├── Demo_Communication_Prediction.ipynb ├── LICENSE ├── README.md ├── data ├── .DS_Store ├── Compass │ ├── met_md.csv │ └── rxn_md.csv ├── demo │ ├── .DS_Store │ ├── compass_res │ │ ├── .DS_Store │ │ ├── reactions.tsv.gz │ │ ├── secretions.tsv.gz │ │ └── uptake.tsv.gz │ ├── raw_scRNA │ │ └── demo_HNSC_200cell.h5ad │ └── scFEA │ │ ├── HNSC_GSE103322_expression_module168_cell5902_batch5902_LR0.008_epoch100_SCimpute_F_lambBal1_lambSca1_lambCellCor1_lambModCor_1e-2_20211011-232316.csv.gz │ │ └── HNSC_balance_20211011-232316.csv.gz ├── images │ ├── example1.png │ ├── example2.png │ └── example3.png ├── mebocost_db │ ├── .DS_Store │ ├── common │ │ ├── .DS_Store │ │ ├── hmdb_blood_metabolite_concentration.tsv │ │ ├── human_mouse_homology_gene_pair.csv │ │ └── metabolite_annotation_HMDB_summary.tsv │ ├── human │ │ ├── .DS_Store │ │ ├── met_sen_October-25-2022_14-52-47.tsv │ │ └── metabolite_associated_gene_reaction_HMDB_summary.tsv │ └── mouse │ │ ├── .DS_Store │ │ ├── metabolite_associated_gene_reaction_HMDB_summary_mouse.tsv │ │ └── mouse_met_sen_October-25-2022_14-52-47.tsv └── scFEA │ └── Human_M168_information.symbols.csv ├── images ├── .DS_Store ├── Mebocost_update.png ├── mebocost_flowchart.png └── mebocost_logo.png ├── mebocost.conf ├── requirements.txt ├── setup.py └── src ├── .DS_Store ├── .ipynb_checkpoints ├── Demo_Communication_Prediction 2-checkpoint.ipynb └── Demo_Communication_Prediction-checkpoint.ipynb ├── mebocost.conf └── mebocost ├── .DS_Store ├── MetEstimator.py ├── __init__.py ├── crosstalk_calculator.py ├── crosstalk_plots.py └── mebocost.py /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2022 Kaifu Chen Lab, Rongbin Zheng 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | * Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | * Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | * Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | ## Welcome to use MEBOCOST: Metabolic Cell-Cell Communication Modeling by Single Cell Transcriptome 4 | 5 | ### What is MEBOCOST and how does it work? 6 | 7 |

8 | 9 | MEBOCOST is a Python-based computational tool for inferring metabolite, such as lipid, mediated cell-cell communication events using single-cell RNA-seq data. MEBOCOST includes a manually curated database of metabolite-sensor partners and defines sender and receiver cells based on rates of metabolite efflux and influx, along with expression levels of enzyme and sensor genes, respectively. 10 | 11 |

12 | 13 | ### Term of Usage 14 | 15 | 1. You agree NOT to make the MEBOCOST data (or any part thereof, modified or not) available to anyone outside your research group. "Make available" includes leaving the data where it may be accessible to outside individuals without your direct knowledge (e.g. on a computer to which people outside your group have login privileges), as well as directly providing it to someone. 16 | 17 | 2. You agree NOT to build another website and/or methods using the MEBOCOST data. Please contact us if you are going to. 18 | 19 | 3. You agree NOT to use the MEBOCOST data for proprietary analysis. You agree to properly cite the MEBOCOST papers and its specific, original contributions if directly related to your work. 20 | 21 | 4. You certify that you are authorized to accept this agreement on behalf of your institution. 22 | 23 | 5. All members of your group with access to the MEBOCOST data agree to the same conditions. 24 | 25 | #### The Flowchart of MEBOCOST 26 | 27 |

28 | 29 | workflow for predicting metabolite mediated cell-cell communication (mCCC) taking scRNA-seq data as input. 30 | 31 |

32 | 33 | 34 | 35 | ### Version control 36 | 37 |

38 | 39 | We keep updating MEBOCOST!!! 40 | 41 |

42 | 43 |
  • 44 | 45 | Changelog for v1.0.4 46 | 47 |
    • 48 | 49 | - Upgrade to up-to-date python version (3.12) 50 | - Integrate COMPASS software to constrain metabolite efflux and influx in mCCC analysis 51 | - Allow users to examine the relationship between communication score and blood metabolite concentration, if the blood metabolite data is available 52 | - Fix bugs for plotting, including remove_unrelevant parameter in network plot, subfigure arrangement in the flow plot, and dendrogram ordering in the dot plot. 53 | - Change lines to curves in the network plot, now it is easier to distinguish sending and receiving signals. 54 | - By default, only output significant mCCC events, rather than complete mCCC table (but still be available in original_table item) 55 | - Provide options to set the range of dot size and line width in all plots. This is useful when generating plots for different samples to compare. 56 | - Provide options to set orders for x and y axis, or rows and columns, in plots. 57 | - Add function to automatically check the format of expression matrix 58 | - deprecated pathway analysis as it will be moved to another module 59 | 60 |
    61 | 62 | ### Installation 63 | 64 | - download and install miniconda environment (Users can skip this step if a python-based environment has been well-established). 65 | 66 | ```{bash} 67 | wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh 68 | 69 | conda create -n mebocost python=3.12 70 | 71 | conda activate mebocost 72 | ``` 73 | 74 | - download MEBOCOST package from github 75 | 76 | ```{bash} 77 | git clone https://github.com/kaifuchenlab/MEBOCOST.git 78 | 79 | cd MEBOCOST 80 | ``` 81 | 82 | - install requirements 83 | 84 | ```{bash} 85 | pip install -r requirements.txt 86 | ``` 87 | 88 | - install MEBOCOST 89 | 90 | ```{bash} 91 | python -m pip install . 92 | ``` 93 | 94 | #### To check whether it has been installed successfully, you can run in python: 95 | 96 | ```{python} 97 | >>from mebocost import mebocost 98 | ``` 99 | 100 | #### if the mebocost can be imported successfully, you are good! 101 | 102 | ### Tutorial 103 | 104 |
  • 105 | 106 | Prediction of cell-cell metabolic communication by scRNA-seq data 107 | 108 |
    • 109 | 110 | ### Cite us 111 | 112 |

    113 | 114 | Please cite us at bioRxiv if you find MEBOCOST is useful to your project. 115 | 116 |

    117 | 118 | ### Contact 119 | 120 | [Rongbin.Zheng\@childrens.harvard.edu](mailto:Rongbin.Zheng@childrens.harvard.edu){.email} 121 | 122 | or 123 | 124 | [Kaifu.Chen\@childrens.harvard.edu](mailto:Kaifu.Chen@childrens.harvard.edu){.email} 125 | 126 |
    127 | 128 | Copy Right \@ Kaifu Chen Lab \@ Boston Childrens Hospital / Harvard Medical School 129 | -------------------------------------------------------------------------------- /data/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/data/.DS_Store -------------------------------------------------------------------------------- /data/demo/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/data/demo/.DS_Store -------------------------------------------------------------------------------- /data/demo/compass_res/.DS_Store: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /data/mebocost_db/common/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/data/mebocost_db/common/.DS_Store -------------------------------------------------------------------------------- /data/mebocost_db/common/hmdb_blood_metabolite_concentration.tsv: -------------------------------------------------------------------------------- 1 | Calcitriol 7.999999999999999e-05 2 | Lipoxin A4 0.000104 3 | Estradiol 0.0001065 4 | 15-Deoxy-d-12,14-PGJ2 0.0001445 5 | Leukotriene B4 0.00016 6 | Melatonin 0.00019 7 | Prostaglandin D2 0.0002 8 | Estrone 0.00021 9 | Thromboxane A2 0.000345 10 | Aldosterone 0.00039575 11 | Prostaglandin F2a 0.0004355 12 | Epinephrine 0.00051 13 | Prostaglandin E2 0.000536 14 | Thyroxine 0.00066 15 | Liothyronine 0.0011 16 | Dihydrotestosterone 0.0012699999999999 17 | Norepinephrine 0.0013 18 | Histamine 0.0023 19 | Biotin 0.0024 20 | Progesterone 0.0025 21 | 3-Methoxytyramine 0.0025 22 | 13-cis-Retinoic acid 0.003 23 | Androstenedione 0.004 24 | Testosterone 0.005295 25 | 9-cis-Retinoic acid 0.0056 26 | Estriol 0.006 27 | Vitamin D3 0.006 28 | 12-HETE 0.00642 29 | Dehydroepiandrosterone 0.010075 30 | 25-Hydroxycholesterol 0.0105 31 | Folic acid 0.01695 32 | Corticosterone 0.025 33 | Kynurenic acid 0.03 34 | Androsterone 0.060325 35 | Calcidiol 0.0634 36 | Spermine 0.09 37 | all-trans-Retinoic acid 0.10725000000000001 38 | Riboflavin 0.10798250000000001 39 | Lithocholic acid 0.11 40 | Thiamine 0.14 41 | Debrisoquine 0.149 42 | Putrescine 0.155 43 | Retinal 0.155 44 | Deoxycytidine 0.2 45 | Thymidine 0.21 46 | Cortisol 0.235 47 | Cytidine 0.255 48 | Adenosine 0.285 49 | Glucosamine 0.29 50 | 27-Hydroxycholesterol 0.3 51 | 5-Methyltetrahydrofolic acid 0.3 52 | Sphingosine 1-phosphate 0.32899999999999996 53 | 5-Aminolevulinic acid 0.35 54 | Deoxyuridine 0.4 55 | beta-Carotene 0.46 56 | Lanosterol 0.48 57 | Glycyl-glycine 0.5 58 | Adenine 0.5 59 | Inosine 0.55 60 | gamma-Aminobutyric acid 0.73 61 | Serotonin 0.7949999999999999 62 | Guanosine 0.8 63 | Tetracosanoic acid 0.93 64 | Fumaric acid 0.9774999999999999 65 | gamma-Linolenic acid 1.08 66 | D-Serine 1.88 67 | Vitamin A 1.951 68 | Dihomo-gamma-linolenic acid 2.076 69 | Uracil 2.175 70 | Chenodeoxycholic acid 2.275 71 | Dehydroascorbic acid 2.36 72 | Anandamide 2.99 73 | Xanthine 3.8945 74 | Deoxyguanosine 5.5 75 | Hypoxanthine 5.58 76 | Succinic acid 6.05 77 | Uridine 6.148 78 | Cytosine 6.4 79 | L-Dopa 7.003615 80 | Malic acid 7.6 81 | Oxoglutaric acid 8.9 82 | Dopamine 9.0142325 83 | Choline 10.5 84 | Phytanic acid 11.975 85 | L-Homoserine 12.0 86 | Myristic acid 13.137 87 | Iron 13.90725 88 | Adenosine monophosphate 14.0 89 | L-Aspartic acid 15.5 90 | Eicosapentaenoic acid 16.869 91 | alpha-Linolenic acid 17.5 92 | Palmitoleic acid 18.0 93 | L-Carnitine 20.81 94 | Hydrogen peroxide 23.5 95 | L-Methionine 27.0 96 | D-Galactose 28.0 97 | alpha-Tocopherol 28.0 98 | D-Fructose 31.0 99 | Betaine 33.3 100 | L-Cysteine 35.75 101 | Creatine 36.7 102 | Hydrogen sulfide 37.6 103 | Arachidonic acid 38.5 104 | L-Asparagine 39.9 105 | Uridine 5'-diphosphate 41.0 106 | Glycogen 41.2 107 | Ethanol 46.68 108 | L-Isoleucine 48.650000000000006 109 | L-Glutamic acid 51.45 110 | D-Mannose 51.5 111 | L-Tryptophan 53.9 112 | Ornithine 54.5 113 | L-Tyrosine 61.0 114 | L-Phenylalanine 64.5 115 | Docosahexaenoic acid 66.973 116 | Pyruvic acid 76.0 117 | L-Leucine 79.15 118 | L-Arginine 80.0 119 | Citric acid 80.2 120 | L-Histidine 89.3 121 | Elaidic acid 100.0 122 | L-Serine 114.55 123 | L-Threonine 121.4 124 | Palmitic acid 122.0 125 | L-Lysine 127.9 126 | Glycerol 133.9 127 | L-Valine 138.75 128 | Uridine diphosphate glucose 155.0 129 | Stearic acid 158.5 130 | ADP 160.0 131 | Linoleic acid 195.2 132 | Glycine 212.4 133 | Oleic acid 240.0 134 | Phosphate 315.885 135 | L-Glutamine 503.515 136 | D-Lactic acid 600.0 137 | Potassium 1050.0 138 | D-Maltose 1169.0 139 | Thymine 1390.0 140 | Adenosine triphosphate 1471.0 141 | L-Lactic acid 1726.284 142 | D-Glucose 2800.0 143 | Urea 3550.0 144 | Cholesterol 4100.0 145 | Chloride ion 8000.0 146 | Sodium 125500.0 147 | -------------------------------------------------------------------------------- /data/mebocost_db/human/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/data/mebocost_db/human/.DS_Store -------------------------------------------------------------------------------- /data/mebocost_db/human/met_sen_October-25-2022_14-52-47.tsv: -------------------------------------------------------------------------------- 1 | ID HMDB_ID standard_metName metName Gene_name Protein_name Evidence Annotation 2 | 0 1 HMDB0006247 25-Hydroxycholesterol 25-Hydroxycholesterol ABCA1 Phospholipid-transporting ATPase ABCA1 16611739 Transporter 3 | 1 3 HMDB0000517 L-Arginine Arginine; L-Arginine SLC7A1 High affinity cationic amino acid transporter 1 33209975; 17325243; 33639836; 23831616; 22144986; 19067360; Recon2 Transporter 4 | 2 4 HMDB0000030 Biotin Biotin SLC5A6 Sodium-dependent multivitamin transporter 27084392 Transporter 5 | 3 5 HMDB0000067 Cholesterol Cholesterol CD36 Platelet glycoprotein 4 21763723; 32531545; 16133421; 10383407; 23247049; 15949682; 12145296; 28928671; 29883404; 34584385; 19718657; 29593722; 25174330; 27890613; 32684173; 18311054; 24371122; 21262584; 16959872; 20338238; 25250848; 23099443; 15168018; 16299001; 26828064; 19147991; 10946357; 23880196; 19016618; 23422832; 21474828; 28122883; 30702457; 21272192; 15136056; 18331615; 17464999; 32058595; 18276752; 31988148; 34603769; 17291449; 20170635; 16503643; 10713080; 10625497; 21674150; 26153221; 12488595; 24733016; 29533793; 12547883; 26582580; 31967154; 28634191; 20112301; 19937569; 21181286; 20360851; 33457418; 21217164; 16123174; 24515116; 18402819; 19028791; 27323079; 18305138; 33211179; 21034810; 11718687; 24162852; 18772361; 32308181; 25703059; 22858201; 28555086; 26759003; 28965954; 16517147; 32982800; 15345670; 19436068; 26832365; 21190831; 25855981; 32952497; 19074161 Transporter 6 | 4 6 HMDB0000073 Dopamine Dopamine SLC6A3 Sodium-dependent dopamine transporter 30967134; 12707943; 27217152; 28924877; 17466074 Transporter 7 | 5 7 HMDB0000148 L-Glutamic acid Glutamate SLC1A5 Neutral amino acid transporter B(0) 29208682 Transporter 8 | 6 8 HMDB0000641 L-Glutamine L-Glutamine; Glutamine SLC1A5 Neutral amino acid transporter B(0) 31535081; 30452920; 33953707; 34525179; 27154413; 25683269; 31881361; 28798141; 28507054; 25337245; 23213057; 32438035; 30025811; 33632871; 30935948; 33505538; 32422185; 30470977; 30671766; 25759021; 32747796; 31150647; 34054543; 31668020; 29208682; 32996252; 29542325; 30541099; 30071532; 34075790; 31866442; 26724577; 27055152; 33457003; 29337138; 32021249 Transporter 9 | 7 9 HMDB0000641 L-Glutamine L-Glutamine; Glutamine SLC38A2 Sodium-coupled neutral amino acid symporter 2 32996252; 25759021; 26724577 Transporter 10 | 8 10 HMDB0000641 L-Glutamine Glutamine SLC3A2 4F2 cell-surface antigen heavy chain 33953707; 30671766 Transporter 11 | 9 11 HMDB0000641 L-Glutamine Glutamine SLC7A5 Large neutral amino acids transporter small subunit 1 33953707; 30671766; 26724577; 33505538 Transporter 12 | 10 12 HMDB0003276 Hydrogen sulfide Hydrogen sulfide CD36 Platelet glycoprotein 4 31262715 Receptor 13 | 11 13 HMDB0015531 Iron Iron SLC11A2 Natural resistance-associated macrophage protein 2 23506870 Transporter 14 | 12 14 HMDB0015531 Iron Iron SLC40A1 Solute carrier family 40 member 1 25209728; 30852438; 27667161; 24644245; 21875943; 20675164; 23506870; 21199650; 33787609; 17181986; 14757427; 15338274; 27773819; 23922661; 29212168; 24121729; 28219768; 28978826; 21175851 Transporter 15 | 13 15 HMDB0001311 D-Lactic acid Lactate SLC16A1 Monocarboxylate transporter 1 32144120; 22428047 Transporter 16 | 14 16 HMDB0000687 L-Leucine Leucine SLC1A5 Neutral amino acid transporter B(0) 33953707; 30071532; 30470977 Transporter 17 | 15 17 HMDB0000687 L-Leucine Leucine SLC3A2 4F2 cell-surface antigen heavy chain 33953707 Transporter 18 | 16 18 HMDB0000687 L-Leucine Leucine SLC7A5 Large neutral amino acids transporter small subunit 1 33953707 Transporter 19 | 17 19 HMDB0001429 Phosphate Phosphate SLC20A2 Sodium-dependent phosphate transporter 2 30721528 Transporter 20 | 18 20 HMDB0000259 Serotonin Serotonin SLC6A4 Sodium-dependent serotonin transporter 33868590; 31342534; 16251523; 25012842 Transporter 21 | 19 