KZI7,P27448 14 | ATPase,alpha/beta subunit,N-terminal P06576,P38606,P25705 15 | Heat shock protein DnaJ,cysteine-rich domain P31689,Q96EY1,O60884 16 | ATPase,F1/V1/A1 complex,alpha/beta subunit,nucleotide-binding domain P06576,P38606,P25705 17 | ATPase,alpha/beta subunit,nucleotide-binding domain,active site P06576,P38606,P25705 18 | Spectrin/alpha-actinin P12814,Q08043,P15924,O43707,P35609 19 | Immunoglobulin E-set Q14315,Q96DL1,O75592,P08581,Q14500,Q7Z4H8,P48050,P61916,Q6UW63 20 | EF-Hand 1,calcium-binding site P0DP23,P12814,P19105,O75746,Q9H4F8,Q15293,Q96AY3,O43707,O43852,P13797,Q14257,Q9Y680,O14950 21 | EF-hand domain Q08043,P60660,Q15293,P35609,Q9Y680,O14950,P12814,P0DP23,P19105,O75746,Q96AY3,O43707,O43852,P13797,Q14257 22 | 26S proteasome subunit P45 P35998,P62191,P62195 23 | G-protein beta WD-40 repeat O43818,P53621,K7ELV2,P78406,P35606,P63244,Q16576,Q96J01 24 | 14-3-3 protein P27348,P62258,P63104 25 | 14-3-3 protein,conserved site P27348,P62258,P63104 26 | 14-3-3 domain P27348,P62258,P63104 27 | Apoptosis regulator,Bcl-2,BH3 motif,conserved site Q07817,Q07820,P10415 28 | Proteasome A-type subunit P25787,O14818,P60900 29 | Proteasome,alpha-subunit,N-terminal domain P25787,O14818,P60900 30 | Chaperone DnaJ,C-terminal P31689,Q96EY1,O60884 31 | HSP40/DnaJ peptide-binding P31689,Q96EY1,O60884 32 | Helicase,C-terminal Q9NR30,Q8TDD1,Q9BUQ8,Q9UHI6,O00148,P38919,Q13838,O94762 33 | Cation efflux protein Q8NEW0,Q6NXT4,Q6PML9 34 | Cation efflux protein transmembrane domain Q8NEW0,Q6NXT4,Q6PML9 35 | Filamin/ABP280 repeat Q14315,Q7Z4H8,Q6UW63 36 | Spectrin repeat P12814,Q08043,O43707,P35609 37 | Helicase,superfamily 1/2,ATP-binding domain Q9NR30,Q8TDD1,Q9BUQ8,Q9UHI6,O00148,P38919,Q13838,O94762 38 | Bromodomain,conserved site P25440,Q9ULI0,Q92793,O60885 39 | Anoctamin/TMEM 16 A1A5B4,Q32M45,Q4KMQ2 40 | RNA helicase,ATP-dependent,DEAD-box,conserved site Q8TDD1,Q9BUQ8,Q9UHI6,P38919 41 | Mitochondrial carrier protein P53007,O75746,Q9BQT8,Q9H936 42 | Tetratricopeptide TPR-1 Q99615,O94826,P31948,O43765 43 | Band 7 protein P27105,P35232,Q99623 44 | WD40-repeat-containing domain K7ELV2,Q9ULV4,P78406,P35606,Q86W42,Q16576,Q96JC1,O43818,B7Z2Y1,P53621,Q6P2E9,Q9H270,Q12770,P63244,Q96J01 45 | von Willebrand factor,type A Q9NWV8,P05556,P12109,P12956,Q9NU22,P13010,P10155 46 | DnaJ domain Q8IXB1,Q99615,P31689,Q96EY1,O60884 47 | Proteasome/cyclosome,regulatory subunit Q13200,Q99460 48 | Apoptosis regulator,Bcl-2/ BclX Q07817,P10415 49 | Transcription factor TFIIB,cyclin-like domain Q00403,Q92994 50 | Insulin-induced protein family O15503,Q9Y5U4 51 | Coatomer,WD associated region P53621,P35606 52 | Ku70/Ku80 C-terminal arm P12956,P13010 53 | Ku70/Ku80,N-terminal alpha/beta P12956,P13010 54 | Ku70/Ku80 beta-barrel domain P12956,P13010 55 | Rab GDI protein P50395,P31150 56 | ATPase,F1 complex beta subunit/V1 complex,C-terminal P06576,P38606 57 | Mago nashi protein P61326,Q96A72 58 | Clathrin/coatomer adaptor,adaptin-like,N-terminal Q9UBF2,O00203,P53618 -------------------------------------------------------------------------------- /www/Examples/IntAct_COVID19/HomoSapiens_Protein_Domains_SMART_FILTERED.txt: -------------------------------------------------------------------------------- 1 | SM00265:BH4 Q07817,Q92843,P10415 2 | SM00033:CH Q14315,P12814,Q08043,O43707,P13797,Q8NHY3,P35609,Q14155 3 | SM00361:RRM_1 P11940,Q14011,Q13310,P19338,P38159 4 | SM00150:SPEC P12814,Q08043,P15924,O43707,P35609 5 | SM00088:PINT Q9UNM6,Q15008,Q14152,O00231 6 | SM00101:14_3_3 P27348,P62258,P63104 7 | SM00948:SM00948 P25787,O14818,P60900 8 | SM00557:IG_FLMN Q14315,Q7Z4H8,Q6UW63 9 | SM00490:HELICc Q9NR30,Q8TDD1,Q9BUQ8,Q9UHI6,O00148,P38919,Q13838,O94762 10 | SM00487:DEXDc Q9NR30,Q8TDD1,Q9BUQ8,Q9UHI6,O00148,P38919,Q13838,O94762 11 | SM00244:PHB P27105,P35232,Q99623 12 | SM00271:DnaJ Q8IXB1,Q99615,P31689,Q96EY1,O60884 13 | -------------------------------------------------------------------------------- /www/Examples/TAU/TAU_KEGG_Annotation_NORMA.txt: -------------------------------------------------------------------------------- 1 | Ribosome RpL10,RpL10Ab,RpL11,RpL12,RpL13,RpL18A,RpL26,RpL3,RpL30,RpL4,RpLP0,RpLP2,RpS10a,RpS10b,RpS11,RpS12,RpS13,RpS15Aa,RpS15Ab,RpS16,RpS17,RpS18,RpS2,RpS23,RpS27,RpS3,RpS3A,RpS4,RpS6,RpS7,RpS8,bonsai,mRpL12,mRpS10,mRpS7,mRpS9,sta 2 | Proteasome Prosalpha6,Prosalpha7,Prosbeta7,Rpn12,Rpn13,Rpn2,Rpn3,Rpn5,Rpn6,Rpt1,Rpt2,Rpt4,Rpt4R,Rpt5,Rpt6,Rpt6R 3 | Spliceosome