21 HMDB0000235 Thiamine Thiamine SLC19A1 Reduced folate transporter 28284395; 32498429 Transporter 22 | 20 22 HMDB0000235 Thiamine Thiamine SLC19A2 Thiamine transporter 1 28284395; 32498429 Transporter 23 | 21 23 HMDB0000338 2-Hydroxyestradiol 2-Hydroxyestradiol ESR1 Estrogen receptor 27312859 Receptor 24 | 22 24 HMDB0006247 25-Hydroxycholesterol 25-Hydroxycholesterol ESR1 Estrogen receptor 21304949 Receptor 25 | 23 25 HMDB0002103 27-Hydroxycholesterol 27-Hydroxycholesterol ESR1 Estrogen receptor 33408073 Receptor 26 | 24 26 HMDB0000022 3-Methoxytyramine 3-Methoxytyramine TAAR1 Trace amine-associated receptor 1 22483291 Receptor 27 | 25 27 HMDB0001149 5-Aminolevulinic acid 5-Aminolevulinic acid TSPO2 Translocator protein 2 31989647 Transporter 28 | 26 28 HMDB0000045 Adenosine monophosphate AMP ADORA1 Adenosine receptor A1 32417395 Receptor 29 | 27 29 HMDB0000895 Acetylcholine Acetylcholine CHRM1 Muscarinic acetylcholine receptor M1 30157420 Receptor 30 | 28 30 HMDB0000895 Acetylcholine Acetylcholine CHRM2 Muscarinic acetylcholine receptor M2 23743182 Receptor 31 | 29 31 HMDB0000895 Acetylcholine Acetylcholine CHRM3 Muscarinic acetylcholine receptor M3 30157420 Receptor 32 | 30 32 HMDB0000895 Acetylcholine Acetylcholine CHRNA1 Acetylcholine receptor subunit alpha 28045942 Receptor 33 | 31 33 HMDB0000895 Acetylcholine Acetylcholine CHRNA2 Neuronal acetylcholine receptor subunit alpha-2 29785025 Receptor 34 | 32 34 HMDB0000895 Acetylcholine Acetylcholine CHRNA4 Neuronal acetylcholine receptor subunit alpha-4 15902904 Receptor 35 | 33 35 HMDB0000895 Acetylcholine Acetylcholine CHRNA7 Neuronal acetylcholine receptor subunit alpha-7 32321403 Receptor 36 | 34 36 HMDB0001178 Adenosine diphosphate ribose Adenosine diphosphate ribose TRPM2 Transient receptor potential cation channel subfamily M member 2 22493272 Receptor 37 | 35 37 HMDB0000050 Adenosine Adenosine ADORA1 Adenosine receptor A1 28598776; 23956030; 31675497; 27747290; 28196272; 33067580 Receptor 38 | 36 38 HMDB0000050 Adenosine Adenosine ADORA2A Adenosine receptor A2a 34255555; 29298852; 28598776; 23956030; 27747290; 17616786; 19635551 Receptor 39 | 37 39 HMDB0000050 Adenosine Adenosine ADORA2B Adenosine receptor A2b 28598776; 23956030; 23540714; 25087184; 27747290; 22504483; 31570448 Receptor 40 | 38 40 HMDB0000050 Adenosine Adenosine ADORA3 Adenosine receptor A3 23956030; 26194548; 28598776 Receptor 41 | 39 41 HMDB0004080 Anandamide Anandamide CNR1 Cannabinoid receptor 1 17935697; 26900150 Receptor 42 | 40 42 HMDB0004080 Anandamide Anandamide CNR2 Cannabinoid receptor 2 26900150; 20133390 Receptor 43 | 41 43 HMDB0004080 Anandamide Anandamide TRPV1 Transient receptor potential cation channel subfamily V member 1 17935697; 29504066; 22568077; 17704831; 23573230; 17591864; 30243113; 22394688; 19647120; 14517174; 16107881 Receptor 44 | 42 44 HMDB0000517 L-Arginine Arginine AVPR2 Vasopressin V2 receptor 24706579 Receptor 45 | 43 45 HMDB0000067 Cholesterol Cholesterol LDLR Low-density lipoprotein receptor 10974047; 19063703; 26520906; 20090943; 26281596; 32855525; 23221398; 25487149; 24900971; 32220355; 34103960; 16741953; 27247956; 32236613; 25023761; 25394495; 32368969; 14978770; 18162663; 19913121; 28919473; 25403094; 27834848; 24675665; 33757439; 22911757; 29535632; 28762182; 22470048; 23580231; 27735997; 30273964; 31437157; 30566603; 16236385; 33423309; 7600118; 28515357; 24603306; 12213890; 24950000; 10669643; 25231171; 32334376; 23937379; 29988450; 26495026; 28012395; 30195495; 30896554; 9351364; 15523646; 20049331; 15358785; 22962999; 22544571; 25797218; 27442011; 20857860; 30584280; 34347016; 28469073; 17184503; 30508567; 33429337; 26686234; 26548330; 30182437; 9502769; 24518357; 15617508; 23654093; 27050279; 32438039; 20041784; 9249773; 22761797; 29301853; 34461308; 32109664; 27888903; 23431047; 26085104; 28145001; 21645898; 22683120; 23623643; 23599654; 22936343; 23422832; 22761969; 8941642; 26523989; 29931853; 24505463; 19916081; 23883163; 30600305; 31100394; 10333389; 28100270; 19888660; 33606190; 21343340; 11164418; 19632679; 22593575; 25548917; 17344580; 18672372; 17331334; 27175606; 28751953; 19322023; 31332430; 31358055; 21657943; 21559365; 10493153; 31647302; 27438015; 31511396; 33747976; 24851052; 29092018; 31753053; 31299237; 21273557; 28555288; 30744358; 21734060; 26246324; 32964731; 24940994; 9664080; 27401460; 24373748; 20176131; 26068142; 27707816; 17531953; 30332439; 30592221; 18039658; 30385871; 30704067; 27084371; 30876530; 20028367; 15450205; 26921684; 15118091; 28099631; 10395289; 19067122; 28169529; 22580899; 25468703; 27031271; 27763549; 29398429; 31167970; 32860619; 9405278; 27459037; 25889601; 26535009; 30576926; 24837748; 30768966; 31767163; 31815695; 16741291; 15677715; 27435541; 32161285; 11291309; 21153157; 25587205; 26721317; 17351764; 23166513; 15654122; 33515402; 29545368; 24443560; 9747026; 32644974; 24352472; 31913546; 29190549; 20887597; 19060325; 25272851; 27909053; 28063230; 17709443; 16185916; 29982529; 30741106; 30486328; 20197419; 32050453; 24412220; 27564380; 31004037; 29169169; 11397707; 32705598; 24489659; 24987033; 22332058; 20073037; 11387232; 32759540; 34558270; 26204136; 29204218; 27918728; 24930699; 20580938; 15904870; 22494195; 24256518; 25413784; 33977967; 11369802; 18799458; 10488949; 9360938; 19433409; 25675507; 12910492; 15888329; 22059152; 32685494; 25754609; 25811180; 18193043; 28013406; 24770487; 30765502; 34615375; 11983917; 32727844; 18187606; 24472543; 26546829; 18771980; 11181749; 26786161; 21377952; 32918994; 16920108; 26040332; 27769814; 17720268; 11445560; 29321129; 25070550; 26700830; 24993279; 25201834; 23862065; 27378433; 28292942; 25504870; 27350674; 28874442; 17766366; 9360301; 20459026; 27998977 Receptor 46 | 44 46 HMDB0000067 Cholesterol Cholesterol SCARB1 Scavenger receptor class B member 1 17379624; 24253048; 29772548; 29285103; 24928939; 23510561; 20926582; 32591337; 24334872; 29516118; 18542840; 26754576; 25245032; 18276752; 25504870; 20064494; 29092018; 31753053; 31017097 Receptor 47 | 45 47 HMDB0003406 D-Serine D-Serine GRIN1 Glutamate receptor ionotropic, NMDA 1 28262924 Receptor 48 | 46 48 HMDB0002961 Dihydrotestosterone Dihydrotestosterone GLP1R Glucagon-like peptide 1 receptor 31669915 Receptor 49 | 47 49 HMDB0002183 Docosahexaenoic acid Docosahexaenoic acid FFAR4 Free fatty acid receptor 4 24005906 Receptor 50 | 48 50 HMDB0000073 Dopamine Dopamine DRD1 D(1A) dopamine receptor 33017522; 30967134; 12047334; 24909515 Receptor 51 | 49 51 HMDB0000073 Dopamine Dopamine DRD2 D(2) dopamine receptor 21070510; 10578238; 30967134; 17476365; 15084894; 20975260; 23717492; 17466074; 24772965; 23232665; 26015071; 29466326; 18192895; 19635551; 22876458; 19931559; 11979061; 18366720; 24834916; 23947671; 23266708; 15542698; 29992511; 9129716; 21592505; 10235293; 16403463; 19803686; 11256581; 12497624; 30651332; 24288745 Receptor 52 | 50 52 HMDB0000073 Dopamine Dopamine DRD3 D(3) dopamine receptor 18366720; 30967134; 12047334; 10578238; 23232665; 29525179; 7914177; 17616385; 17466074; 19931559; 23063408 Receptor 53 | 51 53 HMDB0000073 Dopamine Dopamine DRD4 D(4) dopamine receptor 18366720; 23717434; 30967134; 15627814; 12624717; 15292670; 16182111; 21615938; 22725835; 22356182; 22575564; 12707943; 27217152; 33868590; 14605948; 17466074; 16930369; 19931559 Receptor 54 | 52 54 HMDB0000073 Dopamine Dopamine DRD5 D(1B) dopamine receptor 10578238; 12047334 Receptor 55 | 53 55 HMDB0000073 Dopamine Dopamine TRPV1 Transient receptor potential cation channel subfamily V member 1 24465516 Receptor 56 | 54 56 HMDB0001999 Eicosapentaenoic acid Eicosapentaenoic acid FFAR4 Free fatty acid receptor 4 27489163 Receptor 57 | 55 57 HMDB0000151 Estradiol Estradiol ESR1 Estrogen receptor 28490809; 9925803 Receptor 58 | 56 58 HMDB0000153 Estriol Estriol ESR1 Estrogen receptor 27471150 Receptor 59 | 57 59 HMDB0000145 Estrone Estrone ESR1 Estrogen receptor 9228655 Receptor 60 | 58 60 HMDB0000108 Ethanol Ethanol CHRNA5 Neuronal acetylcholine receptor subunit alpha-5 29944862 Transporter 61 | 59 61 HMDB0000121 Folic acid Folic acid FOLR1 Folate receptor alpha 32581311; Recon2 Transporter 62 | 60 62 HMDB0000121 Folic acid Folic acid FOLR2 Folate receptor beta 32581311; Recon2 Transporter 63 | 61 63 HMDB0000112 gamma-Aminobutyric acid GABA GABBR1 Gamma-aminobutyric acid type B receptor subunit 1 17266109; 22253714; 26298628 Receptor 64 | 62 64 HMDB0000112 gamma-Aminobutyric acid GABA; gamma-Aminobutyric acid GABRG2 Gamma-aminobutyric acid receptor subunit gamma-2 22253714; 27367160; 30695556 Receptor 65 | 63 65 HMDB0000148 L-Glutamic acid Glutamate GRIA1 Glutamate receptor 1 7957959; 20579352 Receptor 66 | 64 66 HMDB0000148 L-Glutamic acid Glutamate GRIA2 Glutamate receptor 2 30695556; 19166514; 26047211; 25411160 Receptor 67 | 65 67 HMDB0000148 L-Glutamic acid Glutamate GRIA3 Glutamate receptor 3 30029590; 32839935 Receptor 68 | 66 68 HMDB0000148 L-Glutamic acid Glutamate GRIA4 Glutamate receptor 4 30029590; 28646511 Receptor 69 | 67 69 HMDB0000148 L-Glutamic acid Glutamate GRID1 Glutamate receptor ionotropic, delta-1 32109663 Receptor 70 | 68 70 HMDB0000148 L-Glutamic acid Glutamate GRID2 Glutamate receptor ionotropic, delta-2 11568633 Receptor 71 | 69 71 HMDB0000148 L-Glutamic acid Glutamate GRIK2 Glutamate receptor ionotropic, kainate 2 30695556 Receptor 72 | 70 72 HMDB0000148 L-Glutamic acid Glutamate GRIK4 Glutamate receptor ionotropic, kainate 4 30029590 Receptor 73 | 71 73 HMDB0000148 L-Glutamic acid Glutamate GRIN3A Glutamate receptor ionotropic, NMDA 3A 30029590 Receptor 74 | 72 74 HMDB0000148 L-Glutamic acid Glutamate GRM1 Metabotropic glutamate receptor 1 7957959; 22892214; 33145952 Receptor 75 | 73 75 HMDB0000148 L-Glutamic acid Glutamate GRM2 Metabotropic glutamate receptor 2 30695556; 25411160; 29113156 Receptor 76 | 74 76 HMDB0000148 L-Glutamic acid Glutamate GRM3 Metabotropic glutamate receptor 3 32839935 Receptor 77 | 75 77 HMDB0000148 L-Glutamic acid Glutamate GRM4 Metabotropic glutamate receptor 4 28646511 Receptor 78 | 76 78 HMDB0000148 L-Glutamic acid Glutamate GRM5 Metabotropic glutamate receptor 5 33053940; 30695556 Receptor 79 | 77 79 HMDB0000148 L-Glutamic acid Glutamate GRM7 Metabotropic glutamate receptor 7 22138407 Receptor 80 | 78 80 HMDB0000148 L-Glutamic acid Glutamate GRM8 Metabotropic glutamate receptor 8 26537360; 24392270 Receptor 81 | 79 81 HMDB0000148 L-Glutamic acid Glutamate TRPV1 Transient receptor potential cation channel subfamily V member 1 23108547; 27157265; 20219639; 21957263; 22394688; 23562495 Receptor 82 | 80 82 HMDB0000123 Glycine Glycine GRIN1 Glutamate receptor ionotropic, NMDA 1 28262924 Receptor 83 | 81 83 HMDB0003178 Heme Heme TLR4 Toll-like receptor 4 33374506; 27821769 Receptor 84 | 82 84 HMDB0003178 Heme Heme TRPV6 Transient receptor potential cation channel subfamily V member 6 27142151 Transporter 85 | 83 85 HMDB0000870 Histamine Histamine HRH1 Histamine H1 receptor 9512916 Receptor 86 | 84 86 HMDB0000870 Histamine Histamine HRH2 Histamine H2 receptor 9792230 Receptor 87 | 85 87 HMDB0000870 Histamine Histamine HRH3 Histamine H3 receptor 8960873 Receptor 88 | 86 88 HMDB0000870 Histamine Histamine HRH4 Histamine H4 receptor 30414378 Receptor 89 | 87 89 HMDB0003125 Hydrogen peroxide Hydrogen peroxide TRPM2 Transient receptor potential cation channel subfamily M member 2 22493272 Receptor 90 | 88 90 HMDB0015531 Iron Iron TFR2 Transferrin receptor protein 2 27013087; 24847265; 20826723; 18565178; 19729324; 11535534; 24055409; 27169626; 11005792; 20593115; 32621410; 17098454; 11673399; 31707638; 27477597; 11358390; 16932966; 27667161; 32054685; 24644245; 20880062; 26608187; 34199599; 20542038; 25635054; 17241880; 17417667; 17181986; 18094142; 24055163; 26029709; 20133002; 19759876; 21150441; 16158226; 17207112; 15521925; 24284962; 15124225; 15317665; 15893030; 21422745; 22460705; 30186425; 16935854; 11027676; 17042772; 12547237; 24556216; 21864651; 34156073; 33323945; 29434729; 17428703; 23582421; 28978826; 30360575; 30034931; 15701302; 12406888 Receptor 91 | 89 91 HMDB0015531 Iron Iron TFRC Transferrin receptor protein 1 21326867; 27773819; 22237814; 31401526; 23115478; 24890018; 33393230; 18603562; 25550467; 33693820; 23416069; 30076742; 32672503; 34389031; 34386079 Receptor 92 | 90 92 HMDB0000517 L-Arginine L-Arginine GPRC6A G-protein coupled receptor family C group 6 member A 22714012 Receptor 93 | 91 93 HMDB0000159 L-Phenylalanine Phenylalanine; L-Phenylalanine GPR142 Probable G-protein coupled receptor 142 27322810 Receptor 94 | 92 94 HMDB0000929 L-Tryptophan L-Tryptophan GPR142 Probable G-protein coupled receptor 142 27322810 Receptor 95 | 93 95 HMDB0001311 D-Lactic acid Lactate HCAR1 Hydroxycarboxylic acid receptor 1 25881750; 34093243; 30728759; 25425080; 33659884; 26677077 Receptor 96 | 94 96 HMDB0001251 Lanosterol Lanosterol HRH2 Histamine H2 receptor 29142437 Receptor 97 | 95 97 HMDB0000673 Linoleic acid Linoleic acid TRPV4 Transient receptor potential cation channel subfamily V member 4 25061872 Receptor 98 | 96 98 HMDB0000761 Lithocholic acid Lithocholic acid GPBAR1 G-protein coupled bile acid receptor 1 26567894; 29290621; 27765751 Receptor 99 | 97 99 HMDB0001389 Melatonin Melatonin MTNR1A Melatonin receptor type 1A 26067916 Receptor 100 | 98 100 HMDB0001389 Melatonin Melatonin MTNR1B Melatonin receptor type 1B 28708046; 19651812; 25132852; 25160745; 33220095; 31901302; 29590381; 26440713 Receptor 101 | 99 101 HMDB0001403 Prostaglandin D2 Prostaglandin D2 PTGDR Prostaglandin D2 receptor 34389612 Receptor 102 | 100 102 HMDB0001403 Prostaglandin D2 Prostaglandin D2 PTGDR2 Prostaglandin D2 receptor 2 29604141 Receptor 103 | 101 103 HMDB0001220 Prostaglandin E2 Prostaglandin E2 PTGER1 Prostaglandin E2 receptor EP1 subtype 17761898 Receptor 104 | 102 104 HMDB0001220 Prostaglandin E2 Prostaglandin E2 PTGER2 Prostaglandin E2 receptor EP2 subtype 17761898 Receptor 105 | 103 105 HMDB0001220 Prostaglandin E2 Prostaglandin E2 PTGER4 Prostaglandin E2 receptor EP4 subtype 33129574 Receptor 106 | 104 106 HMDB0001358 Retinal Retinal STRA6 Receptor for retinol uptake STRA6 27830500 Transporter 107 | 105 107 HMDB0000244 Riboflavin Riboflavin SLC52A1 Solute carrier family 52, riboflavin transporter, member 1 30446350; 29122468 Transporter 108 | 106 108 HMDB0000244 Riboflavin Riboflavin SLC52A2 Solute carrier family 52, riboflavin transporter, member 2 31500345; 22864630 Transporter 109 | 107 109 HMDB0000259 Serotonin Serotonin HTR1A 5-hydroxytryptamine receptor 1A 16251523 Receptor 110 | 108 110 HMDB0000259 Serotonin Serotonin HTR1B 5-hydroxytryptamine receptor 1B 28555718; 29860743; 23964727; 24074042 Receptor 111 | 109 111 HMDB0000259 Serotonin Serotonin HTR1D 5-hydroxytryptamine receptor 1D 20581837 Receptor 112 | 110 112 HMDB0000259 Serotonin Serotonin HTR2A 5-hydroxytryptamine receptor 2A 20521326; 32857933; 16251523; 27959337; 27024926; 32615731 Receptor 113 | 111 113 HMDB0000259 Serotonin Serotonin HTR2B 5-hydroxytryptamine receptor 2B 20581837; 34618686 Receptor 114 | 112 114 HMDB0000259 Serotonin Serotonin HTR2C 5-hydroxytryptamine receptor 2C 27681143 Receptor 115 | 113 115 HMDB0000259 Serotonin Serotonin HTR3A 5-hydroxytryptamine receptor 3A 31342534; 30695556 Receptor 116 | 114 116 HMDB0000259 Serotonin Serotonin HTR3B 5-hydroxytryptamine receptor 3B 23183509 Receptor 117 | 115 117 HMDB0000259 Serotonin Serotonin HTR4 5-hydroxytryptamine receptor 4 30695556 Receptor 118 | 116 118 HMDB0000259 Serotonin Serotonin HTR6 5-hydroxytryptamine receptor 6 18256283 Receptor 119 | 117 119 HMDB0000259 Serotonin Serotonin TRPC6 Short transient receptor potential channel 6 24259679 Receptor 120 | 118 120 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1PR1 Sphingosine 1-phosphate receptor 1 24977489; 25197261 Receptor 121 | 119 121 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1PR2 Sphingosine 1-phosphate receptor 2 26518876; 25363242; 26669941 Receptor 122 | 120 122 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1PR3 Sphingosine 1-phosphate receptor 3 28943478 Receptor 123 | 121 123 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1PR5 Sphingosine 1-phosphate receptor 5 24977489 Receptor 124 | 122 124 HMDB0000254 Succinic acid Succinate SUCNR1 Succinate receptor 1 25352636; 34270263; 33916314; 26808164; 33279412; 34301438; 29894669; 34233171 Receptor 125 | 123 125 HMDB0000234 Testosterone Testosterone GPRC6A G-protein coupled receptor family C group 6 member A 26785252; 29468843; 24032653; 24998176; 22374969; 24193547; 25093461; 27673554; 33474566; 28180060; 26440882; 31558901 Receptor 126 | 124 126 HMDB0001452 Thromboxane A2 Thromboxane A2 TBXA2R Thromboxane A2 receptor 9774254 Receptor 127 | 125 127 HMDB0000158 L-Tyrosine Tyrosine GPR35 G-protein coupled receptor 35 22523636 Receptor 128 | 126 128 HMDB0000305 Vitamin A Vitamin A STRA6 Receptor for retinol uptake STRA6 21782034; 19112531; 25481334; 22665496; 27830501; 32597569; 21704730; 23591992; 26729422; 31956331; 26373900; Recon2 Transporter 129 | 127 129 HMDB0000292 Xanthine Xanthine ADORA1 Adenosine receptor A1 31675497 Receptor 130 | 128 130 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid GABBR2 Gamma-aminobutyric acid type B receptor subunit 2 30610899 Receptor 131 | 129 131 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid GABRA1 Gamma-aminobutyric acid receptor subunit alpha-1 30891080 Receptor 132 | 130 132 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid GABRA4 Gamma-aminobutyric acid receptor subunit alpha-4 33594062 Receptor 133 | 131 133 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid GABRB2 Gamma-aminobutyric acid receptor subunit beta-2 33594062 Receptor 134 | 132 141 HMDB0000123 Glycine Glycine SLC16A10 Monocarboxylate transporter 10 HMDB Transporter 135 | 133 142 HMDB0000097 Choline Choline SLC22A1 Solute carrier family 22 member 1 HMDB Transporter 136 | 134 143 HMDB0001256 Spermine Spermine SLC22A1 Solute carrier family 22 member 1 HMDB; Recon2 Transporter 137 | 135 144 HMDB0001414 Putrescine Putrescine SLC22A4 Solute carrier family 22 member 4 HMDB Transporter 138 | 136 145 HMDB0001256 Spermine Spermine SLC22A4 Solute carrier family 22 member 4 HMDB Transporter 139 | 137 146 HMDB0000064 Creatine Creatine SLC16A12 Monocarboxylate transporter 12 23578822 Transporter 140 | 138 148 HMDB0000123 Glycine Glycine SLC36A1 Proton-coupled amino acid transporter 1 HMDB Transporter 141 | 139 149 HMDB0000097 Choline Choline SLC44A1 Choline transporter-like protein 1 HMDB Transporter 142 | 140 150 HMDB0000097 Choline Choline SLC44A2 Choline transporter-like protein 2 HMDB Transporter 143 | 141 151 HMDB0000097 Choline Choline SLC44A3 Choline transporter-like protein 3 HMDB Transporter 144 | 142 152 HMDB0000097 Choline Choline SLC44A4 Choline transporter-like protein 4 HMDB Transporter 145 | 143 153 HMDB0000097 Choline Choline SLC5A7 High affinity choline transporter 1 HMDB Transporter 146 | 144 154 HMDB0000243 Pyruvic acid Pyruvate SLC16A11 Monocarboxylate transporter 11 https://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC16A11 Transporter 147 | 145 155 HMDB0000243 Pyruvic acid Pyruvate SLC16A1 Monocarboxylate transporter 1 31882442 Transporter 148 | 146 156 HMDB0000254 Succinic acid Succinate SLC13A5 Na(+)/citrate cotransporter 31882442 Transporter 149 | 147 157 HMDB0000094 Citric acid Citrate SLC13A5 Na(+)/citrate cotransporter 33597751 Transporter 150 | 148 158 HMDB0000134 Fumaric acid Fumarate SLC13A5 Na(+)/citrate cotransporter 31882442 Transporter 151 | 149 159 HMDB0000156 Malic acid Malate SLC13A5 Na(+)/citrate cotransporter 31882442 Transporter 152 | 150 160 HMDB0000156 Malic acid Malate SLC1A3 Excitatory amino acid transporter 1 https://en.wikipedia.org/wiki/Excitatory_amino_acid_transporter_1 Transporter 153 | 151 161 HMDB0000187 L-Serine Serine SLC7A10 Asc-type amino acid transporter 1 33269112 Transporter 154 | 152 162 HMDB0000187 L-Serine Serine SLC3A2 4F2 cell-surface antigen heavy chain 33269112 Transporter 155 | 153 163 HMDB0000187 L-Serine Serine SLC1A4 Neutral amino acid transporter A 33269112 Transporter 156 | 154 164 HMDB0000187 L-Serine Serine SLC1A5 Neutral amino acid transporter B(0) 33269112 Transporter 157 | 155 165 HMDB0000574 L-Cysteine Cysteine SLC7A11 Cystine/glutamate transporter 33000412 Transporter 158 | 156 166 HMDB0000696 L-Methionine Methionine SLC7A5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 159 | 157 167 HMDB0000168 L-Asparagine Asparagine SLC1A5 Neutral amino acid transporter B(0) 33420487 Transporter 160 | 158 168 HMDB0000641 L-Glutamine Glutamine SLC6A14 Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) 26724577 Transporter 161 | 159 169 HMDB0000641 L-Glutamine Glutamine SLC6A19 Sodium-dependent neutral amino acid transporter B(0)AT1 26724577 Transporter 162 | 160 170 HMDB0000641 L-Glutamine Glutamine SLC7A6 Y+L amino acid transporter 2 26724577 Transporter 163 | 161 171 HMDB0000641 L-Glutamine Glutamine SLC7A7 Y+L amino acid transporter 1 26724577 Transporter 164 | 162 172 HMDB0000641 L-Glutamine Glutamine SLC38A1 Sodium-coupled neutral amino acid symporter 1 26724577 Transporter 165 | 163 173 HMDB0000641 L-Glutamine Glutamine SLC38A3 Sodium-coupled neutral amino acid transporter 3 26724577 Transporter 166 | 164 174 HMDB0000641 L-Glutamine Glutamine SLC38A5 Sodium-coupled neutral amino acid transporter 5 26724577 Transporter 167 | 165 175 HMDB0000641 L-Glutamine Glutamine SLC38A7 Sodium-coupled neutral amino acid transporter 7 26724577 Transporter 168 | 166 176 HMDB0000641 L-Glutamine Glutamine SLC38A8 Putative sodium-coupled neutral amino acid transporter 8 26724577 Transporter 169 | 167 177 HMDB0000112 gamma-Aminobutyric acid GABA SLC6A1 Sodium- and chloride-dependent GABA transporter 1 https://en.wikipedia.org/wiki/GABA_transporter Transporter 170 | 168 178 HMDB0000112 gamma-Aminobutyric acid GABA SLC6A13 Sodium- and chloride-dependent GABA transporter 2 https://en.wikipedia.org/wiki/GABA_transporter Transporter 171 | 169 179 HMDB0000112 gamma-Aminobutyric acid GABA SLC6A11 Sodium- and chloride-dependent GABA transporter 3 https://en.wikipedia.org/wiki/GABA_transporter Transporter 172 | 170 180 HMDB0000112 gamma-Aminobutyric acid GABA SLC6A12 Sodium- and chloride-dependent betaine transporter https://en.wikipedia.org/wiki/GABA_transporter Transporter 173 | 171 181 HMDB0000112 gamma-Aminobutyric acid GABA SLC6A8 Sodium- and chloride-dependent creatine transporter 1 https://en.wikipedia.org/wiki/GABA_transporter Transporter 174 | 172 182 HMDB0000112 gamma-Aminobutyric acid GABA SLC6A6 Sodium- and chloride-dependent taurine transporter https://en.wikipedia.org/wiki/GABA_transporter Transporter 175 | 173 183 HMDB0000158 L-Tyrosine Tyrosine SLC7A5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 176 | 174 184 HMDB0000191 L-Aspartic acid Aspartate SLC1A2 Excitatory amino acid transporter 2 31269432 Transporter 177 | 175 185 HMDB0000177 L-Histidine Histidine SLC7A5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 178 | 176 186 HMDB0000159 L-Phenylalanine Phenylalanine SLC7A5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 179 | 177 187 HMDB0000883 L-Valine Valine SLC43A1 Large neutral amino acids transporter small subunit 3 31997805; Recon2 Transporter 180 | 178 188 HMDB0000172 L-Isoleucine Isoleucine SLC43A1 Large neutral amino acids transporter small subunit 3 31997805; Recon2 Transporter 181 | 179 189 HMDB0000687 L-Leucine Leucine SLC43A1 Large neutral amino acids transporter small subunit 3 31997805; Recon2 Transporter 182 | 180 190 HMDB0000034 Adenine Adenine SLC28A3 Solute carrier family 28 member 3 33972798 Transporter 183 | 181 191 HMDB0000034 Adenine Adenine SLC29A3 Equilibrative nucleoside transporter 3 33972798 Transporter 184 | 182 192 HMDB0000034 Adenine Adenine SLC35F5 Solute carrier family 35 member F5 33972798 Transporter 185 | 183 193 HMDB0000062 L-Carnitine L-Carnitine SLC22A5 Organic cation/carnitine transporter 2 Recon2 Transporter 186 | 184 194 HMDB0000641 L-Glutamine L-glutamine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 187 | 185 195 HMDB0000187 L-Serine L-serine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 188 | 186 196 HMDB0000159 L-Phenylalanine L-phenylalanine SLC43A2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 189 | 187 197 HMDB0000159 L-Phenylalanine L-phenylalanine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 190 | 188 198 HMDB0000159 L-Phenylalanine L-phenylalanine SLC16A10 Monocarboxylate transporter 10 Recon2 Transporter 191 | 189 199 HMDB0000687 L-Leucine L-leucine SLC43A2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 192 | 190 200 HMDB0000574 L-Cysteine L-cysteine SLC43A2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 193 | 191 201 HMDB0000696 L-Methionine L-methionine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 194 | 192 202 HMDB0000696 L-Methionine L-methionine SLC43A2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 195 | 193 203 HMDB0000158 L-Tyrosine L-tyrosine SLC16A10 Monocarboxylate transporter 10 Recon2 Transporter 196 | 194 204 HMDB0000168 L-Asparagine L-asparagine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 197 | 195 205 HMDB0000167 L-Threonine L-threonine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 198 | 196 206 HMDB0000883 L-Valine L-valine SLC43A2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 199 | 197 207 HMDB0000929 L-Tryptophan L-tryptophan SLC36A4 Neutral amino acid uniporter 4 Recon2 Transporter 200 | 198 208 HMDB0000929 L-Tryptophan L-tryptophan SLC16A10 Monocarboxylate transporter 10 Recon2 Transporter 201 | 199 209 HMDB0000172 L-Isoleucine L-isoleucine SLC43A2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 202 | 200 210 HMDB0000517 L-Arginine L-argininium(1+) SLC38A4 Sodium-coupled neutral amino acid transporter 4 Recon2 Transporter 203 | 201 211 HMDB0000517 L-Arginine L-argininium(1+) SLC7A2 Cationic amino acid transporter 2 Recon2 Transporter 204 | 202 212 HMDB0000517 L-Arginine L-argininium(1+) SLC7A3 Cationic amino acid transporter 3 Recon2 Transporter 205 | 203 213 HMDB0000177 L-Histidine L-histidine SLC38A4 Sodium-coupled neutral amino acid transporter 4 Recon2 Transporter 206 | 204 214 HMDB0000182 L-Lysine L-lysinium(1+) SLC38A4 Sodium-coupled neutral amino acid transporter 4 Recon2 Transporter 207 | 205 215 HMDB0000182 L-Lysine L-lysinium(1+) SLC7A2 Cationic amino acid transporter 2 Recon2 Transporter 208 | 206 216 HMDB0000182 L-Lysine L-lysinium(1+) SLC7A1 High affinity cationic amino acid transporter 1 Recon2 Transporter 209 | 207 217 HMDB0000182 L-Lysine L-lysinium(1+) SLC7A3 Cationic amino acid transporter 3 Recon2 Transporter 210 | 208 218 HMDB0000214 Ornithine Ornithine SLC7A2 Cationic amino acid transporter 2 Recon2 Transporter 211 | 209 219 HMDB0000214 Ornithine Ornithine SLC7A1 High affinity cationic amino acid transporter 1 Recon2 Transporter 212 | 210 220 HMDB0000214 Ornithine Ornithine SLC7A3 Cationic amino acid transporter 3 Recon2 Transporter 213 | 211 221 HMDB0000143 D-Galactose D-Galactose SLC2A2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 214 | 212 222 HMDB0000143 D-Galactose D-Galactose SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 215 | 213 223 HMDB0000143 D-Galactose D-Galactose SLC2A8 Solute carrier family 2, facilitated glucose transporter member 8 Recon2 Transporter 216 | 214 224 HMDB0000143 D-Galactose D-Galactose SLC2A10 Solute carrier family 2, facilitated glucose transporter member 10 Recon2 Transporter 217 | 215 225 HMDB0000143 D-Galactose D-Galactose SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 218 | 216 226 HMDB0001043 Arachidonic acid arachidonate SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 219 | 217 227 HMDB0000122 D-Glucose D-glucose SLC2A9 Solute carrier family 2, facilitated glucose transporter member 9 Recon2 Transporter 220 | 218 228 HMDB0000122 D-Glucose D-glucose SLC2A2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 221 | 219 229 HMDB0000122 D-Glucose D-glucose SLC2A6 Solute carrier family 2, facilitated glucose transporter member 6 Recon2 Transporter 222 | 220 230 HMDB0000122 D-Glucose D-glucose SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 223 | 221 231 HMDB0000122 D-Glucose D-glucose SLC2A4 Solute carrier family 2, facilitated glucose transporter member 4 Recon2 Transporter 224 | 222 232 HMDB0000122 D-Glucose D-glucose SLC2A8 Solute carrier family 2, facilitated glucose transporter member 8 Recon2 Transporter 225 | 223 233 HMDB0000122 D-Glucose D-glucose SLC2A7 Solute carrier family 2, facilitated glucose transporter member 7 Recon2 Transporter 226 | 224 234 HMDB0000122 D-Glucose D-glucose SLC2A12 Solute carrier family 2, facilitated glucose transporter member 12 Recon2 Transporter 227 | 225 235 HMDB0000122 D-Glucose D-glucose SLC2A10 Solute carrier family 2, facilitated glucose transporter member 10 Recon2 Transporter 228 | 226 236 HMDB0000122 D-Glucose D-glucose SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 229 | 227 237 HMDB0001264 Dehydroascorbic acid dehydroascorbide(1-) SLC2A4 Solute carrier family 2, facilitated glucose transporter member 4 Recon2 Transporter 230 | 228 238 HMDB0001264 Dehydroascorbic acid dehydroascorbide(1-) SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 231 | 229 239 HMDB0001264 Dehydroascorbic acid dehydroascorbide(1-) SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 232 | 230 240 HMDB0000073 Dopamine dopaminium(1+) SLC22A3 Solute carrier family 22 member 3 Recon2 Transporter 233 | 231 241 HMDB0000073 Dopamine dopaminium(1+) SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 234 | 232 242 HMDB0000073 Dopamine dopaminium(1+) SLC22A5 Organic cation/carnitine transporter 2 Recon2 Transporter 235 | 233 243 HMDB0000169 D-Mannose D-Mannose SLC2A2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 236 | 234 244 HMDB0000169 D-Mannose D-Mannose SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 237 | 235 245 HMDB0000169 D-Mannose D-Mannose SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 238 | 236 246 HMDB0000050 Adenosine Adenosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 239 | 237 247 HMDB0000050 Adenosine Adenosine SLC29A1 Equilibrative nucleoside transporter 1 Recon2 Transporter 240 | 238 248 HMDB0000216 Norepinephrine Norepinephrine SLC22A1 Solute carrier family 22 member 1 Recon2 Transporter 241 | 239 249 HMDB0000216 Norepinephrine Norepinephrine SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 242 | 240 250 HMDB0000216 Norepinephrine Norepinephrine SLC22A3 Solute carrier family 