B52,CG10077,CG10777,CG16941,Hrb98DE,LS2,Prp8,Ref1,SF2,Tango4,U2A,U2af50,mago 4 | Phagosome Act79B,Cnx99A,Cp1,Dhc64C,Dlic,Hrs,Mtl,Rab5,Rac1,Vha100-1,Vha100-2,Vha68-2,betaTub56D 5 | Carbon metabolism AcCoAS,CG10932,CG11876,CG11899,CG12262,CG3011,CG32026,CG33791,Cat,Eno,Mdh2,Men,Men-b,Nc73EF,Pfk,PyK,Tpi,l(1)G0156 6 | Oxidative phosphorylation ATPsynCF6,ATPsynbeta,COX4,COX5A,COX6B,ND-15,ND-51,ND-51L1,ND-B16.6,ND-PDSW,NP15.6,Vha100-1,Vha100-2,Vha68-2,sun 7 | RNA degradation CG2091,Eno,Hsc70-5,Hsp60,Hsp60C,Not1,Not3,Pfk,me31B,pAbp 8 | RNA transport CG9769,Fmr1,Mtor,Rae1,Ref1,Trip1,eIF-3p66,eIF3-S10,eIF3-S8,eIF3-S9,eIF4G,emb,mago,pAbp,smt3 9 | Glycolysis AcCoAS,Aldh,CG11876,Eno,ImpL3,Pfk,PyK,Tpi 10 | Pyruvate metabolism ACC,AcCoAS,Aldh,CG10932,CG11876,ImpL3,Mdh2,Men,Men-b,PyK 11 | -------------------------------------------------------------------------------- /www/Examples/TAU/TAU_Louvain.txt: -------------------------------------------------------------------------------- 1 | Group-1 Mgstl,KP78a,CG9257,par-1,CG31064,LpR1,Rab39,LpR2,CG3529,Lam,LamC,Sap-r,Vps60,lqf,ninaC,Hrs,Arr2,Arr1,Rab5,CG32683,pins,chp 2 | Group-2 Sc2,Uch,Prx2540-1,Ace,CG4572,Sgt,CG14715,CG10359,Ect3,CalpB,Prx5,Ost48,Hsp60C,Prx2540-2,Hsp60,Ubqn,Hsp70Ab,Ugt,Iswi,Trap1,Cat,Hsc70-5,CG8209,DnaJ-H,p47,Rad23,Cnx99A,pont,Cp1,cathD,Uba2,Pfk,Gdi,Uch-L5,Rpt4R,Prosalpha1,mor,Bap55,Ufd1-like,TER94,Hsc70-3,PyK,Hsp83,ERp60,arm,Rpt1,Rpn13,Rpt2,Rpn5,Rpt6R,Rpn2,Pdi,CaBP1,Gp93,Rpt4,Hop,CG1416,Prosalpha6,Rpt5,Prosalpha7,Rpn6,CG8258,Rpt6,Rpn3,Rpn12,Prosbeta7,Usp5,CG2918,CG2852,CG1354,CG6891,HDAC6,Hsp27,His1,CG11577 3 | Group-3 shep,CG5590,CG17597,ScpX,Mfe2 4 | Group-4 CG4882,EfTuM,Rbp2,eEF1delta,CG10576,Nacalpha,mRpS34,vig,CG4679,mRpS35,mRpS7,mRpL44,mRpS22,eIF4G,bonsai,mRpS10,Srp54k,mRpL12,Tctp,eIF-2gamma,mRpS23,mRpS18B,ade3,mRpS9,mRpS5,Srp19,Srp72,eIF-3p66,Cctgamma,Ef1beta,Tango7,RpL10Ab,Trip1,eIF3-S10,eIF3-S9,Tcp-1eta,RpL13,RpS11,eIF3-S8,RpS6,RpS2,RpL12,RpS7,RpL10,RpS8,RpL30,RpS10a,RpS17,RpLP0,eRF1,Elf,RpS15Aa,RpS27,RpS18,RpS10b,RpS3A,RpS16,RpS15Ab,RpL3,Tcp-1zeta,T-cp1,RpS3,RpL26,RpS12,CG5642,CG9769,CG7033,Cct5,RpLP2,RpS23,RpS14a,Rack1,RpL11,RpS13,RpL18A,RpS4,RpL4,sta,wuho,bsf,kra,Hsp67Bc,su(r),FeCH,CG8635 5 | Group-5 nito,bol,Kap-alpha3,CG2082,lig,clu,Dbp80,Plc21C,Hrb27C,bel,Dp1,Lpin,Pkc53E,Nlp,rin,poe,CG43367,emb,fne,RanBPM,yps,Art4,CG10077,mub,AGO1,glo,Srp54,Rbp9,Rae1,Mtor,Ref1,mago,B52,LS2,U2af50,Fmr1,Top2,heph,Hrb98DE,Tudor-SN,SF2,me31B,CG16941,Prp8,Tango4,U2A,smt3,pAbp,Not1,Not3,CG2091,Capr,Gbeta76C,CG10777,CG6617,CG3800,tyf,CG11505 6 | Group-6 CG6178,frj,CG9090,Ssadh,l(1)G0156,CG32026,Men-b,CG11899,CG16935,AGBE,ImpL3,Nc73EF,CG3902,CG11876,Pdk,Vha100-1,AcCoAS,ACC,Mdh2,Cyt-c-p,Aldh,CG15093,ND-51L1,ND-51,Vha68-2,Vha100-2,ND-15,CG12262,yip2,ade5,CG11089,COX6B,CG11752,COX4,COX5A,Eno,Tpi,ND-PDSW,NP15.6,ATPsynbeta,ATPsynCF6,CG10932,CG33791,CG3011,Men,sun,porin,ND-B16.6,CG7603,Mpcp 7 | Group-7 Ndg,trol,Cg25C,vkg,LanA,LanB2,Glt 8 | Group-8 Lar,CG31715,PlexA,gammaSnap2,CG10186,Klp10A,Mtl,bai,Act79B,Abl,Tim17b,p115,Sec24AB,robl,tsr,flr,FKBP59,bic,BicD,CadN,syd,Rac1,zip,alphaCOP,zetaCOP,CG7048,CG7770,Dlic,Dhc64C,betaCOP,cpa,cpb,epsilonCOP,beta'COP,Klc,Khc,alpha-Cat,deltaCOP,RhoGDI,Dscam1,Tim9a,sqh,dock,Dscam2,CG8498,CLIP-190,betaTub56D 9 | Group-9 Mapmodulin,Aats-val,Aats-his,Aats-asp,CG33123,Aats-ile,Aats-arg,CG31739 10 | -------------------------------------------------------------------------------- /www/Examples/TAU/TAU_expressions.txt: -------------------------------------------------------------------------------- 1 | CG7603 red 2 | His1 red 3 | Act79B red 4 | Gbeta76C red 5 | CG11876 red 6 | Kap-alpha3 red 7 | CG2082 red 8 | LanA red 9 | Vha68-2 red 10 | CalpB red 11 | Ssadh red 12 | CG43367 red 13 | l(1)G0156 red 14 | CG9090 red 15 | Prx5 red 16 | CG1354 red 17 | porin red 18 | GstD9 red 19 | CG32026 red 20 | Aldh red 21 | Glt red 22 | Tpi red 23 | PyK red 24 | ATPsynbeta red 25 | Eno red 26 | Mtl red 27 | Arr1 red 28 | Mpcp red 29 | Arr2 red 30 | Ndg red 31 | FeCH red 32 | Nc73EF red 33 | CG10932 red 34 | CG33791 red 35 | betaTub56D red 36 | Cyt-c-p red 37 | CG16935 red 38 | Prx2540-2 red 39 | GstE4 red 40 | pins red 41 | chp red 42 | Men-b red 43 | GstD3 red 44 | HDAC6 red 45 | CG10359 red 46 | mago red 47 | LamC red 48 | Ace red 49 | Mdh2 red 50 | ninaC red 51 | LanB2 red 52 | Cg25C red 53 | sun red 54 | vkg red 55 | Pfk red 56 | Prx2540-1 red 57 | EfTuM red 58 | Vha100-1 red 59 | Vha100-2 red 60 | AGBE red 61 | frj red 62 | DnaJ-H red 63 | trol red 64 | Men green 