22 member 3 Recon2 Transporter 243 | 241 251 HMDB0000097 Choline Choline SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 244 | 242 252 HMDB0000097 Choline Choline SLC22A5 Organic cation/carnitine transporter 2 Recon2 Transporter 245 | 243 253 HMDB0000259 Serotonin serotonin(1+) SLC22A1 Solute carrier family 22 member 1 Recon2 Transporter 246 | 244 254 HMDB0000259 Serotonin serotonin(1+) SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 247 | 245 255 HMDB0000660 D-Fructose D-Fructose SLC2A2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 248 | 246 256 HMDB0000660 D-Fructose D-Fructose SLC2A7 Solute carrier family 2, facilitated glucose transporter member 7 Recon2 Transporter 249 | 247 257 HMDB0000660 D-Fructose D-Fructose SLC2A8 Solute carrier family 2, facilitated glucose transporter member 8 Recon2 Transporter 250 | 248 258 HMDB0000660 D-Fructose D-Fructose SLC2A5 Solute carrier family 2, facilitated glucose transporter member 5 Recon2 Transporter 251 | 249 259 HMDB0001220 Prostaglandin E2 prostaglandin E2(1-) SLC22A1 Solute carrier family 22 member 1 Recon2 Transporter 252 | 250 260 HMDB0001220 Prostaglandin E2 prostaglandin E2(1-) SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 253 | 251 261 HMDB0000296 Uridine Uridine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 254 | 252 262 HMDB0000296 Uridine Uridine SLC29A1 Equilibrative nucleoside transporter 1 Recon2 Transporter 255 | 253 263 HMDB0000220 Palmitic acid Hexadecanoate (n-C16:0) SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 256 | 254 264 HMDB0000305 Vitamin A retinol RBP1 Retinol-binding protein 1 Recon2 Transporter 257 | 255 265 HMDB0000305 Vitamin A retinol RBP4 Retinol-binding protein 4 Recon2 Transporter 258 | 256 266 HMDB0000305 Vitamin A retinol RBP2 Retinol-binding protein 2 Recon2 Transporter 259 | 257 267 HMDB0000195 Inosine Inosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 260 | 258 268 HMDB0000195 Inosine Inosine SLC29A1 Equilibrative nucleoside transporter 1 Recon2 Transporter 261 | 259 269 HMDB0000089 Cytidine Cytidine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 262 | 260 270 HMDB0000089 Cytidine Cytidine SLC29A1 Equilibrative nucleoside transporter 1 Recon2 Transporter 263 | 261 271 HMDB0000207 Oleic acid octadecenoate (n-C18:1) SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 264 | 262 272 HMDB0000870 Histamine histamium SLC22A3 Solute carrier family 22 member 3 Recon2 Transporter 265 | 263 273 HMDB0000870 Histamine histamium SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 266 | 264 274 HMDB0000870 Histamine histamium SLC22A5 Organic cation/carnitine transporter 2 Recon2 Transporter 267 | 265 275 HMDB0000265 Liothyronine 3,3',5-triiodo-L-thyronine SLC16A2 Monocarboxylate transporter 8 Recon2 Transporter 268 | 266 276 HMDB0003550 Calcidiol calcidiol CUBN Cubilin Recon2 Transporter 269 | 267 277 HMDB0003550 Calcidiol calcidiol LRP2 Low-density lipoprotein receptor-related protein 2 Recon2 Transporter 270 | 268 278 HMDB0003550 Calcidiol calcidiol GC Vitamin D-binding protein Recon2 Transporter 271 | 269 279 HMDB0000181 L-Dopa L-dopa SLC16A10 Monocarboxylate transporter 10 Recon2 Transporter 272 | 270 280 HMDB0001396 5-Methyltetrahydrofolic acid 5-Methyltetrahydrofolate FOLR1 Folate receptor alpha Recon2 Transporter 273 | 271 281 HMDB0000895 Acetylcholine acetylcholine SLC22A1 Solute carrier family 22 member 1 Recon2 Transporter 274 | 272 282 HMDB0000012 Deoxyuridine Deoxyuridine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 275 | 273 283 HMDB0000133 Guanosine Guanosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 276 | 274 284 HMDB0000133 Guanosine Guanosine SLC29A1 Equilibrative nucleoside transporter 1 Recon2 Transporter 277 | 275 285 HMDB0000157 Hypoxanthine Hypoxanthine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 278 | 276 286 HMDB0000248 Thyroxine L-thyroxine SLC16A2 Monocarboxylate transporter 8 Recon2 Transporter 279 | 277 287 HMDB0000273 Thymidine Thymidine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 280 | 278 288 HMDB0000273 Thymidine Thymidine SLC29A1 Equilibrative nucleoside transporter 1 Recon2 Transporter 281 | 279 289 HMDB0001139 Prostaglandin F2a prostaglandin F2alpha(1-) SLC22A1 Solute carrier family 22 member 1 Recon2 Transporter 282 | 280 290 HMDB0001139 Prostaglandin F2a prostaglandin F2alpha(1-) SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 283 | 281 291 HMDB0000673 Linoleic acid linoleate SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 284 | 282 292 HMDB0000034 Adenine Adenine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 285 | 283 293 HMDB0000300 Uracil uracil SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 286 | 284 294 HMDB0000101 Deoxyadenosine 2-deoxyadenosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 287 | 285 295 HMDB0000085 Deoxyguanosine Deoxyguanosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 288 | 286 296 HMDB0000163 D-Maltose Maltose SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 289 | 287 297 HMDB0000876 Vitamin D3 calciol GOT2 Aspartate aminotransferase, mitochondrial Recon2 Transporter 290 | 288 298 HMDB0000876 Vitamin D3 calciol CD36 Platelet glycoprotein 4 Recon2 Transporter 291 | 289 299 HMDB0000294 Urea Urea SLC5A1 Sodium/glucose cotransporter 1 Recon2 Transporter 292 | 290 300 HMDB0000294 Urea Urea SLC14A2 Urea transporter 2 Recon2 Transporter 293 | 291 301 HMDB0000294 Urea Urea SLC5A5 Sodium/iodide cotransporter Recon2 Transporter 294 | 292 302 HMDB0000294 Urea Urea SLC14A1 Urea transporter 1 Recon2 Transporter 295 | 293 303 HMDB0000071 Deoxyinosine Deoxyinosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 296 | 294 304 HMDB0000014 Deoxycytidine Deoxycytidine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 297 | 295 305 HMDB0002925 Dihomo-gamma-linolenic acid dihomo-gamma-linolenic acid (n-6) SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 298 | 296 306 HMDB0000262 Thymine Thymine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 299 | 297 307 HMDB0000806 Myristic acid tetradecanoate (n-C14:0) SLC27A2 Long-chain fatty acid transport protein 2 Recon2 Transporter 300 | 298 308 HMDB0000827 Stearic acid octadecanoate (n-C18:0) SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 301 | 299 309 HMDB0003073 gamma-Linolenic acid gamma-linolenate SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 302 | 300 310 HMDB0001388 alpha-Linolenic acid alpha-linolenate SLC27A5 Long-chain fatty acid transport protein 5 Recon2 Transporter 303 | 301 311 HMDB0000132 Guanine Guanine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 304 | 302 312 HMDB0001514 Glucosamine D-Glucosamine SLC2A2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 305 | 303 313 HMDB0001514 Glucosamine D-Glucosamine SLC2A4 Solute carrier family 2, facilitated glucose transporter member 4 Recon2 Transporter 306 | 304 314 HMDB0001514 Glucosamine D-Glucosamine SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 307 | 305 315 HMDB0003178 Heme Protoheme SLC46A1 Proton-coupled folate transporter Recon2 Transporter 308 | 306 316 HMDB0003178 Heme Protoheme LRP1 Prolow-density lipoprotein receptor-related protein 1 Recon2 Transporter 309 | 307 317 HMDB0001178 Adenosine diphosphate ribose ADPribose CD38 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 Recon2 Transporter 310 | 308 318 HMDB0000190 L-Lactic acid L-Lactic acid HCAR1 Hydroxycarboxylic acid receptor 1 30728759, 31259764 Receptor 311 | 309 319 HMDB0015531 Iron Iron TFR1 24847265 Receptor 312 | 310 320 HMDB0000538 Adenosine triphosphate ATP P2RX1 P2X purinoceptor 1 24335194 Receptor 313 | 311 321 HMDB0000538 Adenosine triphosphate ATP P2RX2 P2X purinoceptor 2 24335194 Receptor 314 | 312 322 HMDB0000538 Adenosine triphosphate ATP P2RX3 P2X purinoceptor 3 24335194 Receptor 315 | 313 323 HMDB0000538 Adenosine triphosphate ATP P2RX4 P2X purinoceptor 4 24335194 Receptor 316 | 314 324 HMDB0000538 Adenosine triphosphate ATP P2RX5 P2X purinoceptor 5 24335194 Receptor 317 | 315 325 HMDB0000538 Adenosine triphosphate ATP P2RX6 P2X purinoceptor 6 24335194 Receptor 318 | 316 326 HMDB0000538 Adenosine triphosphate ATP P2RX7 P2X purinoceptor 7 24335194 Receptor 319 | 317 327 HMDB0001341 ADP ADP P2RY1 P2Y purinoceptor 1 24335194 Receptor 320 | 318 328 HMDB0000538 Adenosine triphosphate ATP P2RY1 P2Y purinoceptor 1 24335194 Receptor 321 | 319 329 HMDB0000538 Adenosine triphosphate ATP P2RY2 P2Y purinoceptor 2 24335194 Receptor 322 | 320 330 HMDB0000285 Uridine triphosphate UTP P2RY2 P2Y purinoceptor 2 24335194 Receptor 323 | 321 331 HMDB0000285 Uridine triphosphate UTP P2RY4 P2Y purinoceptor 4 24335194 Receptor 324 | 322 332 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2RY4 P2Y purinoceptor 4 24335194 Receptor 325 | 323 333 HMDB0000285 Uridine triphosphate UTP P2RY6 P2Y purinoceptor 6 24335194 Receptor 326 | 324 334 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2RY6 P2Y purinoceptor 6 24335194 Receptor 327 | 325 335 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2RY11 P2Y purinoceptor 11 24335194 Receptor 328 | 326 336 HMDB0000285 Uridine triphosphate UTP P2RY11 P2Y purinoceptor 11 24335194 Receptor 329 | 327 337 HMDB0001341 ADP ADP P2RY12 P2Y purinoceptor 12 24335194 Receptor 330 | 328 338 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2RY12 P2Y purinoceptor 12 24335194 Receptor 331 | 329 339 HMDB0001341 ADP ADP P2RY13 P2Y purinoceptor 13 24335194 Receptor 332 | 330 340 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2RY13 P2Y purinoceptor 13 24335194 Receptor 333 | 331 341 HMDB0000286 Uridine diphosphate glucose Uridine diphosphate glucose P2RY14 P2Y purinoceptor 14 24335194 Receptor 334 | 332 342 HMDB0000067 Cholesterol Cholesterol NPC1L1 NPC1-like intracellular cholesterol transporter 1 21763723 Receptor 335 | 333 343 HMDB0002961 Dihydrotestosterone Dihydrotestosterone AR Androgen receptor https://en.wikipedia.org/wiki/Androgen_receptor Nuclear Receptor 336 | 334 344 HMDB0000234 Testosterone Testosterone AR Androgen receptor https://en.wikipedia.org/wiki/Androgen_receptor Nuclear Receptor 337 | 335 345 HMDB0000131 Glycerol Glycerol AQP3 Aquaporin-3 32213983 Receptor 338 | 336 346 HMDB0000043 Betaine Betaine SLC6A12 Sodium- and chloride-dependent betaine transporter 32213983 Transporter 339 | 337 347 HMDB0000895 Acetylcholine Acetylcholine CHRM4 Muscarinic acetylcholine receptor M4 https://gpcrdb.org/ligand/statistics Receptor 340 | 338 348 HMDB0000895 Acetylcholine Acetylcholine CHRM5 Muscarinic acetylcholine receptor M5 https://gpcrdb.org/ligand/statistics Receptor 341 | 339 349 HMDB0000208 Oxoglutaric acid Oxoglutaric acid OXGR1 2-oxoglutarate receptor 1 https://gpcrdb.org/ligand/statistics Receptor 342 | 340 350 HMDB0000248 Thyroxine Thyroxine THRA Thyroid hormone receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 343 | 341 351 HMDB0000248 Thyroxine Thyroxine THRB Thyroid hormone receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 344 | 342 352 HMDB0000305 Vitamin A Vitamin A RARA Retinoic acid receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 345 | 343 353 HMDB0001358 Retinal Retinal RARA Retinoic acid receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 346 | 344 354 HMDB0000561 beta-Carotene beta-Carotene RARA Retinoic acid receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 347 | 345 355 HMDB0000305 Vitamin A Vitamin A RARB Retinoic acid receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 348 | 346 356 HMDB0001358 Retinal Retinal RARB Retinoic acid receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 349 | 347 357 HMDB0000561 beta-Carotene beta-Carotene RARB Retinoic acid receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 350 | 348 358 HMDB0000305 Vitamin A Vitamin A RARG Retinoic acid receptor gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 351 | 349 359 HMDB0001358 Retinal Retinal RARG Retinoic acid receptor gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 352 | 350 360 HMDB0000561 beta-Carotene beta-Carotene RARG Retinoic acid receptor gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 353 | 351 361 HMDB0003178 Heme Heme NR1D1 Nuclear receptor subfamily 1 group D member 1 https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 354 | 352 362 HMDB0003178 Heme Heme NR1D2 Nuclear receptor subfamily 1 group D member 2 https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 355 | 353 363 HMDB0000067 Cholesterol Cholesterol RORA Nuclear receptor ROR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 356 | 354 364 HMDB0000067 Cholesterol Cholesterol RORB Nuclear receptor ROR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 357 | 355 365 HMDB0000067 Cholesterol Cholesterol RORC Nuclear receptor ROR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 358 | 356 366 HMDB0000876 Vitamin D3 Vitamin D3 VDR Vitamin D3 receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 359 | 357 367 HMDB0001358 Retinal Retinal RXRA Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 360 | 358 368 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid RXRA Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 361 | 359 369 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid RXRA Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 362 | 360 370 HMDB0006219 13-cis-Retinoic acid 13-cis-Retinoic acid RXRA Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 363 | 361 371 HMDB0001358 Retinal Retinal RXRB Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 364 | 362 372 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid RXRB Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 365 | 363 373 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid RXRB Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 366 | 364 374 HMDB0006219 13-cis-Retinoic acid 13-cis-Retinoic acid RXRB Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 367 | 365 375 HMDB0001358 Retinal Retinal RXRG Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 368 | 366 376 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid RXRG Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 369 | 367 377 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid RXRG Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 370 | 368 378 HMDB0006219 13-cis-Retinoic acid 13-cis-Retinoic acid RXRG Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 371 | 369 379 HMDB0006216 11-cis-Retinol 11-cis-Retinol NR2F2 COUP transcription factor 2 https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 372 | 370 380 HMDB0000063 Cortisol Cortisol NR3C1 Glucocorticoid receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 373 | 371 381 HMDB0000037 Aldosterone Aldosterone NR3C2 Mineralocorticoid receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 374 | 372 382 HMDB0001830 Progesterone Progesterone PGR Progesterone receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 375 | 373 383 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid VDR Vitamin D3 receptor 15824121 Nuclear Receptor 376 | 374 384 HMDB0000053 Androstenedione Androstenedione AR Androgen receptor 16524719; 28457967; 12647261; 20534728; 24861263; 23856005; 18645714; 23258647 Nuclear Receptor 377 | 375 385 HMDB0000031 Androsterone Androsterone AR Androgen receptor 21303972; 24861263; 12647261 Nuclear Receptor 378 | 376 386 HMDB0003550 Calcidiol Calcidiol VDR Vitamin D3 receptor 25201891; 33348854 Nuclear Receptor 379 | 377 387 HMDB0001903 Calcitriol Calcitriol VDR Vitamin D3 receptor 29657326; 15077124; 20303786; 28008815; 9211344; 8574944; 9211349; 19667157; 16061850; 10079704; 17629157; 15225804; 21337382; 19371337; 21647319; 16048257; 29367669; 22276021; 29113124; 24597598; 27530414; 12899526; 9144338; 20798257; 12465754; 18290711; 33348854; 33354999; 26000306; 15861036; 12753260; 10633458; 16886687; 17489022; 19034868; 19705334; 25614680; 33211721; 22213328; 8147918; 24060611; 7552094; 20592360; 22720752 Nuclear Receptor 380 | 378 389 HMDB0000151 Estradiol Estradiol ESR2 Estrogen receptor beta 25765287; 20173016 Nuclear Receptor 381 | 379 390 HMDB0000761 Lithocholic acid Lithocholic acid VDR Vitamin D3 receptor 32863311; 24343899; 20888898; 20006981; 29074825; 19244278; 18180267; 15489543; 19581390; 32213983; 14525957; 16724925; 15824121 Nuclear Receptor 382 | 380 391 HMDB0000216 Norepinephrine Norepinephrine ADRA1A Alpha-1A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 383 | 381 392 HMDB0000068 Epinephrine Epinephrine ADRA1A Alpha-1A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 384 | 382 393 HMDB0000216 Norepinephrine Norepinephrine ADRA1B Alpha-1B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 385 | 383 394 HMDB0000068 Epinephrine Epinephrine ADRA1B Alpha-1B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 386 | 384 395 HMDB0000216 Norepinephrine Norepinephrine ADRA1D Alpha-1D adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 387 | 385 396 HMDB0000068 Epinephrine Epinephrine ADRA1D Alpha-1D adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 388 | 386 397 HMDB0000216 Norepinephrine Norepinephrine ADRA2A Alpha-2A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 389 | 387 398 HMDB0000068 Epinephrine Epinephrine ADRA2A Alpha-2A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 390 | 388 399 HMDB0000216 Norepinephrine Norepinephrine ADRA2B Alpha-2B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 391 | 389 400 HMDB0000068 Epinephrine Epinephrine ADRA2B Alpha-2B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 392 | 390 401 HMDB0000216 Norepinephrine Norepinephrine ADRA2C Alpha-2C adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 393 | 391 402 HMDB0000068 Epinephrine Epinephrine ADRA2C Alpha-2C adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 394 | 392 403 HMDB0000216 Norepinephrine Norepinephrine ADRB1 Beta-1 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 395 | 393 404 HMDB0000068 Epinephrine Epinephrine ADRB1 Beta-1 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 396 | 394 405 HMDB0000216 Norepinephrine Norepinephrine ADRB2 Beta-2 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 397 | 395 406 HMDB0000068 Epinephrine Epinephrine ADRB2 Beta-2 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 398 | 396 407 HMDB0000216 Norepinephrine Norepinephrine ADRB3 Beta-3 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 399 | 397 408 HMDB0000068 Epinephrine Epinephrine ADRB3 Beta-3 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 400 | 398 409 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid RARA Retinoic acid receptor alpha 20615454 Nuclear Receptor 401 | 399 410 HMDB0001085 Leukotriene B4 Leukotriene B4 PPARA Peroxisome proliferator-activated receptor alpha 20615454 Nuclear Receptor 402 | 400 411 HMDB0001547 Corticosterone Corticosterone NR3C1 Glucocorticoid receptor 20615454 Nuclear Receptor 403 | 401 412 HMDB0000518 Chenodeoxycholic acid Chenodeoxycholic acid NR1H4 Bile acid receptor 20615454 Nuclear Receptor 404 | 402 413 HMDB0006247 25-Hydroxycholesterol 25-Hydroxycholesterol NR1H3 Oxysterols receptor LXR-alpha 20615454 Nuclear Receptor 405 | 403 414 HMDB0000121 Folic acid Folic acid SLC19A1 Reduced folate transporter 28284395 Transporter 406 | 404 415 HMDB0000235 Thiamine Thiamine SLC19A3 Thiamine transporter 2 28284395 Transporter 407 | 405 416 HMDB0000190 L-Lactic acid Lactate SLC16A1 Monocarboxylate transporter 1 32144120; 22428047 Transporter 408 | 406 417 HMDB0000077 Dehydroepiandrosterone Dehydroepiandrosterone AR Androgen receptor 21303972; 24861263; 12647261 Nuclear Receptor 409 | 407 418 HMDB0000586 Potassium Potassium ABCC8 ATP-binding cassette sub-family C member 8 https://en.wikipedia.org/wiki/ABCC8; 23226049; 24399968; 22050960; 24700710 Transporter 410 | 408 420 HMDB0006111 12-HETE 12-HETE GPR31 12-(S)-hydroxy-5,8,10,14-eicosatetraenoic acid receptor 32918516 Receptor 411 | 409 421 HMDB0000757 Glycogen Glycogen STBD1 Starch-binding domain-containing protein 1 20810658; 21893048; 32927708; 24837458 Receptor 412 | 410 423 HMDB0000715 Kynurenic acid Kynurenic acid GPR35 G-protein coupled receptor 35 22523636; 23123095; 30141532; 29414686; 16754668 Receptor 413 | 411 424 HMDB0004385 Lipoxin A4 Lipoxin A4 ESR1 Estrogen receptor 24587003 Receptor 414 | 412 425 HMDB0000588 Sodium Sodium SLC5A1 Sodium/glucose cotransporter 1 Recon2 Transporter 415 | 413 426 HMDB0000588 Sodium Sodium SLC5A5 Sodium/iodide cotransporter Recon2 Transporter 416 | 414 427 HMDB0000588 Sodium Sodium SLC5A3 Sodium/myo-inositol cotransporter Recon2 Transporter 417 | 415 428 HMDB0000719 L-Homoserine L-homoserine SLC43A1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 418 | 416 429 HMDB0000492 Chloride ion Chloride SLC17A1 Sodium-dependent phosphate transport protein 1 Recon2 Transporter 419 | 417 430 HMDB0003229 Palmitoleic acid Hexadecenoate (n-C16:1) SLC27A2 Long-chain fatty acid transport protein 2 Recon2 Transporter 420 | 418 431 HMDB0012238 Iodide iodide SLC5A8 Sodium-coupled monocarboxylate transporter 1 Recon2 Transporter 421 | 419 432 HMDB0002003 Tetracosanoic acid lignocerate SLC27A2 Long-chain fatty acid transport protein 2 Recon2 Transporter 422 | 420 433 HMDB0001893 alpha-Tocopherol (+)-alpha-tocopherol SCARB1 Scavenger receptor class B member 1 Recon2 Transporter 423 | 421 434 HMDB0001893 alpha-Tocopherol (+)-alpha-tocopherol NPC1L1 NPC1-like intracellular cholesterol transporter 1 Recon2 Transporter 424 | 422 435 HMDB0000573 Elaidic acid elaidate SLC27A2 Long-chain fatty acid transport protein 2 Recon2 Transporter 425 | 423 436 HMDB0002086 Adenosylcobalamin Adenosylcobalamin CUBN Cubilin Recon2 Transporter 426 | 424 437 HMDB0002086 Adenosylcobalamin Adenosylcobalamin AMN Protein amnionless [Cleaved into: Soluble protein amnionless] Recon2 Transporter 427 | 425 438 HMDB0000630 Cytosine cytosine SLC29A2 Equilibrative nucleoside transporter 2 Recon2 Transporter 428 | 426 439 HMDB0006543 Debrisoquine debrisoquine SLC22A2 Solute carrier family 22 member 2 Recon2 Transporter 429 | 427 440 HMDB0011733 Glycyl-glycine Glycyl-glycine SLC15A1 Solute carrier family 15 member 1 Recon2 Transporter 430 | 428 441 HMDB0000295 Uridine 5'-diphosphate Uridine 5'-diphosphate P2RY6 P2Y purinoceptor 6 24335194 Receptor 431 | 429 442 HMDB0000801 Phytanic acid Phytanic acid PPARA Peroxisome proliferator-activated receptor alpha 11923221 Nuclear Receptor 432 | 430 443 HMDB0000801 Phytanic acid Phytanic acid PPARG Peroxisome proliferator-activated receptor gamma 11923221 Nuclear Receptor 433 | 431 444 HMDB0005079 15-Deoxy-d-12,14-PGJ2 15-Deoxy-d-12,14-PGJ2 PPARG Peroxisome proliferator-activated receptor gamma 20615454 Nuclear Receptor 434 | -------------------------------------------------------------------------------- /data/mebocost_db/mouse/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/data/mebocost_db/mouse/.DS_Store -------------------------------------------------------------------------------- /data/mebocost_db/mouse/mouse_met_sen_October-25-2022_14-52-47.tsv: -------------------------------------------------------------------------------- 1 | ID HMDB_ID standard_metName metName Gene_name Protein_name Evidence Annotation 2 | 0 1 HMDB0006247 25-Hydroxycholesterol 25-Hydroxycholesterol Abca1 Phospholipid-transporting ATPase ABCA1 16611739 Transporter 3 | 1 3 HMDB0000517 L-Arginine Arginine; L-Arginine Slc7a1 High affinity cationic amino acid transporter 1 33209975; 17325243; 33639836; 23831616; 22144986; 19067360; Recon2 Transporter 4 | 2 4 HMDB0000030 Biotin Biotin Slc5a6 Sodium-dependent multivitamin transporter 27084392 Transporter 5 | 3 5 HMDB0000067 Cholesterol Cholesterol Cd36 Platelet glycoprotein 4 21763723; 32531545; 16133421; 10383407; 23247049; 15949682; 12145296; 28928671; 29883404; 34584385; 19718657; 29593722; 25174330; 27890613; 32684173; 18311054; 24371122; 21262584; 16959872; 20338238; 25250848; 23099443; 15168018; 16299001; 26828064; 19147991; 10946357; 23880196; 19016618; 23422832; 21474828; 28122883; 30702457; 21272192; 15136056; 18331615; 17464999; 32058595; 18276752; 31988148; 34603769; 17291449; 20170635; 16503643; 10713080; 10625497; 21674150; 26153221; 12488595; 24733016; 29533793; 12547883; 26582580; 31967154; 28634191; 20112301; 19937569; 21181286; 20360851; 33457418; 21217164; 16123174; 24515116; 18402819; 19028791; 27323079; 18305138; 33211179; 21034810; 11718687; 24162852; 18772361; 32308181; 25703059; 22858201; 28555086; 26759003; 28965954; 16517147; 32982800; 15345670; 19436068; 26832365; 21190831; 25855981; 32952497; 19074161 Transporter 6 | 4 6 HMDB0000073 Dopamine Dopamine Slc6a3 Sodium-dependent dopamine transporter 30967134; 12707943; 27217152; 28924877; 17466074 Transporter 7 | 5 7 HMDB0000148 L-Glutamic acid Glutamate Slc1a5 Neutral amino acid transporter B(0) 29208682 Transporter 8 | 6 8 HMDB0000641 L-Glutamine L-Glutamine; Glutamine Slc1a5 Neutral amino acid transporter B(0) 31535081; 30452920; 33953707; 34525179; 27154413; 25683269; 31881361; 28798141; 28507054; 25337245; 23213057; 32438035; 30025811; 33632871; 30935948; 33505538; 32422185; 30470977; 30671766; 25759021; 32747796; 31150647; 34054543; 31668020; 29208682; 32996252; 29542325; 30541099; 30071532; 34075790; 31866442; 26724577; 27055152; 33457003; 29337138; 32021249 Transporter 9 | 7 9 HMDB0000641 L-Glutamine L-Glutamine; Glutamine Slc38a2 Sodium-coupled neutral amino acid symporter 2 32996252; 25759021; 26724577 Transporter 10 | 8 10 HMDB0000641 L-Glutamine Glutamine Slc3a2 4F2 cell-surface antigen heavy chain 33953707; 30671766 Transporter 11 | 9 11 HMDB0000641 L-Glutamine Glutamine Slc7a5 Large neutral amino acids transporter small subunit 1 33953707; 30671766; 26724577; 33505538 Transporter 12 | 10 12 HMDB0003276 Hydrogen sulfide Hydrogen sulfide Cd36 Platelet glycoprotein 4 31262715 Receptor 13 | 11 13 HMDB0015531 Iron Iron Slc11a2 Natural resistance-associated macrophage protein 2 23506870 Transporter 14 | 12 14 HMDB0015531 Iron Iron Slc40a1 Solute carrier family 40 member 1 25209728; 30852438; 27667161; 24644245; 21875943; 20675164; 23506870; 21199650; 33787609; 17181986; 14757427; 15338274; 27773819; 23922661; 29212168; 24121729; 28219768; 28978826; 21175851 Transporter 15 | 13 15 HMDB0001311 D-Lactic acid Lactate Slc16a1 Monocarboxylate transporter 1 32144120; 22428047 Transporter 16 | 14 16 HMDB0000687 L-Leucine Leucine Slc1a5 Neutral amino acid transporter B(0) 33953707; 30071532; 30470977 Transporter 17 | 15 17 HMDB0000687 L-Leucine Leucine Slc3a2 4F2 cell-surface antigen heavy chain 33953707 Transporter 18 | 16 18 HMDB0000687 L-Leucine Leucine Slc7a5 Large neutral amino acids transporter small subunit 1 33953707 Transporter 19 | 17 19 HMDB0001429 Phosphate Phosphate Slc20a2 Sodium-dependent phosphate transporter 2 30721528 Transporter 20 | 18 20 HMDB0000259 Serotonin Serotonin Slc6a4 Sodium-dependent serotonin transporter 33868590; 31342534; 16251523; 25012842 Transporter 21 | 19 21 HMDB0000235 Thiamine Thiamine Slc19a1 Reduced folate transporter 28284395; 32498429 Transporter 22 | 20 22 HMDB0000235 Thiamine Thiamine Slc19a2 Thiamine transporter 1 28284395; 32498429 Transporter 23 | 21 23 HMDB0000338 2-Hydroxyestradiol 2-Hydroxyestradiol Esr1 Estrogen receptor 27312859 Receptor 24 | 22 24 HMDB0006247 25-Hydroxycholesterol 25-Hydroxycholesterol Esr1 Estrogen receptor 21304949 Receptor 25 | 23 25 HMDB0002103 27-Hydroxycholesterol 27-Hydroxycholesterol Esr1 Estrogen receptor 33408073 Receptor 26 | 24 26 HMDB0000022 3-Methoxytyramine 3-Methoxytyramine Taar1 Trace amine-associated receptor 1 22483291 Receptor 27 | 25 27 HMDB0001149 5-Aminolevulinic acid 5-Aminolevulinic acid Tspo2 Translocator protein 2 31989647 Transporter 28 | 26 28 HMDB0000045 Adenosine monophosphate AMP Adora1 Adenosine receptor A1 32417395 Receptor 29 | 27 29 HMDB0000895 Acetylcholine Acetylcholine Chrm1 Muscarinic acetylcholine receptor M1 30157420 Receptor 30 | 28 30 HMDB0000895 Acetylcholine Acetylcholine Chrm2 Muscarinic acetylcholine receptor M2 23743182 Receptor 31 | 29 31 HMDB0000895 Acetylcholine Acetylcholine Chrm3 Muscarinic acetylcholine receptor M3 30157420 Receptor 32 | 30 32 HMDB0000895 Acetylcholine Acetylcholine Chrna1 Acetylcholine receptor subunit alpha 28045942 Receptor 33 | 31 33 HMDB0000895 Acetylcholine Acetylcholine Chrna2 Neuronal acetylcholine receptor subunit alpha-2 29785025 Receptor 34 | 32 34 HMDB0000895 Acetylcholine Acetylcholine Chrna4 Neuronal acetylcholine receptor subunit alpha-4 15902904 Receptor 35 | 33 35 HMDB0000895 Acetylcholine Acetylcholine Chrna7 Neuronal acetylcholine receptor subunit alpha-7 32321403 Receptor 36 | 34 36 HMDB0001178 Adenosine diphosphate ribose Adenosine diphosphate ribose Trpm2 Transient receptor potential cation channel subfamily M member 2 22493272 Receptor 37 | 35 37 HMDB0000050 Adenosine Adenosine Adora1 Adenosine receptor A1 28598776; 23956030; 31675497; 27747290; 28196272; 33067580 Receptor 38 | 36 38 HMDB0000050 Adenosine Adenosine Adora2a Adenosine receptor A2a 34255555; 29298852; 28598776; 23956030; 27747290; 17616786; 19635551 Receptor 39 | 37 39 HMDB0000050 Adenosine Adenosine Adora2b Adenosine receptor A2b 28598776; 23956030; 23540714; 25087184; 27747290; 22504483; 31570448 Receptor 40 | 38 40 HMDB0000050 Adenosine Adenosine Adora3 Adenosine receptor A3 23956030; 26194548; 28598776 Receptor 41 | 39 41 HMDB0004080 Anandamide Anandamide Cnr1 Cannabinoid receptor 1 17935697; 26900150 Receptor 42 | 40 42 HMDB0004080 Anandamide Anandamide Cnr2 Cannabinoid receptor 2 26900150; 20133390 Receptor 43 | 41 43 HMDB0004080 Anandamide Anandamide Trpv1 Transient receptor potential cation channel subfamily V member 1 17935697; 29504066; 22568077; 17704831; 23573230; 17591864; 30243113; 22394688; 19647120; 14517174; 16107881 Receptor 44 | 42 44 HMDB0000517 L-Arginine Arginine Avpr2 Vasopressin V2 receptor 24706579 Receptor 45 | 43 45 HMDB0000067 Cholesterol Cholesterol Ldlr Low-density lipoprotein receptor 10974047; 19063703; 26520906; 20090943; 26281596; 32855525; 23221398; 25487149; 24900971; 32220355; 34103960; 16741953; 27247956; 32236613; 25023761; 25394495; 32368969; 14978770; 18162663; 19913121; 28919473; 25403094; 27834848; 24675665; 33757439; 22911757; 29535632; 28762182; 22470048; 23580231; 27735997; 30273964; 31437157; 30566603; 16236385; 33423309; 7600118; 28515357; 24603306; 12213890; 24950000; 10669643; 25231171; 32334376; 23937379; 29988450; 26495026; 28012395; 30195495; 30896554; 9351364; 15523646; 20049331; 15358785; 22962999; 22544571; 25797218; 27442011; 20857860; 30584280; 34347016; 