65 | p47 green 66 | mRpS10 green 67 | NP15.6 green 68 | RpS15Ab green 69 | Not3 green 70 | Tim17b green 71 | eIF4G green 72 | cathD green 73 | CG12262 green 74 | Prosalpha7 green 75 | Usp5 green 76 | yip2 green 77 | Dscam1 green 78 | CG2918 green 79 | cpa green 80 | RpS4 green 81 | ade3 green 82 | CG8209 green 83 | CG11505 green 84 | FKBP59 green 85 | RpS11 green 86 | Rab39 green 87 | RpL13 green 88 | CG1371 green 89 | Prp8 green 90 | Prosalpha6 green 91 | Rpn12 green 92 | Rpn2 green 93 | Rpn5 green 94 | Nacalpha green 95 | Hsp60 green 96 | Tudor-SN green 97 | Rpt5 green 98 | Rpt4 green 99 | lqf green 100 | Rpt1 green 101 | Top2 green 102 | Rpn6 green 103 | ND-PDSW green 104 | sta green 105 | sqh green 106 | CG6178 green 107 | CG32683 green 108 | Aats-asp green 109 | LpR2 green 110 | eIF-2gamma green 111 | RpL11 green 112 | Elf green 113 | ERp60 green 114 | Sec24AB green 115 | CG11089 green 116 | Rae1 green 117 | CG3011 green 118 | Abl green 119 | Rpt6R green 120 | Uch green 121 | Trap1 green 122 | CG7048 green 123 | Rpt6 green 124 | CG10186 green 125 | wuho green 126 | Aats-arg green 127 | Lam green 128 | Hsp60C green 129 | Trip1 green 130 | RpS3 green 131 | Tctp green 132 | CG31064 green 133 | Dscam2 green 134 | emb green 135 | Uba2 green 136 | pAbp green 137 | Capr green 138 | CG4972 green 139 | Aats-his green 140 | Aats-ile green 141 | PlexA green 142 | Cctgamma green 143 | Rab5 green 144 | zip green 145 | Mi-2 green 146 | AcCoAS green 147 | su(r) green 148 | mRpS23 green 149 | arm green 150 | CG10077 green 151 | Ref1 green 152 | RpS7 green 153 | CG10777 green 154 | Aats-val green 155 | ImpL3 green 156 | Pdi green 157 | Sgt green 158 | beta'COP green 159 | alphaCOP green 160 | Fmr1 green 161 | CG31715 green 162 | mRpS7 green 163 | Ef1beta green 164 | ND-B16.6 green 165 | ScpX green 166 | Cat green 167 | lig green 168 | CG10576 green 169 | p115 green 170 | ade5 green 171 | Bap55 green 172 | Hsp83 green 173 | RpL4 green 174 | Prosbeta7 green 175 | RpLP2 green 176 | CG4572 green 177 | CG31739 green 178 | Tim9a green 179 | pont green 180 | Hsc70-5 green 181 | Hsp27 green 182 | bic green 183 | Hsp67Bc green 184 | KP78a green 185 | CG3529 green 186 | BicD green 187 | RpS12 green 188 | bsf green 189 | Hsc70-3 green 190 | Hrb98DE green 191 | RpS8 green 192 | CG8498 green 193 | Dp1 green 194 | Ost48 green 195 | Srp54k green 196 | Rad23 green 197 | Tango4 green 198 | kra green 199 | Hsp70Ab green 200 | RpS15Aa green 201 | tyf green 202 | Lpin green 203 | Cnx99A green 204 | mRpS18B green 205 | eEF1delta green 206 | CG3800 green 207 | RpL18A green 208 | par-1 green 209 | me31B green 210 | COX4 green 211 | eIF3-S10 green 212 | CG11752 green 213 | CG14715 green 214 | Mtor green 215 | U2af50 green 216 | mRpS5 green 217 | Khc green 218 | Cct5 green 219 | RpL12 green 220 | yps green 221 | B52 green 222 | CG1416 green 223 | bonsai green 224 | TER94 green 225 | Lar green 226 | alpha-Cat green 227 | glo green 228 | CadN green 229 | CG7033 green 230 | CG2091 green 231 | RpS17 green 232 | Art4 green 233 | syd green 234 | RpL3 green 235 | Tcp-1eta green 236 | CG4679 green 237 | Srp54 green 238 | mRpS34 green 239 | vig green 240 | Srp72 green 241 | ND-15 green 242 | Mapmodulin green 243 | Rack1 green 244 | Cp1 green 245 | Dlic green 246 | RpS18 green 247 | fne green 248 | RpS14a green 249 | eIF3-S8 green 250 | CG5642 green 251 | RpLP0 green 252 | gammaSnap2 green 253 | robl green 254 | RpS16 green 255 | Ugt green 256 | Hrs green 257 | Klc green 258 | eIF-3p66 green 259 | ND-51L1 green 260 | betaCOP green 261 | zetaCOP green 262 | Ubqn green 263 | rin green 264 | eRF1 green 265 | LS2 green 266 | Dbp80 green 267 | Ufd1-like green 268 | eIF3-S9 green 269 | ND-51 green 270 | COX6B green 271 | mRpS9 green 272 | CG33123 green 273 | CG9769 green 274 | bel green 275 | Sap-r green 276 | deltaCOP green 277 | Rbp9 green 278 | RpS13 green 279 | CG9257 green 280 | mRpL12 green 281 | Mfe2 green 282 | CaBP1 green 283 | AGO1 green 284 | Mgstl green 285 | CG17597 green 286 | CG6617 green 287 | mub green 288 | ATPsynCF6 green 289 | Rbp2 green 290 | Uch-L5 green 291 | dock green 292 | LpR1 green 293 | CG6891 green 294 | RpL10 green 295 | heph green 296 | Hop green 297 | RpL10Ab green 298 | COX5A green 299 | RpL30 green 300 | mRpS22 green 301 | Tcp-1zeta green 302 | Nlp green 303 | Rpt4R green 304 | Ect3 green 305 | poe green 306 | Vps60 green 307 | tsr green 308 | RanBPM green 309 | Plc21C green 310 | mor green 311 | epsilonCOP green 312 | Rpt2 green 313 | ACC green 314 | Rpn3 green 315 | bol green 316 | RpS10a green 317 | CG4882 green 318 | CG8258 green 319 | bai green 320 | shep green 321 | Srp19 green 322 | CG2852 green 323 | CG11899 green 324 | clu green 325 | Iswi green 326 | Dhc64C green 327 | RpS6 green 328 | RpS10b green 329 | CG5590 green 330 | Klp10A green 331 | Gdi green 332 | RpS2 green 333 | RpS27 green 334 | Not1 green 335 | flr green 336 | Pkc53E green 337 | CG11577 green 338 | CG15093 green 339 | CLIP-190 green 340 | smt3 green 341 | Rac1 green 342 | cpb green 343 | CG16941 green 344 | RhoGDI green 345 | Prosalpha1 green 346 | mRpL44 green 347 | Gp93 green 348 | Pdk green 349 | RpS23 green 350 | T-cp1 green 351 | RpL26 green 352 | CG3902 green 353 | CG7770 green 354 | mRpS35 green 355 | CG8635 green 356 | RpS3A green 357 | Tango7 green 358 | Hrb27C green 359 | nito green 360 | Sc2 green 361 | U2A green 362 | Rpn13 green 363 | SF2 green 364 | -------------------------------------------------------------------------------- /www/Examples/TP53/string_expression_colors.txt: -------------------------------------------------------------------------------- 1 | CDKN1A blue 2 | TP53 blue 3 | MDM4 blue 4 | BCL2L1 red 5 | CHEK2 red 6 | ATM red 7 | TP53BP2 red 8 | CDKN2A blue 9 | EP300 red 10 | CREBBP red 11 | -------------------------------------------------------------------------------- /www/Examples/TP53/string_interactions.txt: -------------------------------------------------------------------------------- 1 | Source Target Weight 2 | CDKN1A TP53 70 3 | TP53 MDM2 2 4 | MDM4 TP53 3 5 | BCL2L1 TP53 4 6 | CHEK2 ATM 5 7 | TP53 EP300 20 8 | ATM TP53 7 9 | TP53 CREBB 1 10 | MDM4 MDM2 1 11 | CHEK2 TP53 1 12 | TP53BP2 TP53 1 13 | CDKN2A TP53 1 14 | CDKN2A MDM2 1 15 | ATM MDM2 2 16 | EP300 CREBBP 1 17 | MDM4 ATM 2 18 | CHEK2 MDM4 1 19 | CHEK2 MDM2 1 20 | CDKN2A CDKN1A 1 21 | CDKN2A MDM4 1 22 | EP300 MDM2 1 23 | CDKN1A EP300 1 24 | CREBBP MDM2 1 25 | CDKN1A MDM2 1 26 | CDKN2A BCL2L1 1 27 | BCL2L1 MDM2 2 28 | CDKN2A ATM 1 29 | CDKN1A MDM4 1 30 | CDKN1A CHEK2 1 31 | CDKN1A ATM 2 32 | CDKN1A CREBBP 1 33 | CDKN1A BCL2L1 1 34 | CDKN2A CHEK2 1 35 | ATM EP300 1 36 | TP53BP2 BCL2L1 3 37 | CDKN2A EP300 3 38 | BCL2L1 ATM 3 39 | MDM4 EP300 1 40 | ATM CREBBP 1 41 | CHEK2 EP300 1 42 | TP53BP2 MDM2 1 43 | CHEK2 BCL2L1 1 44 | CDKN2A CREBBP 1 45 | TP53BP2 EP300 1 46 | BCL2L1 EP300 1 47 | MDM4 BCL2L1 1 48 | -------------------------------------------------------------------------------- /www/Examples/TP53/string_interactions_groups_comma_duplicate.txt: -------------------------------------------------------------------------------- 1 | Group-1 BCL2L1,MDM4,MDM2,CHEK2 2 | Group-2 CDKN2A,ATM,TP53BP2,MDM2 3 | Group-3 CHEK2,MDM2 4 | Group-4 TP53,EP300 5 | Group-5 MDM4,MDM2 6 | -------------------------------------------------------------------------------- /www/Figures/Banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PavlopoulosLab/NORMA/8a43f009ca81ac4a2c27793c0d8b95f81109fcee/www/Figures/Banner.png -------------------------------------------------------------------------------- /www/Figures/Community_detection_algorithms.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PavlopoulosLab/NORMA/8a43f009ca81ac4a2c27793c0d8b95f81109fcee/www/Figures/Community_detection_algorithms.png -------------------------------------------------------------------------------- /www/Figures/Convex_Hulls.PNG: 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(!require(stringr)) 12 | install.packages('stringr') 13 | 14 | library(stringi) 15 | library(stringr) 16 | library(plyr) 17 | library(tidyr) 18 | library(dplyr) 19 | library(purrr) 20 | 21 | network<- read.delim(choose.files()) 22 | annotations <- read.delim(choose.files(),header = F) 23 | 24 | column1<- unique(network$Source) 25 | column2<- unique(network$Target) 26 | 27 | df1<- data.frame(V1= column1) 28 | df2<- data.frame(V1= column2) 29 | 30 | unique_nodes_network <- suppressMessages(full_join(df1, df2)) 31 | 32 | annotations2<- as.character(annotations[,2]) 33 | genes <- strsplit(annotations2, ',') 34 | 35 | unique_nodes_annotations<- as.data.frame(unique(unlist(genes))) 36 | colnames(unique_nodes_annotations)<- 'V1' 37 | 38 | merged <- suppressMessages(full_join(unique_nodes_network, unique_nodes_annotations)) 39 | 40 | 41 | words_to_be_removed <- suppressMessages(anti_join(merged,unique_nodes_network)) 42 | 43 | annotations_new<- data.frame() 44 | if(!is.null(words_to_be_removed)){ 45 | for(i in 1:length(annotations[,2])){ 46 | x <- annotations[i,2] 47 | candidates <- strsplit(as.character(x), ',') 48 | line<-'' 49 | for(j in 1:length(candidates[[1]])){ 50 | word<-as.character(c(candidates[[1]])[j]) 51 | if(!