28469073; 17184503; 30508567; 33429337; 26686234; 26548330; 30182437; 9502769; 24518357; 15617508; 23654093; 27050279; 32438039; 20041784; 9249773; 22761797; 29301853; 34461308; 32109664; 27888903; 23431047; 26085104; 28145001; 21645898; 22683120; 23623643; 23599654; 22936343; 23422832; 22761969; 8941642; 26523989; 29931853; 24505463; 19916081; 23883163; 30600305; 31100394; 10333389; 28100270; 19888660; 33606190; 21343340; 11164418; 19632679; 22593575; 25548917; 17344580; 18672372; 17331334; 27175606; 28751953; 19322023; 31332430; 31358055; 21657943; 21559365; 10493153; 31647302; 27438015; 31511396; 33747976; 24851052; 29092018; 31753053; 31299237; 21273557; 28555288; 30744358; 21734060; 26246324; 32964731; 24940994; 9664080; 27401460; 24373748; 20176131; 26068142; 27707816; 17531953; 30332439; 30592221; 18039658; 30385871; 30704067; 27084371; 30876530; 20028367; 15450205; 26921684; 15118091; 28099631; 10395289; 19067122; 28169529; 22580899; 25468703; 27031271; 27763549; 29398429; 31167970; 32860619; 9405278; 27459037; 25889601; 26535009; 30576926; 24837748; 30768966; 31767163; 31815695; 16741291; 15677715; 27435541; 32161285; 11291309; 21153157; 25587205; 26721317; 17351764; 23166513; 15654122; 33515402; 29545368; 24443560; 9747026; 32644974; 24352472; 31913546; 29190549; 20887597; 19060325; 25272851; 27909053; 28063230; 17709443; 16185916; 29982529; 30741106; 30486328; 20197419; 32050453; 24412220; 27564380; 31004037; 29169169; 11397707; 32705598; 24489659; 24987033; 22332058; 20073037; 11387232; 32759540; 34558270; 26204136; 29204218; 27918728; 24930699; 20580938; 15904870; 22494195; 24256518; 25413784; 33977967; 11369802; 18799458; 10488949; 9360938; 19433409; 25675507; 12910492; 15888329; 22059152; 32685494; 25754609; 25811180; 18193043; 28013406; 24770487; 30765502; 34615375; 11983917; 32727844; 18187606; 24472543; 26546829; 18771980; 11181749; 26786161; 21377952; 32918994; 16920108; 26040332; 27769814; 17720268; 11445560; 29321129; 25070550; 26700830; 24993279; 25201834; 23862065; 27378433; 28292942; 25504870; 27350674; 28874442; 17766366; 9360301; 20459026; 27998977 Receptor 46 | 44 46 HMDB0000067 Cholesterol Cholesterol Scarb1 Scavenger receptor class B member 1 17379624; 24253048; 29772548; 29285103; 24928939; 23510561; 20926582; 32591337; 24334872; 29516118; 18542840; 26754576; 25245032; 18276752; 25504870; 20064494; 29092018; 31753053; 31017097 Receptor 47 | 45 47 HMDB0003406 D-Serine D-Serine Grin1 Glutamate receptor ionotropic, NMDA 1 28262924 Receptor 48 | 46 48 HMDB0002961 Dihydrotestosterone Dihydrotestosterone Glp1r Glucagon-like peptide 1 receptor 31669915 Receptor 49 | 47 49 HMDB0002183 Docosahexaenoic acid Docosahexaenoic acid Ffar4 Free fatty acid receptor 4 24005906 Receptor 50 | 48 50 HMDB0000073 Dopamine Dopamine Drd1 D(1A) dopamine receptor 33017522; 30967134; 12047334; 24909515 Receptor 51 | 49 51 HMDB0000073 Dopamine Dopamine Drd2 D(2) dopamine receptor 21070510; 10578238; 30967134; 17476365; 15084894; 20975260; 23717492; 17466074; 24772965; 23232665; 26015071; 29466326; 18192895; 19635551; 22876458; 19931559; 11979061; 18366720; 24834916; 23947671; 23266708; 15542698; 29992511; 9129716; 21592505; 10235293; 16403463; 19803686; 11256581; 12497624; 30651332; 24288745 Receptor 52 | 50 52 HMDB0000073 Dopamine Dopamine Drd3 D(3) dopamine receptor 18366720; 30967134; 12047334; 10578238; 23232665; 29525179; 7914177; 17616385; 17466074; 19931559; 23063408 Receptor 53 | 51 53 HMDB0000073 Dopamine Dopamine Drd4 D(4) dopamine receptor 18366720; 23717434; 30967134; 15627814; 12624717; 15292670; 16182111; 21615938; 22725835; 22356182; 22575564; 12707943; 27217152; 33868590; 14605948; 17466074; 16930369; 19931559 Receptor 54 | 52 54 HMDB0000073 Dopamine Dopamine Drd5 D(1B) dopamine receptor 10578238; 12047334 Receptor 55 | 53 55 HMDB0000073 Dopamine Dopamine Trpv1 Transient receptor potential cation channel subfamily V member 1 24465516 Receptor 56 | 54 56 HMDB0001999 Eicosapentaenoic acid Eicosapentaenoic acid Ffar4 Free fatty acid receptor 4 27489163 Receptor 57 | 55 57 HMDB0000151 Estradiol Estradiol Esr1 Estrogen receptor 28490809; 9925803 Receptor 58 | 56 58 HMDB0000153 Estriol Estriol Esr1 Estrogen receptor 27471150 Receptor 59 | 57 59 HMDB0000145 Estrone Estrone Esr1 Estrogen receptor 9228655 Receptor 60 | 58 60 HMDB0000108 Ethanol Ethanol Chrna5 Neuronal acetylcholine receptor subunit alpha-5 29944862 Transporter 61 | 59 61 HMDB0000121 Folic acid Folic acid Folr1 Folate receptor alpha 32581311; Recon2 Transporter 62 | 60 62 HMDB0000121 Folic acid Folic acid Folr2 Folate receptor beta 32581311; Recon2 Transporter 63 | 61 63 HMDB0000112 gamma-Aminobutyric acid GABA Gabbr1 Gamma-aminobutyric acid type B receptor subunit 1 17266109; 22253714; 26298628 Receptor 64 | 62 64 HMDB0000112 gamma-Aminobutyric acid GABA; gamma-Aminobutyric acid Gabrg2 Gamma-aminobutyric acid receptor subunit gamma-2 22253714; 27367160; 30695556 Receptor 65 | 63 65 HMDB0000148 L-Glutamic acid Glutamate Gria1 Glutamate receptor 1 7957959; 20579352 Receptor 66 | 64 66 HMDB0000148 L-Glutamic acid Glutamate Gria2 Glutamate receptor 2 30695556; 19166514; 26047211; 25411160 Receptor 67 | 65 67 HMDB0000148 L-Glutamic acid Glutamate Gria3 Glutamate receptor 3 30029590; 32839935 Receptor 68 | 66 68 HMDB0000148 L-Glutamic acid Glutamate Gria4 Glutamate receptor 4 30029590; 28646511 Receptor 69 | 67 69 HMDB0000148 L-Glutamic acid Glutamate Grid1 Glutamate receptor ionotropic, delta-1 32109663 Receptor 70 | 68 70 HMDB0000148 L-Glutamic acid Glutamate Grid2 Glutamate receptor ionotropic, delta-2 11568633 Receptor 71 | 69 71 HMDB0000148 L-Glutamic acid Glutamate Grik2 Glutamate receptor ionotropic, kainate 2 30695556 Receptor 72 | 70 72 HMDB0000148 L-Glutamic acid Glutamate Grik4 Glutamate receptor ionotropic, kainate 4 30029590 Receptor 73 | 71 73 HMDB0000148 L-Glutamic acid Glutamate Grin3a Glutamate receptor ionotropic, NMDA 3A 30029590 Receptor 74 | 72 74 HMDB0000148 L-Glutamic acid Glutamate Grm1 Metabotropic glutamate receptor 1 7957959; 22892214; 33145952 Receptor 75 | 73 75 HMDB0000148 L-Glutamic acid Glutamate Grm2 Metabotropic glutamate receptor 2 30695556; 25411160; 29113156 Receptor 76 | 74 76 HMDB0000148 L-Glutamic acid Glutamate Grm3 Metabotropic glutamate receptor 3 32839935 Receptor 77 | 75 77 HMDB0000148 L-Glutamic acid Glutamate Grm4 Metabotropic glutamate receptor 4 28646511 Receptor 78 | 76 78 HMDB0000148 L-Glutamic acid Glutamate Grm5 Metabotropic glutamate receptor 5 33053940; 30695556 Receptor 79 | 77 79 HMDB0000148 L-Glutamic acid Glutamate Grm7 Metabotropic glutamate receptor 7 22138407 Receptor 80 | 78 80 HMDB0000148 L-Glutamic acid Glutamate Grm8 Metabotropic glutamate receptor 8 26537360; 24392270 Receptor 81 | 79 81 HMDB0000148 L-Glutamic acid Glutamate Trpv1 Transient receptor potential cation channel subfamily V member 1 23108547; 27157265; 20219639; 21957263; 22394688; 23562495 Receptor 82 | 80 82 HMDB0000123 Glycine Glycine Grin1 Glutamate receptor ionotropic, NMDA 1 28262924 Receptor 83 | 81 83 HMDB0003178 Heme Heme Tlr4 Toll-like receptor 4 33374506; 27821769 Receptor 84 | 82 84 HMDB0003178 Heme Heme Trpv6 Transient receptor potential cation channel subfamily V member 6 27142151 Transporter 85 | 83 85 HMDB0000870 Histamine Histamine Hrh1 Histamine H1 receptor 9512916 Receptor 86 | 84 86 HMDB0000870 Histamine Histamine Hrh2 Histamine H2 receptor 9792230 Receptor 87 | 85 87 HMDB0000870 Histamine Histamine Hrh3 Histamine H3 receptor 8960873 Receptor 88 | 86 88 HMDB0000870 Histamine Histamine Hrh4 Histamine H4 receptor 30414378 Receptor 89 | 87 89 HMDB0003125 Hydrogen peroxide Hydrogen peroxide Trpm2 Transient receptor potential cation channel subfamily M member 2 22493272 Receptor 90 | 88 90 HMDB0015531 Iron Iron Tfr2 Transferrin receptor protein 2 27013087; 24847265; 20826723; 18565178; 19729324; 11535534; 24055409; 27169626; 11005792; 20593115; 32621410; 17098454; 11673399; 31707638; 27477597; 11358390; 16932966; 27667161; 32054685; 24644245; 20880062; 26608187; 34199599; 20542038; 25635054; 17241880; 17417667; 17181986; 18094142; 24055163; 26029709; 20133002; 19759876; 21150441; 16158226; 17207112; 15521925; 24284962; 15124225; 15317665; 15893030; 21422745; 22460705; 30186425; 16935854; 11027676; 17042772; 12547237; 24556216; 21864651; 34156073; 33323945; 29434729; 17428703; 23582421; 28978826; 30360575; 30034931; 15701302; 12406888 Receptor 91 | 89 91 HMDB0015531 Iron Iron Tfrc Transferrin receptor protein 1 21326867; 27773819; 22237814; 31401526; 23115478; 24890018; 33393230; 18603562; 25550467; 33693820; 23416069; 30076742; 32672503; 34389031; 34386079 Receptor 92 | 90 92 HMDB0000517 L-Arginine L-Arginine Gprc6a G-protein coupled receptor family C group 6 member A 22714012 Receptor 93 | 91 93 HMDB0000159 L-Phenylalanine Phenylalanine; L-Phenylalanine Gpr142 Probable G-protein coupled receptor 142 27322810 Receptor 94 | 92 94 HMDB0000929 L-Tryptophan L-Tryptophan Gpr142 Probable G-protein coupled receptor 142 27322810 Receptor 95 | 93 95 HMDB0001311 D-Lactic acid Lactate Hcar1 Hydroxycarboxylic acid receptor 1 25881750; 34093243; 30728759; 25425080; 33659884; 26677077 Receptor 96 | 94 96 HMDB0001251 Lanosterol Lanosterol Hrh2 Histamine H2 receptor 29142437 Receptor 97 | 95 97 HMDB0000673 Linoleic acid Linoleic acid Trpv4 Transient receptor potential cation channel subfamily V member 4 25061872 Receptor 98 | 96 98 HMDB0000761 Lithocholic acid Lithocholic acid Gpbar1 G-protein coupled bile acid receptor 1 26567894; 29290621; 27765751 Receptor 99 | 97 99 HMDB0001389 Melatonin Melatonin Mtnr1a Melatonin receptor type 1A 26067916 Receptor 100 | 98 100 HMDB0001389 Melatonin Melatonin Mtnr1b Melatonin receptor type 1B 28708046; 19651812; 25132852; 25160745; 33220095; 31901302; 29590381; 26440713 Receptor 101 | 99 101 HMDB0001403 Prostaglandin D2 Prostaglandin D2 Ptgdr Prostaglandin D2 receptor 34389612 Receptor 102 | 100 102 HMDB0001403 Prostaglandin D2 Prostaglandin D2 Ptgdr2 Prostaglandin D2 receptor 2 29604141 Receptor 103 | 101 103 HMDB0001220 Prostaglandin E2 Prostaglandin E2 Ptger1 Prostaglandin E2 receptor EP1 subtype 17761898 Receptor 104 | 102 104 HMDB0001220 Prostaglandin E2 Prostaglandin E2 Ptger2 Prostaglandin E2 receptor EP2 subtype 17761898 Receptor 105 | 103 105 HMDB0001220 Prostaglandin E2 Prostaglandin E2 Ptger4 Prostaglandin E2 receptor EP4 subtype 33129574 Receptor 106 | 104 106 HMDB0001358 Retinal Retinal Stra6 Receptor for retinol uptake STRA6 27830500 Transporter 107 | 105 107 HMDB0000244 Riboflavin Riboflavin Slc52a2 Solute carrier family 52, riboflavin transporter, member 1 30446350; 29122468 Transporter 108 | 106 108 HMDB0000244 Riboflavin Riboflavin Slc52a2 Solute carrier family 52, riboflavin transporter, member 2 31500345; 22864630 Transporter 109 | 107 109 HMDB0000259 Serotonin Serotonin Htr1a 5-hydroxytryptamine receptor 1A 16251523 Receptor 110 | 108 110 HMDB0000259 Serotonin Serotonin Htr1b 5-hydroxytryptamine receptor 1B 28555718; 29860743; 23964727; 24074042 Receptor 111 | 109 111 HMDB0000259 Serotonin Serotonin Htr1d 5-hydroxytryptamine receptor 1D 20581837 Receptor 112 | 110 112 HMDB0000259 Serotonin Serotonin Htr2a 5-hydroxytryptamine receptor 2A 20521326; 32857933; 16251523; 27959337; 27024926; 32615731 Receptor 113 | 111 113 HMDB0000259 Serotonin Serotonin Htr2b 5-hydroxytryptamine receptor 2B 20581837; 34618686 Receptor 114 | 112 114 HMDB0000259 Serotonin Serotonin Htr2c 5-hydroxytryptamine receptor 2C 27681143 Receptor 115 | 113 115 HMDB0000259 Serotonin Serotonin Htr3a 5-hydroxytryptamine receptor 3A 31342534; 30695556 Receptor 116 | 114 116 HMDB0000259 Serotonin Serotonin Htr3b 5-hydroxytryptamine receptor 3B 23183509 Receptor 117 | 115 117 HMDB0000259 Serotonin Serotonin Htr4 5-hydroxytryptamine receptor 4 30695556 Receptor 118 | 116 118 HMDB0000259 Serotonin Serotonin Htr6 5-hydroxytryptamine receptor 6 18256283 Receptor 119 | 117 119 HMDB0000259 Serotonin Serotonin Trpc6 Short transient receptor potential channel 6 24259679 Receptor 120 | 118 120 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1pr1 Sphingosine 1-phosphate receptor 1 24977489; 25197261 Receptor 121 | 119 121 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1pr2 Sphingosine 1-phosphate receptor 2 26518876; 25363242; 26669941 Receptor 122 | 120 122 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1pr3 Sphingosine 1-phosphate receptor 3 28943478 Receptor 123 | 121 123 HMDB0000277 Sphingosine 1-phosphate Sphingosine 1-phosphate S1pr5 Sphingosine 1-phosphate receptor 5 24977489 Receptor 124 | 122 124 HMDB0000254 Succinic acid Succinate Sucnr1 Succinate receptor 1 25352636; 34270263; 33916314; 26808164; 33279412; 34301438; 29894669; 34233171 Receptor 125 | 123 125 HMDB0000234 Testosterone Testosterone Gprc6a G-protein coupled receptor family C group 6 member A 26785252; 29468843; 24032653; 24998176; 22374969; 24193547; 25093461; 27673554; 33474566; 28180060; 26440882; 31558901 Receptor 126 | 124 126 HMDB0001452 Thromboxane A2 Thromboxane A2 Tbxa2r Thromboxane A2 receptor 9774254 Receptor 127 | 125 127 HMDB0000158 L-Tyrosine Tyrosine Gpr35 G-protein coupled receptor 35 22523636 Receptor 128 | 126 128 HMDB0000305 Vitamin A Vitamin A Stra6 Receptor for retinol uptake STRA6 21782034; 19112531; 25481334; 22665496; 27830501; 32597569; 21704730; 23591992; 26729422; 31956331; 26373900; Recon2 Transporter 129 | 127 129 HMDB0000292 Xanthine Xanthine Adora1 Adenosine receptor A1 31675497 Receptor 130 | 128 130 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid Gabbr2 Gamma-aminobutyric acid type B receptor subunit 2 30610899 Receptor 131 | 129 131 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid Gabra1 Gamma-aminobutyric acid receptor subunit alpha-1 30891080 Receptor 132 | 130 132 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid Gabra4 Gamma-aminobutyric acid receptor subunit alpha-4 33594062 Receptor 133 | 131 133 HMDB0000112 gamma-Aminobutyric acid gamma-Aminobutyric acid Gabrb2 Gamma-aminobutyric acid receptor subunit beta-2 33594062 Receptor 134 | 132 141 HMDB0000123 Glycine Glycine Slc16a10 Monocarboxylate transporter 10 HMDB Transporter 135 | 133 142 HMDB0000097 Choline Choline Slc22a1 Solute carrier family 22 member 1 HMDB Transporter 136 | 134 143 HMDB0001256 Spermine Spermine Slc22a1 Solute carrier family 22 member 1 HMDB; Recon2 Transporter 137 | 135 144 HMDB0001414 Putrescine Putrescine Slc22a4 Solute carrier family 22 member 4 HMDB Transporter 138 | 136 145 HMDB0001256 Spermine Spermine Slc22a4 Solute carrier family 22 member 4 HMDB Transporter 139 | 137 146 HMDB0000064 Creatine Creatine Slc16a12 Monocarboxylate transporter 12 23578822 Transporter 140 | 138 148 HMDB0000123 Glycine Glycine Slc36a1 Proton-coupled amino acid transporter 1 HMDB Transporter 141 | 139 149 HMDB0000097 Choline Choline Slc44a1 Choline transporter-like protein 1 HMDB Transporter 142 | 140 150 HMDB0000097 Choline Choline Slc44a2 Choline transporter-like protein 2 HMDB Transporter 143 | 141 151 HMDB0000097 Choline Choline Slc44a3 Choline transporter-like protein 3 HMDB Transporter 144 | 142 152 HMDB0000097 Choline Choline Slc44a4 Choline transporter-like protein 4 HMDB Transporter 145 | 143 153 HMDB0000097 Choline Choline Slc5a7 High affinity choline transporter 1 HMDB Transporter 146 | 144 154 HMDB0000243 Pyruvic acid Pyruvate Slc16a11 Monocarboxylate transporter 11 https://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC16A11 Transporter 147 | 145 155 HMDB0000243 Pyruvic acid Pyruvate Slc16a1 Monocarboxylate transporter 1 31882442 Transporter 148 | 146 156 HMDB0000254 Succinic acid Succinate Slc13a5 Na(+)/citrate cotransporter 31882442 Transporter 149 | 147 157 HMDB0000094 Citric acid Citrate Slc13a5 Na(+)/citrate cotransporter 33597751 Transporter 150 | 148 158 HMDB0000134 Fumaric acid Fumarate Slc13a5 Na(+)/citrate cotransporter 31882442 Transporter 151 | 149 159 HMDB0000156 Malic acid Malate Slc13a5 Na(+)/citrate cotransporter 31882442 Transporter 152 | 150 160 HMDB0000156 Malic acid Malate Slc1a3 Excitatory amino acid transporter 1 https://en.wikipedia.org/wiki/Excitatory_amino_acid_transporter_1 Transporter 153 | 151 161 HMDB0000187 L-Serine Serine Slc7a10 Asc-type amino acid transporter 1 33269112 Transporter 154 | 152 162 HMDB0000187 L-Serine Serine Slc3a2 4F2 cell-surface antigen heavy chain 33269112 Transporter 155 | 153 163 HMDB0000187 L-Serine Serine Slc1a4 Neutral amino acid transporter A 33269112 Transporter 156 | 154 164 HMDB0000187 L-Serine Serine Slc1a5 Neutral amino acid transporter B(0) 33269112 Transporter 157 | 155 165 HMDB0000574 L-Cysteine Cysteine Slc7a11 Cystine/glutamate transporter 33000412 Transporter 158 | 156 166 HMDB0000696 L-Methionine Methionine Slc7a5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 159 | 157 167 HMDB0000168 L-Asparagine Asparagine Slc1a5 Neutral amino acid transporter B(0) 33420487 Transporter 160 | 158 168 HMDB0000641 L-Glutamine Glutamine Slc6a14 Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) 26724577 Transporter 161 | 159 169 HMDB0000641 L-Glutamine Glutamine Slc6a19 Sodium-dependent neutral amino acid transporter B(0)AT1 26724577 Transporter 162 | 160 170 HMDB0000641 L-Glutamine Glutamine Slc7a6 Y+L amino acid transporter 2 26724577 Transporter 163 | 161 171 HMDB0000641 L-Glutamine Glutamine Slc7a7 Y+L amino acid transporter 1 26724577 Transporter 164 | 162 172 HMDB0000641 L-Glutamine Glutamine Slc38a1 Sodium-coupled neutral amino acid symporter 1 26724577 Transporter 165 | 163 173 HMDB0000641 L-Glutamine Glutamine Slc38a3 Sodium-coupled neutral amino acid transporter 3 26724577 Transporter 166 | 164 174 HMDB0000641 L-Glutamine Glutamine Slc38a5 Sodium-coupled neutral amino acid transporter 5 26724577 Transporter 167 | 165 175 HMDB0000641 L-Glutamine Glutamine Slc38a7 Sodium-coupled neutral amino acid transporter 7 26724577 Transporter 168 | 166 176 HMDB0000641 L-Glutamine Glutamine Slc38a8 Putative sodium-coupled neutral amino acid transporter 8 26724577 Transporter 169 | 167 177 HMDB0000112 gamma-Aminobutyric acid GABA Slc6a1 Sodium- and chloride-dependent GABA transporter 1 https://en.wikipedia.org/wiki/GABA_transporter Transporter 170 | 168 178 HMDB0000112 gamma-Aminobutyric acid GABA Slc6a13 Sodium- and chloride-dependent GABA transporter 2 https://en.wikipedia.org/wiki/GABA_transporter Transporter 171 | 169 179 HMDB0000112 gamma-Aminobutyric acid GABA Slc6a11 Sodium- and chloride-dependent GABA transporter 3 https://en.wikipedia.org/wiki/GABA_transporter Transporter 172 | 170 180 HMDB0000112 gamma-Aminobutyric acid GABA Slc6a12 Sodium- and chloride-dependent betaine transporter https://en.wikipedia.org/wiki/GABA_transporter Transporter 173 | 171 181 HMDB0000112 gamma-Aminobutyric acid GABA Slc6a8 Sodium- and chloride-dependent creatine transporter 1 https://en.wikipedia.org/wiki/GABA_transporter Transporter 174 | 172 182 HMDB0000112 gamma-Aminobutyric acid GABA Slc6a6 Sodium- and chloride-dependent taurine transporter https://en.wikipedia.org/wiki/GABA_transporter Transporter 175 | 173 183 HMDB0000158 L-Tyrosine Tyrosine Slc7a5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 176 | 174 184 HMDB0000191 L-Aspartic acid Aspartate Slc1a2 Excitatory amino acid transporter 2 31269432 Transporter 177 | 175 185 HMDB0000177 L-Histidine Histidine Slc7a5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 178 | 176 186 HMDB0000159 L-Phenylalanine Phenylalanine Slc7a5 Large neutral amino acids transporter small subunit 1 32377929 Transporter 179 | 177 187 HMDB0000883 L-Valine Valine Slc43a1 Large neutral amino acids transporter small subunit 3 31997805; Recon2 Transporter 180 | 178 188 HMDB0000172 L-Isoleucine Isoleucine Slc43a1 Large neutral amino acids transporter small subunit 3 31997805; Recon2 Transporter 181 | 179 189 HMDB0000687 L-Leucine Leucine Slc43a1 Large neutral amino acids transporter small subunit 3 31997805; Recon2 Transporter 182 | 180 190 HMDB0000034 Adenine Adenine Slc28a3 Solute carrier family 28 member 3 33972798 Transporter 183 | 181 191 HMDB0000034 Adenine Adenine Slc29a3 Equilibrative nucleoside transporter 3 33972798 Transporter 184 | 182 192 HMDB0000034 Adenine Adenine Slc35f5 Solute carrier family 35 member F5 33972798 Transporter 185 | 183 193 HMDB0000062 L-Carnitine L-Carnitine Slc22a21 Organic cation/carnitine transporter 2 Recon2 Transporter 186 | 183 193 HMDB0000062 L-Carnitine L-Carnitine Slc22a5 Organic cation/carnitine transporter 2 Recon2 Transporter 187 | 184 194 HMDB0000641 L-Glutamine L-glutamine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 188 | 185 195 HMDB0000187 L-Serine L-serine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 189 | 186 196 HMDB0000159 L-Phenylalanine L-phenylalanine Slc43a2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 190 | 187 197 HMDB0000159 L-Phenylalanine L-phenylalanine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 191 | 188 198 HMDB0000159 L-Phenylalanine L-phenylalanine Slc16a10 Monocarboxylate transporter 10 Recon2 Transporter 192 | 189 199 HMDB0000687 L-Leucine L-leucine Slc43a2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 193 | 190 200 HMDB0000574 L-Cysteine L-cysteine Slc43a2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 194 | 191 201 HMDB0000696 L-Methionine L-methionine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 195 | 192 202 HMDB0000696 L-Methionine L-methionine Slc43a2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 196 | 193 203 HMDB0000158 L-Tyrosine L-tyrosine Slc16a10 Monocarboxylate transporter 10 Recon2 Transporter 197 | 194 204 HMDB0000168 L-Asparagine L-asparagine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 198 | 195 205 HMDB0000167 L-Threonine L-threonine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 199 | 196 206 HMDB0000883 L-Valine L-valine Slc43a2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 200 | 197 207 HMDB0000929 L-Tryptophan L-tryptophan Slc36a4 Neutral amino acid uniporter 4 Recon2 Transporter 201 | 198 208 HMDB0000929 L-Tryptophan L-tryptophan Slc16a10 Monocarboxylate transporter 10 Recon2 Transporter 202 | 199 209 HMDB0000172 L-Isoleucine L-isoleucine Slc43a2 Large neutral amino acids transporter small subunit 4 Recon2 Transporter 203 | 200 210 HMDB0000517 L-Arginine L-argininium(1+) Slc38a4 Sodium-coupled neutral amino acid transporter 4 Recon2 Transporter 204 | 201 211 HMDB0000517 L-Arginine L-argininium(1+) Slc7a2 Cationic amino acid transporter 2 Recon2 Transporter 205 | 202 212 HMDB0000517 L-Arginine L-argininium(1+) Slc7a3 Cationic amino acid transporter 3 Recon2 Transporter 206 | 203 213 HMDB0000177 L-Histidine L-histidine Slc38a4 Sodium-coupled neutral amino acid transporter 4 Recon2 Transporter 207 | 204 214 HMDB0000182 L-Lysine L-lysinium(1+) Slc38a4 Sodium-coupled neutral amino acid transporter 4 Recon2 Transporter 208 | 205 215 HMDB0000182 L-Lysine L-lysinium(1+) Slc7a2 Cationic amino acid transporter 2 Recon2 Transporter 209 | 206 216 HMDB0000182 L-Lysine L-lysinium(1+) Slc7a1 High affinity cationic amino acid transporter 1 Recon2 Transporter 210 | 207 217 HMDB0000182 L-Lysine L-lysinium(1+) Slc7a3 Cationic amino acid transporter 3 Recon2 Transporter 211 | 208 218 HMDB0000214 Ornithine Ornithine Slc7a2 Cationic amino acid transporter 2 Recon2 Transporter 212 | 209 219 HMDB0000214 Ornithine Ornithine Slc7a1 High affinity cationic amino acid transporter 1 Recon2 Transporter 213 | 210 220 HMDB0000214 Ornithine Ornithine Slc7a3 Cationic amino acid transporter 3 Recon2 Transporter 214 | 211 221 HMDB0000143 D-Galactose D-Galactose Slc2a2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 215 | 212 222 HMDB0000143 D-Galactose D-Galactose Slc2a3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 216 | 213 223 HMDB0000143 D-Galactose D-Galactose Slc2a8 Solute carrier family 2, facilitated glucose transporter member 8 Recon2 Transporter 217 | 214 224 HMDB0000143 D-Galactose D-Galactose Slc2a10 Solute carrier family 2, facilitated glucose transporter member 10 Recon2 Transporter 218 | 215 225 HMDB0000143 D-Galactose D-Galactose Slc2a1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 219 | 216 226 HMDB0001043 Arachidonic acid arachidonate Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 220 | 217 227 HMDB0000122 D-Glucose D-glucose Slc2a9 Solute carrier family 2, facilitated glucose transporter member 9 Recon2 Transporter 221 | 218 228 HMDB0000122 D-Glucose D-glucose Slc2a2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 222 | 219 229 HMDB0000122 D-Glucose D-glucose Slc2a6 Solute carrier family 2, facilitated glucose transporter member 6 Recon2 Transporter 223 | 220 230 HMDB0000122 D-Glucose D-glucose Slc2a3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 224 | 221 231 HMDB0000122 D-Glucose D-glucose Slc2a4 Solute carrier family 2, facilitated glucose transporter member 4 Recon2 Transporter 225 | 222 232 HMDB0000122 D-Glucose D-glucose Slc2a8 Solute carrier family 2, facilitated glucose transporter member 8 Recon2 Transporter 226 | 223 233 HMDB0000122 D-Glucose D-glucose Slc2a7 Solute carrier family 2, facilitated glucose transporter member 7 Recon2 Transporter 227 | 224 234 HMDB0000122 D-Glucose D-glucose Slc2a12 Solute carrier family 2, facilitated glucose transporter member 12 Recon2 Transporter 228 | 225 235 HMDB0000122 D-Glucose D-glucose Slc2a10 Solute carrier family 2, facilitated glucose transporter member 10 Recon2 Transporter 229 | 226 236 HMDB0000122 D-Glucose D-glucose Slc2a1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 230 | 227 237 HMDB0001264 Dehydroascorbic acid dehydroascorbide(1-) Slc2a4 Solute carrier family 2, facilitated glucose transporter member 4 Recon2 Transporter 231 | 228 238 HMDB0001264 Dehydroascorbic acid dehydroascorbide(1-) Slc2a3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 232 | 229 239 HMDB0001264 Dehydroascorbic acid dehydroascorbide(1-) Slc2a1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 233 | 230 240 HMDB0000073 Dopamine dopaminium(1+) Slc22a3 Solute carrier family 22 member 3 Recon2 Transporter 234 | 231 241 HMDB0000073 Dopamine dopaminium(1+) Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 235 | 232 242 HMDB0000073 Dopamine dopaminium(1+) Slc22a21 Organic cation/carnitine transporter 2 Recon2 Transporter 236 | 232 242 HMDB0000073 Dopamine dopaminium(1+) Slc22a5 Organic cation/carnitine transporter 2 Recon2 Transporter 237 | 233 243 HMDB0000169 D-Mannose D-Mannose Slc2a2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 238 | 234 244 HMDB0000169 D-Mannose D-Mannose Slc2a3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 239 | 235 245 HMDB0000169 D-Mannose D-Mannose Slc2a1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 240 | 236 246 HMDB0000050 Adenosine Adenosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 241 | 237 247 HMDB0000050 Adenosine Adenosine Slc29a1 Equilibrative nucleoside transporter 1 Recon2 Transporter 242 | 238 248 HMDB0000216 Norepinephrine Norepinephrine Slc22a1 Solute carrier family 22 member 1 Recon2 Transporter 243 | 239 249 HMDB0000216 Norepinephrine Norepinephrine Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 244 | 240 250 HMDB0000216 Norepinephrine Norepinephrine Slc22a3 Solute carrier family 22 member 3 Recon2 Transporter 245 | 241 251 HMDB0000097 Choline Choline Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 246 | 242 252 HMDB0000097 Choline Choline Slc22a21 Organic cation/carnitine transporter 2 Recon2 Transporter 247 | 242 252 HMDB0000097 Choline Choline Slc22a5 Organic cation/carnitine transporter 2 Recon2 Transporter 248 | 243 253 HMDB0000259 Serotonin serotonin(1+) Slc22a1 Solute carrier family 22 member 1 Recon2 Transporter 249 | 244 254 HMDB0000259 Serotonin serotonin(1+) Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 250 | 245 255 HMDB0000660 D-Fructose D-Fructose Slc2a2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 251 | 246 256 HMDB0000660 D-Fructose D-Fructose Slc2a7 Solute carrier family 2, facilitated glucose transporter member 7 Recon2 Transporter 252 | 247 257 HMDB0000660 D-Fructose D-Fructose Slc2a8 Solute carrier family 2, facilitated glucose transporter member 8 Recon2 Transporter 253 | 248 258 HMDB0000660 D-Fructose D-Fructose Slc2a5 Solute carrier family 2, facilitated glucose transporter member 5 Recon2 Transporter 254 | 249 259 HMDB0001220 Prostaglandin E2 prostaglandin E2(1-) Slc22a1 Solute carrier family 22 member 1 Recon2 Transporter 255 | 250 260 HMDB0001220 Prostaglandin E2 prostaglandin E2(1-) Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 256 | 251 261 HMDB0000296 Uridine Uridine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 257 | 252 262 HMDB0000296 Uridine Uridine Slc29a1 Equilibrative nucleoside transporter 1 Recon2 Transporter 258 | 253 263 HMDB0000220 Palmitic acid Hexadecanoate (n-C16:0) Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 259 | 254 264 HMDB0000305 Vitamin A retinol Rbp1 Retinol-binding protein 1 Recon2 Transporter 260 | 255 265 HMDB0000305 Vitamin A retinol Rbp4 Retinol-binding protein 4 Recon2 Transporter 261 | 256 266 HMDB0000305 Vitamin A retinol Rbp2 Retinol-binding protein 2 Recon2 Transporter 262 | 257 267 HMDB0000195 Inosine Inosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 263 | 258 268 HMDB0000195 Inosine Inosine Slc29a1 Equilibrative nucleoside transporter 1 Recon2 Transporter 264 | 259 269 HMDB0000089 Cytidine Cytidine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 265 | 260 270 HMDB0000089 Cytidine Cytidine Slc29a1 Equilibrative nucleoside transporter 1 Recon2 Transporter 266 | 261 271 HMDB0000207 Oleic acid octadecenoate (n-C18:1) Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 267 | 262 272 HMDB0000870 Histamine histamium Slc22a3 Solute carrier family 22 member 3 Recon2 Transporter 268 | 263 273 HMDB0000870 Histamine histamium Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 269 | 264 274 HMDB0000870 Histamine histamium Slc22a21 Organic cation/carnitine transporter 2 Recon2 Transporter 270 | 264 274 HMDB0000870 Histamine histamium Slc22a5 Organic cation/carnitine transporter 2 Recon2 Transporter 271 | 265 275 HMDB0000265 Liothyronine 3,3',5-triiodo-L-thyronine Slc16a2 Monocarboxylate transporter 8 Recon2 Transporter 272 | 266 276 HMDB0003550 Calcidiol calcidiol Cubn Cubilin Recon2 Transporter 273 | 267 277 HMDB0003550 Calcidiol calcidiol Lrp2 Low-density lipoprotein receptor-related protein 2 Recon2 Transporter 274 | 268 278 HMDB0003550 Calcidiol calcidiol Gc Vitamin D-binding protein Recon2 Transporter 