(word %in% words_to_be_removed$V1)) 52 | line<-paste(line,word, sep=',') 53 | } 54 | line <- gsub('^,', '', line) 55 | if(nchar(line)>0) 56 | { 57 | annotations_new[i,1] <- annotations[i,1] 58 | annotations_new[i,2] <- line 59 | } 60 | } 61 | annotations_new<-na.omit(annotations_new) 62 | } else { 63 | annotations_new<-annotations 64 | } 65 | colnames(annotations_new)<- c('Annotations','Nodes') 66 | 67 | write.table(annotations_new, file = 'annotations_cleaned.txt', row.names = F, col.names = F, sep = "\t") 68 | 69 | -------------------------------------------------------------------------------- /www/favicon.ico: -------------------------------------------------------------------------------- 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| .introjs-disableInteraction { 40 | z-index: 99999999 !important; 41 | position: absolute; 42 | background-color: white; 43 | opacity: 0; 44 | filter: alpha(opacity=0); 45 | } 46 | 47 | .introjs-relativePosition, 48 | tr.introjs-showElement > td, 49 | tr.introjs-showElement > th { 50 | position: relative; 51 | } 52 | 53 | .introjs-helperLayer { 54 | box-sizing: content-box; 55 | position: absolute; 56 | z-index: 9999998; 57 | background-color: #FFF; 58 | background-color: rgba(255,255,255,.9); 59 | border: 1px solid #777; 60 | border: 1px solid rgba(0,0,0,.5); 61 | border-radius: 4px; 62 | box-shadow: 0 2px 15px rgba(0,0,0,.4); 63 | -webkit-transition: all 0.3s ease-out; 64 | -moz-transition: all 0.3s ease-out; 65 | -ms-transition: all 0.3s ease-out; 66 | -o-transition: all 0.3s ease-out; 67 | transition: all 0.3s ease-out; 68 | } 69 | 70 | .introjs-tooltipReferenceLayer { 71 | box-sizing: content-box; 72 | position: absolute; 73 | visibility: hidden; 74 | z-index: 100000000; 75 | background-color: transparent; 76 | -webkit-transition: all 0.3s ease-out; 77 | -moz-transition: all 0.3s ease-out; 78 | -ms-transition: all 0.3s ease-out; 79 | -o-transition: all 0.3s ease-out; 80 | transition: all 0.3s ease-out; 81 | } 82 | 83 | .introjs-helperLayer *, 84 | .introjs-helperLayer *:before, 85 | .introjs-helperLayer *:after { 86 | -webkit-box-sizing: content-box; 87 | -moz-box-sizing: content-box; 88 | -ms-box-sizing: content-box; 89 | -o-box-sizing: content-box; 90 | box-sizing: content-box; 91 | } 92 | 93 | .introjs-helperNumberLayer { 94 | box-sizing: content-box; 95 | position: absolute; 96 | visibility: visible; 97 | top: -16px; 98 | left: -16px; 99 | z-index: 9999999999 !important; 100 | padding: 2px; 101 | font-family: Arial, verdana, tahoma; 102 | font-size: 13px; 103 | font-weight: bold; 104 | color: white; 105 | text-align: center; 106 | text-shadow: 1px 1px 1px rgba(0,0,0,.3); 107 | background: #ff3019; /* Old browsers */ 108 | background: -webkit-linear-gradient(top, #ff3019 0%, #cf0404 100%); /* Chrome10+,Safari5.1+ */ 109 | background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #ff3019), color-stop(100%, #cf0404)); /* Chrome,Safari4+ */ 110 | background: -moz-linear-gradient(top, #ff3019 0%, #cf0404 100%); /* FF3.6+ */ 111 | background: -ms-linear-gradient(top, #ff3019 0%, #cf0404 100%); /* IE10+ */ 112 | background: -o-linear-gradient(top, #ff3019 0%, #cf0404 100%); /* Opera 11.10+ */ 113 | background: linear-gradient(to bottom, #ff3019 0%, #cf0404 100%); /* W3C */ 114 | width: 20px; 115 | height:20px; 116 | line-height: 20px; 117 | border: 3px solid white; 118 | border-radius: 50%; 119 | filter: "progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3019', endColorstr='#cf0404', GradientType=0)"; /* IE6-9 */ 120 | filter: "progid:DXImageTransform.Microsoft.Shadow(direction=135, strength=2, color=ff0000)"; /* IE10 text shadows */ 121 | box-shadow: 0 2px 5px rgba(0,0,0,.4); 122 | } 123 | 124 | .introjs-arrow { 125 | border: 5px solid transparent; 126 | content:''; 127 | position: absolute; 128 | } 129 | .introjs-arrow.top { 130 | top: -10px; 131 | border-bottom-color:white; 132 | } 133 | .introjs-arrow.top-right { 134 | top: -10px; 135 | right: 10px; 136 | border-bottom-color:white; 137 | } 138 | .introjs-arrow.top-middle { 139 | top: -10px; 140 | left: 50%; 141 | margin-left: -5px; 142 | border-bottom-color:white; 143 | } 144 | .introjs-arrow.right { 145 | right: -10px; 146 | top: 10px; 147 | border-left-color:white; 148 | } 149 | .introjs-arrow.right-bottom { 150 | bottom:10px; 151 | right: -10px; 152 | border-left-color:white; 153 | } 154 | .introjs-arrow.bottom { 155 | bottom: -10px; 156 | border-top-color:white; 157 | } 158 | .introjs-arrow.bottom-right { 159 | bottom: -10px; 160 | right: 10px; 161 | border-top-color:white; 162 | } 163 | .introjs-arrow.bottom-middle { 164 | bottom: -10px; 165 | left: 50%; 166 | margin-left: -5px; 167 | border-top-color:white; 168 | } 169 | .introjs-arrow.left { 170 | left: -10px; 171 | top: 10px; 172 | border-right-color:white; 173 | } 174 | .introjs-arrow.left-bottom { 175 | left: -10px; 176 | bottom:10px; 177 | border-right-color:white; 178 | } 179 | 180 | .introjs-tooltip { 181 | box-sizing: content-box; 182 | position: absolute; 183 | visibility: visible; 184 | padding: 10px; 185 | background-color: white; 186 | min-width: 200px; 187 | max-width: 300px; 188 | border-radius: 3px; 189 | box-shadow: 0 1px 10px rgba(0,0,0,.4); 190 | -webkit-transition: opacity 0.1s ease-out; 191 | -moz-transition: opacity 0.1s ease-out; 192 | -ms-transition: opacity 0.1s ease-out; 193 | -o-transition: opacity 0.1s ease-out; 194 | transition: opacity 0.1s ease-out; 195 | } 196 | 197 | .introjs-tooltipbuttons { 198 | text-align: right; 199 | white-space: nowrap; 200 | } 201 | 202 | /* 203 | Buttons style by http://nicolasgallagher.com/lab/css3-github-buttons/ 204 | Changed by Afshin Mehrabani 205 | */ 206 | .introjs-button { 207 | box-sizing: content-box; 208 | position: relative; 209 | overflow: visible; 210 | display: inline-block; 211 | padding: 0.3em 0.8em; 212 | border: 1px solid #d4d4d4; 213 | margin: 0; 214 | text-decoration: none; 215 | text-shadow: 1px 1px 0 #fff; 216 | font: 11px/normal sans-serif; 217 | color: #333; 218 | white-space: nowrap; 219 | cursor: pointer; 220 | outline: none; 221 | background-color: #ececec; 222 | background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#f4f4f4), to(#ececec)); 223 | background-image: -moz-linear-gradient(#f4f4f4, #ececec); 224 | background-image: -o-linear-gradient(#f4f4f4, #ececec); 225 | background-image: linear-gradient(#f4f4f4, #ececec); 226 | -webkit-background-clip: padding; 227 | -moz-background-clip: padding; 228 | -o-background-clip: padding-box; 229 | /*background-clip: padding-box;*/ /* commented out due to Opera 11.10 bug */ 230 | -webkit-border-radius: 0.2em; 231 | -moz-border-radius: 0.2em; 232 | border-radius: 0.2em; 233 | /* IE hacks */ 234 | zoom: 1; 235 | *display: inline; 236 | margin-top: 10px; 237 | } 238 | 239 | .introjs-button:hover { 240 | border-color: #bcbcbc; 241 | text-decoration: none; 242 | box-shadow: 0px 1px 1px #e3e3e3; 243 | } 244 | 245 | .introjs-button:focus, 246 | .introjs-button:active { 247 | background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ececec), to(#f4f4f4)); 248 | background-image: -moz-linear-gradient(#ececec, #f4f4f4); 249 | background-image: -o-linear-gradient(#ececec, #f4f4f4); 250 | background-image: linear-gradient(#ececec, #f4f4f4); 251 | } 252 | 253 | /* overrides extra padding on button elements in Firefox */ 254 | .introjs-button::-moz-focus-inner { 255 | padding: 0; 256 | border: 0; 257 | } 258 | 259 | .introjs-skipbutton { 260 | box-sizing: content-box; 261 | margin-right: 5px; 262 | color: #7a7a7a; 263 | } 264 | 265 | .introjs-prevbutton { 266 | -webkit-border-radius: 0.2em 0 0 0.2em; 267 | -moz-border-radius: 0.2em 0 0 0.2em; 268 | border-radius: 0.2em 0 0 0.2em; 269 | border-right: none; 270 | } 271 | 272 | .introjs-prevbutton.introjs-fullbutton { 273 | border: 1px solid #d4d4d4; 274 | -webkit-border-radius: 0.2em; 275 | -moz-border-radius: 0.2em; 276 | border-radius: 0.2em; 277 | } 278 | 279 | .introjs-nextbutton { 280 | -webkit-border-radius: 0 0.2em 0.2em 0; 281 | -moz-border-radius: 0 0.2em 0.2em 0; 282 | border-radius: 0 0.2em 0.2em 0; 283 | } 284 | 285 | .introjs-nextbutton.introjs-fullbutton { 286 | -webkit-border-radius: 0.2em; 287 | -moz-border-radius: 0.2em; 288 | border-radius: 0.2em; 289 | } 290 | 291 | .introjs-disabled, .introjs-disabled:hover, .introjs-disabled:focus { 292 | color: #9a9a9a; 293 | border-color: #d4d4d4; 294 | box-shadow: none; 295 | cursor: default; 296 | background-color: #f4f4f4; 297 | background-image: none; 298 | text-decoration: none; 299 | } 300 | 301 | .introjs-hidden { 302 | display: none; 303 | } 304 | 305 | .introjs-bullets { 306 | text-align: center; 307 | } 308 | .introjs-bullets ul { 309 | box-sizing: content-box; 310 | clear: both; 311 | margin: 15px auto 0; 312 | padding: 0; 313 | display: inline-block; 314 | } 315 | .introjs-bullets ul li { 316 | box-sizing: content-box; 317 | list-style: none; 318 | float: left; 319 | margin: 0 2px; 320 | } 321 | .introjs-bullets ul li a { 322 | box-sizing: content-box; 323 | display: block; 324 | width: 6px; 325 | height: 6px; 326 | background: #ccc; 327 | border-radius: 10px; 328 | -moz-border-radius: 10px; 329 | -webkit-border-radius: 10px; 330 | text-decoration: none; 331 | cursor: pointer; 332 | } 333 | .introjs-bullets ul li a:hover { 334 | background: #999; 335 | } 336 | .introjs-bullets ul li a.active { 337 | background: #999; 338 | } 339 | 340 | .introjs-progress { 341 | box-sizing: content-box; 342 | overflow: hidden; 343 | height: 10px; 344 | margin: 10px 0 5px 0; 345 | border-radius: 4px; 346 | background-color: #ecf0f1 347 | } 348 | .introjs-progressbar { 349 | box-sizing: content-box; 350 | float: left; 351 | width: 0%; 352 | height: 100%; 353 | font-size: 10px; 354 | line-height: 10px; 355 | text-align: center; 356 | background-color: #08c; 357 | } 358 | 359 | .introjsFloatingElement { 360 | position: absolute; 361 | height: 0; 362 | width: 0; 363 | left: 50%; 364 | top: 50%; 365 | } 366 | 367 | .introjs-fixedTooltip { 368 | position: fixed; 369 | } 370 | 371 | .introjs-hint { 372 | box-sizing: content-box; 373 | position: absolute; 374 | background: transparent; 375 | width: 20px; 376 | height: 15px; 377 | cursor: pointer; 378 | } 379 | .introjs-hint:focus { 380 | border: 0; 381 | outline: 0; 382 | } 383 | .introjs-hidehint { 384 | display: none; 385 | } 386 | 387 | .introjs-fixedhint { 388 | position: fixed; 389 | } 390 | 391 | .introjs-hint:hover > .introjs-hint-pulse { 392 | border: 5px solid rgba(60, 60, 60, 0.57); 393 | } 394 | 395 | .introjs-hint-pulse { 396 | box-sizing: content-box; 397 | width: 10px; 398 | height: 10px; 399 | border: 5px solid rgba(60, 60, 60, 0.27); 400 | -webkit-border-radius: 30px; 401 | -moz-border-radius: 30px; 402 | border-radius: 30px; 403 | background-color: rgba(136, 136, 136, 0.24); 404 | z-index: 10; 405 | position: absolute; 406 | -webkit-transition: all 0.2s ease-out; 407 | -moz-transition: all 0.2s ease-out; 408 | -ms-transition: all 0.2s ease-out; 409 | -o-transition: all 0.2s ease-out; 410 | transition: all 0.2s ease-out; 411 | } 412 | .introjs-hint-no-anim .introjs-hint-dot { 413 | -webkit-animation: none; 414 | -moz-animation: none; 415 | animation: none; 416 | } 417 | .introjs-hint-dot { 418 | box-sizing: content-box; 419 | border: 10px solid rgba(146, 146, 146, 0.36); 420 | background: transparent; 421 | -webkit-border-radius: 60px; 422 | -moz-border-radius: 60px; 423 | border-radius: 60px; 424 | height: 50px; 425 | width: 50px; 426 | -webkit-animation: introjspulse 3s ease-out; 427 | -moz-animation: introjspulse 3s ease-out; 428 | animation: introjspulse 3s ease-out; 429 | -webkit-animation-iteration-count: infinite; 430 | -moz-animation-iteration-count: infinite; 431 | animation-iteration-count: infinite; 432 | position: absolute; 433 | top: -25px; 434 | left: -25px; 435 | z-index: 1; 436 | opacity: 0; 437 | } 438 | 439 | @-webkit-keyframes introjspulse { 440 | 0% { 441 | -webkit-transform: scale(0); 442 | opacity: 0.0; 443 | } 444 | 25% { 445 | -webkit-transform: scale(0); 446 | opacity: 0.1; 447 | } 448 | 50% { 449 | -webkit-transform: scale(0.1); 450 | opacity: 0.3; 451 | } 452 | 75% { 453 | -webkit-transform: scale(0.5); 454 | opacity: 0.5; 455 | } 456 | 100% { 457 | -webkit-transform: scale(1); 458 | opacity: 0.0; 459 | } 460 | } 461 | 462 | @-moz-keyframes introjspulse { 463 | 0% { 464 | -moz-transform: scale(0); 465 | opacity: 0.0; 466 | } 467 | 25% { 468 | -moz-transform: scale(0); 469 | opacity: 0.1; 470 | } 471 | 50% { 472 | -moz-transform: scale(0.1); 473 | opacity: 0.3; 474 | } 475 | 75% { 476 | -moz-transform: scale(0.5); 477 | opacity: 0.5; 478 | } 479 | 100% { 480 | -moz-transform: scale(1); 481 | opacity: 0.0; 482 | } 483 | } 484 | 485 | @keyframes introjspulse { 486 | 0% { 487 | transform: scale(0); 488 | opacity: 0.0; 489 | } 490 | 25% { 491 | transform: scale(0); 492 | opacity: 0.1; 493 | } 494 | 50% { 495 | transform: scale(0.1); 496 | opacity: 0.3; 497 | } 498 | 75% { 499 | transform: scale(0.5); 500 | opacity: 0.5; 501 | } 502 | 100% { 503 | transform: scale(1); 504 | opacity: 0.0; 505 | } 506 | } -------------------------------------------------------------------------------- /www/introbutton.js: -------------------------------------------------------------------------------- 1 | document.addEventListener('DOMContentLoaded', function() { 2 | var selector = document.getElementById("btnAddNetwork"); 3 | selector.setAttribute("data-step", "1"); 4 | selector.setAttribute("data-intro", "The network file is an obligatory, 2-column (or 3-column for weighted), tab-delimited file, containing all network connections of an undirected network. This file must contain headers, namely: 'Source' and 'Target'. Press this button to upload your network file"); 5 | selector.setAttribute("data-position", "bottom"); 6 | 7 | selector = document.getElementById("uiLoadGraphOptionsOutput"); 8 | selector.setAttribute("data-step", "2"); 9 | selector.setAttribute("data-intro", "If the network is weighted (3 columns), check this box to allow weighted visualization."); 10 | selector.setAttribute("data-position", "bottom"); 11 | 12 | selector = document.getElementById("btnAddNetwork2"); 13 | selector.setAttribute("data-step", "3"); 14 | selector.setAttribute("data-intro", "The annotation file is an obligatory, 2-column, tab-delimited file which contains information about the defined groups. The first column contains the group names whereas the second column contains the node names in a group separated by a comma (,) and without spaces. No headers are allowed. Press this button to upload your annotation file"); 15 | selector.setAttribute("data-position", "bottom"); 16 | 17 | selector = document.getElementById("btnAddExpression"); 18 | selector.setAttribute("data-step", "4"); 19 | selector.setAttribute("data-intro", "The expression file is an optional, 2-column, tab-delimited file to allow node coloring (e.g. gene expressions). The first column contains the node names and the second column the node colors (color names or hex codes (e.g. Green or #00ff00, Red or #ff0000, Yellow or #ffff00)). Press this button to upload your node - coloring file"); 20 | selector.setAttribute("data-position", "bottom"); 21 | 22 | selector = document.getElementById("introButton"); 23 | selector.setAttribute("data-step", "5"); 24 | selector.setAttribute("data-intro", "For more details, please check Help Pages tab."); 25 | selector.setAttribute("data-position", "bottom"); 26 | 27 | document.getElementById("introButton").onclick = function(){ 28 | introJs().start(); 29 | }; 30 | }, false); 31 | -------------------------------------------------------------------------------- /www/norma.css: -------------------------------------------------------------------------------- 1 | body{ 2 | text-align: justify; 3 | } 4 | 5 | hr {border-top: 1px solid #000000;} 6 | 7 | td { 8 | line-height: 1.2 !important; 9 | } 10 | 11 | .well{ 12 | margin-bottom: 0 !important; 13 | padding-top: 0 !important; 14 | padding-bottom: 0 !important; 15 | } 16 | 17 | .box-panel { 18 | border-radius: 0 0 5px 5px; 19 | border-width: 1px; 20 | border-color: #d7d7d7; 21 | border-style: none solid solid solid; 22 | } 23 | 24 | .box-panel-padding { 25 | padding: 20px 20px 20px 20px; 26 | } 27 | 28 | .tabBox-panel { 29 | padding: 20px 20px 20px 20px; 30 | border-width: 1px; 31 | border-color: #d7d7d7; 32 | border-radius: 0px 0px 8px 8px; 33 | border-style: none solid solid solid; 34 | background: #ffffff; 35 | } 36 | 37 | .centerBlock { 38 | float: none; 39 | margin: 0 auto; 40 | } 41 | 42 | .dataTables_wrapper td { 43 | line-height: 80%; 44 | } 45 | 46 | .strategies{ 47 | background-color: #fff7f1; 48 | border: 1px solid #ff9300; 49 | border-radius: 25px; 50 | padding: 5px; 51 | padding-bottom: 0; 52 | font-size: 1.2em; 53 | display: block; 54 | } 55 | 56 | .strategies > div{ 57 | display: inline-block; 58 | width: 45% !important; 59 | margin: 20px; 60 | margin-bottom: 5px; 61 | } 62 | 63 | .strategies > div:nth-child(5){ 64 | position: relative; 65 | top: -87px; 66 | } 67 | 68 | .irs-single{ 69 | background-color: #2C8160 !important; 70 | } 71 | 72 | .irs-bar{ 73 | background: #2C8160 !important; 74 | } 75 | 76 | .layout_strat_img{ 77 | margin-left: auto; 78 | margin-right: auto; 79 | display: block; 80 | } 81 | 82 | #introButton{ 83 | width: 100%; 84 | margin-top: 15px; 85 | } 86 | 87 | @media only screen and (max-width: 991px) { 88 | .strategies > div:nth-child(5){ 89 | top: 0; 90 | } 91 | } 92 | --------------------------------------------------------------------------------