275 | 269 279 HMDB0000181 L-Dopa L-dopa Slc16a10 Monocarboxylate transporter 10 Recon2 Transporter 276 | 270 280 HMDB0001396 5-Methyltetrahydrofolic acid 5-Methyltetrahydrofolate Folr1 Folate receptor alpha Recon2 Transporter 277 | 271 281 HMDB0000895 Acetylcholine acetylcholine Slc22a1 Solute carrier family 22 member 1 Recon2 Transporter 278 | 272 282 HMDB0000012 Deoxyuridine Deoxyuridine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 279 | 273 283 HMDB0000133 Guanosine Guanosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 280 | 274 284 HMDB0000133 Guanosine Guanosine Slc29a1 Equilibrative nucleoside transporter 1 Recon2 Transporter 281 | 275 285 HMDB0000157 Hypoxanthine Hypoxanthine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 282 | 276 286 HMDB0000248 Thyroxine L-thyroxine Slc16a2 Monocarboxylate transporter 8 Recon2 Transporter 283 | 277 287 HMDB0000273 Thymidine Thymidine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 284 | 278 288 HMDB0000273 Thymidine Thymidine Slc29a1 Equilibrative nucleoside transporter 1 Recon2 Transporter 285 | 279 289 HMDB0001139 Prostaglandin F2a prostaglandin F2alpha(1-) Slc22a1 Solute carrier family 22 member 1 Recon2 Transporter 286 | 280 290 HMDB0001139 Prostaglandin F2a prostaglandin F2alpha(1-) Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 287 | 281 291 HMDB0000673 Linoleic acid linoleate Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 288 | 282 292 HMDB0000034 Adenine Adenine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 289 | 283 293 HMDB0000300 Uracil uracil Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 290 | 284 294 HMDB0000101 Deoxyadenosine 2-deoxyadenosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 291 | 285 295 HMDB0000085 Deoxyguanosine Deoxyguanosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 292 | 286 296 HMDB0000163 D-Maltose Maltose Slc2a3 Solute carrier family 2, facilitated glucose transporter member 3 Recon2 Transporter 293 | 287 297 HMDB0000876 Vitamin D3 calciol Got2 Aspartate aminotransferase, mitochondrial Recon2 Transporter 294 | 288 298 HMDB0000876 Vitamin D3 calciol Cd36 Platelet glycoprotein 4 Recon2 Transporter 295 | 289 299 HMDB0000294 Urea Urea Slc5a1 Sodium/glucose cotransporter 1 Recon2 Transporter 296 | 290 300 HMDB0000294 Urea Urea Slc14a2 Urea transporter 2 Recon2 Transporter 297 | 291 301 HMDB0000294 Urea Urea Slc5a5 Sodium/iodide cotransporter Recon2 Transporter 298 | 292 302 HMDB0000294 Urea Urea Slc14a1 Urea transporter 1 Recon2 Transporter 299 | 293 303 HMDB0000071 Deoxyinosine Deoxyinosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 300 | 294 304 HMDB0000014 Deoxycytidine Deoxycytidine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 301 | 295 305 HMDB0002925 Dihomo-gamma-linolenic acid dihomo-gamma-linolenic acid (n-6) Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 302 | 296 306 HMDB0000262 Thymine Thymine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 303 | 297 307 HMDB0000806 Myristic acid tetradecanoate (n-C14:0) Slc27a2 Long-chain fatty acid transport protein 2 Recon2 Transporter 304 | 298 308 HMDB0000827 Stearic acid octadecanoate (n-C18:0) Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 305 | 299 309 HMDB0003073 gamma-Linolenic acid gamma-linolenate Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 306 | 300 310 HMDB0001388 alpha-Linolenic acid alpha-linolenate Slc27a5 Long-chain fatty acid transport protein 5 Recon2 Transporter 307 | 301 311 HMDB0000132 Guanine Guanine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 308 | 302 312 HMDB0001514 Glucosamine D-Glucosamine Slc2a2 Solute carrier family 2, facilitated glucose transporter member 2 Recon2 Transporter 309 | 303 313 HMDB0001514 Glucosamine D-Glucosamine Slc2a4 Solute carrier family 2, facilitated glucose transporter member 4 Recon2 Transporter 310 | 304 314 HMDB0001514 Glucosamine D-Glucosamine Slc2a1 Solute carrier family 2, facilitated glucose transporter member 1 Recon2 Transporter 311 | 305 315 HMDB0003178 Heme Protoheme Slc46a1 Proton-coupled folate transporter Recon2 Transporter 312 | 306 316 HMDB0003178 Heme Protoheme Lrp1 Prolow-density lipoprotein receptor-related protein 1 Recon2 Transporter 313 | 307 317 HMDB0001178 Adenosine diphosphate ribose ADPribose Cd38 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 Recon2 Transporter 314 | 308 318 HMDB0000190 L-Lactic acid L-Lactic acid Hcar1 Hydroxycarboxylic acid receptor 1 30728759, 31259764 Receptor 315 | 310 320 HMDB0000538 Adenosine triphosphate ATP P2rx1 P2X purinoceptor 1 24335194 Receptor 316 | 311 321 HMDB0000538 Adenosine triphosphate ATP P2rx2 P2X purinoceptor 2 24335194 Receptor 317 | 312 322 HMDB0000538 Adenosine triphosphate ATP P2rx3 P2X purinoceptor 3 24335194 Receptor 318 | 313 323 HMDB0000538 Adenosine triphosphate ATP P2rx4 P2X purinoceptor 4 24335194 Receptor 319 | 314 324 HMDB0000538 Adenosine triphosphate ATP P2rx5 P2X purinoceptor 5 24335194 Receptor 320 | 315 325 HMDB0000538 Adenosine triphosphate ATP P2rx6 P2X purinoceptor 6 24335194 Receptor 321 | 316 326 HMDB0000538 Adenosine triphosphate ATP P2rx7 P2X purinoceptor 7 24335194 Receptor 322 | 317 327 HMDB0001341 ADP ADP P2ry1 P2Y purinoceptor 1 24335194 Receptor 323 | 318 328 HMDB0000538 Adenosine triphosphate ATP P2ry1 P2Y purinoceptor 1 24335194 Receptor 324 | 319 329 HMDB0000538 Adenosine triphosphate ATP P2ry2 P2Y purinoceptor 2 24335194 Receptor 325 | 320 330 HMDB0000285 Uridine triphosphate UTP P2ry2 P2Y purinoceptor 2 24335194 Receptor 326 | 321 331 HMDB0000285 Uridine triphosphate UTP P2ry4 P2Y purinoceptor 4 24335194 Receptor 327 | 322 332 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2ry4 P2Y purinoceptor 4 24335194 Receptor 328 | 323 333 HMDB0000285 Uridine triphosphate UTP P2ry6 P2Y purinoceptor 6 24335194 Receptor 329 | 324 334 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2ry6 P2Y purinoceptor 6 24335194 Receptor 330 | 327 337 HMDB0001341 ADP ADP P2ry12 P2Y purinoceptor 12 24335194 Receptor 331 | 328 338 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2ry12 P2Y purinoceptor 12 24335194 Receptor 332 | 329 339 HMDB0001341 ADP ADP P2ry13 P2Y purinoceptor 13 24335194 Receptor 333 | 330 340 HMDB0000538 Adenosine triphosphate Adenosine triphosphate P2ry13 P2Y purinoceptor 13 24335194 Receptor 334 | 331 341 HMDB0000286 Uridine diphosphate glucose Uridine diphosphate glucose P2ry14 P2Y purinoceptor 14 24335194 Receptor 335 | 332 342 HMDB0000067 Cholesterol Cholesterol Npc1l1 NPC1-like intracellular cholesterol transporter 1 21763723 Receptor 336 | 333 343 HMDB0002961 Dihydrotestosterone Dihydrotestosterone Ar Androgen receptor https://en.wikipedia.org/wiki/Androgen_receptor Nuclear Receptor 337 | 334 344 HMDB0000234 Testosterone Testosterone Ar Androgen receptor https://en.wikipedia.org/wiki/Androgen_receptor Nuclear Receptor 338 | 335 345 HMDB0000131 Glycerol Glycerol Aqp3 Aquaporin-3 32213983 Receptor 339 | 336 346 HMDB0000043 Betaine Betaine Slc6a12 Sodium- and chloride-dependent betaine transporter 32213983 Transporter 340 | 337 347 HMDB0000895 Acetylcholine Acetylcholine Chrm4 Muscarinic acetylcholine receptor M4 https://gpcrdb.org/ligand/statistics Receptor 341 | 338 348 HMDB0000895 Acetylcholine Acetylcholine Chrm5 Muscarinic acetylcholine receptor M5 https://gpcrdb.org/ligand/statistics Receptor 342 | 339 349 HMDB0000208 Oxoglutaric acid Oxoglutaric acid Oxgr1 2-oxoglutarate receptor 1 https://gpcrdb.org/ligand/statistics Receptor 343 | 340 350 HMDB0000248 Thyroxine Thyroxine Thra Thyroid hormone receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 344 | 341 351 HMDB0000248 Thyroxine Thyroxine Thrb Thyroid hormone receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 345 | 342 352 HMDB0000305 Vitamin A Vitamin A Rara Retinoic acid receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 346 | 343 353 HMDB0001358 Retinal Retinal Rara Retinoic acid receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 347 | 344 354 HMDB0000561 beta-Carotene beta-Carotene Rara Retinoic acid receptor alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 348 | 345 355 HMDB0000305 Vitamin A Vitamin A Rarb Retinoic acid receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 349 | 346 356 HMDB0001358 Retinal Retinal Rarb Retinoic acid receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 350 | 347 357 HMDB0000561 beta-Carotene beta-Carotene Rarb Retinoic acid receptor beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 351 | 348 358 HMDB0000305 Vitamin A Vitamin A Rarg Retinoic acid receptor gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 352 | 349 359 HMDB0001358 Retinal Retinal Rarg Retinoic acid receptor gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 353 | 350 360 HMDB0000561 beta-Carotene beta-Carotene Rarg Retinoic acid receptor gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 354 | 351 361 HMDB0003178 Heme Heme Nr1d1 Nuclear receptor subfamily 1 group D member 1 https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 355 | 352 362 HMDB0003178 Heme Heme Nr1d2 Nuclear receptor subfamily 1 group D member 2 https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 356 | 353 363 HMDB0000067 Cholesterol Cholesterol Rora Nuclear receptor ROR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 357 | 354 364 HMDB0000067 Cholesterol Cholesterol Rorb Nuclear receptor ROR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 358 | 355 365 HMDB0000067 Cholesterol Cholesterol Rorc Nuclear receptor ROR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 359 | 356 366 HMDB0000876 Vitamin D3 Vitamin D3 Vdr Vitamin D3 receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 360 | 357 367 HMDB0001358 Retinal Retinal Rxra Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 361 | 358 368 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid Rxra Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 362 | 359 369 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid Rxra Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 363 | 360 370 HMDB0006219 13-cis-Retinoic acid 13-cis-Retinoic acid Rxra Retinoic acid receptor RXR-alpha https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 364 | 361 371 HMDB0001358 Retinal Retinal Rxrb Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 365 | 362 372 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid Rxrb Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 366 | 363 373 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid Rxrb Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 367 | 364 374 HMDB0006219 13-cis-Retinoic acid 13-cis-Retinoic acid Rxrb Retinoic acid receptor RXR-beta https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 368 | 365 375 HMDB0001358 Retinal Retinal Rxrg Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 369 | 366 376 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid Rxrg Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 370 | 367 377 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid Rxrg Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 371 | 368 378 HMDB0006219 13-cis-Retinoic acid 13-cis-Retinoic acid Rxrg Retinoic acid receptor RXR-gamma https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 372 | 369 379 HMDB0006216 11-cis-Retinol 11-cis-Retinol Nr2f2 COUP transcription factor 2 https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 373 | 370 380 HMDB0000063 Cortisol Cortisol Nr3c1 Glucocorticoid receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 374 | 371 381 HMDB0000037 Aldosterone Aldosterone Nr3c2 Mineralocorticoid receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 375 | 372 382 HMDB0001830 Progesterone Progesterone Pgr Progesterone receptor https://en.wikipedia.org/wiki/Nuclear_receptor#Ligands Nuclear Receptor 376 | 373 383 HMDB0002369 9-cis-Retinoic acid 9-cis-Retinoic acid Vdr Vitamin D3 receptor 15824121 Nuclear Receptor 377 | 374 384 HMDB0000053 Androstenedione Androstenedione Ar Androgen receptor 16524719; 28457967; 12647261; 20534728; 24861263; 23856005; 18645714; 23258647 Nuclear Receptor 378 | 375 385 HMDB0000031 Androsterone Androsterone Ar Androgen receptor 21303972; 24861263; 12647261 Nuclear Receptor 379 | 376 386 HMDB0003550 Calcidiol Calcidiol Vdr Vitamin D3 receptor 25201891; 33348854 Nuclear Receptor 380 | 377 387 HMDB0001903 Calcitriol Calcitriol Vdr Vitamin D3 receptor 29657326; 15077124; 20303786; 28008815; 9211344; 8574944; 9211349; 19667157; 16061850; 10079704; 17629157; 15225804; 21337382; 19371337; 21647319; 16048257; 29367669; 22276021; 29113124; 24597598; 27530414; 12899526; 9144338; 20798257; 12465754; 18290711; 33348854; 33354999; 26000306; 15861036; 12753260; 10633458; 16886687; 17489022; 19034868; 19705334; 25614680; 33211721; 22213328; 8147918; 24060611; 7552094; 20592360; 22720752 Nuclear Receptor 381 | 378 389 HMDB0000151 Estradiol Estradiol Esr2 Estrogen receptor beta 25765287; 20173016 Nuclear Receptor 382 | 379 390 HMDB0000761 Lithocholic acid Lithocholic acid Vdr Vitamin D3 receptor 32863311; 24343899; 20888898; 20006981; 29074825; 19244278; 18180267; 15489543; 19581390; 32213983; 14525957; 16724925; 15824121 Nuclear Receptor 383 | 380 391 HMDB0000216 Norepinephrine Norepinephrine Adra1a Alpha-1A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 384 | 381 392 HMDB0000068 Epinephrine Epinephrine Adra1a Alpha-1A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 385 | 382 393 HMDB0000216 Norepinephrine Norepinephrine Adra1b Alpha-1B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 386 | 383 394 HMDB0000068 Epinephrine Epinephrine Adra1b Alpha-1B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 387 | 384 395 HMDB0000216 Norepinephrine Norepinephrine Adra1d Alpha-1D adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 388 | 385 396 HMDB0000068 Epinephrine Epinephrine Adra1d Alpha-1D adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 389 | 386 397 HMDB0000216 Norepinephrine Norepinephrine Adra2a Alpha-2A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 390 | 387 398 HMDB0000068 Epinephrine Epinephrine Adra2a Alpha-2A adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 391 | 388 399 HMDB0000216 Norepinephrine Norepinephrine Adra2b Alpha-2B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 392 | 389 400 HMDB0000068 Epinephrine Epinephrine Adra2b Alpha-2B adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 393 | 390 401 HMDB0000216 Norepinephrine Norepinephrine Adra2c Alpha-2C adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 394 | 391 402 HMDB0000068 Epinephrine Epinephrine Adra2c Alpha-2C adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 395 | 392 403 HMDB0000216 Norepinephrine Norepinephrine Adrb1 Beta-1 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 396 | 393 404 HMDB0000068 Epinephrine Epinephrine Adrb1 Beta-1 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 397 | 394 405 HMDB0000216 Norepinephrine Norepinephrine Adrb2 Beta-2 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 398 | 395 406 HMDB0000068 Epinephrine Epinephrine Adrb2 Beta-2 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 399 | 396 407 HMDB0000216 Norepinephrine Norepinephrine Adrb3 Beta-3 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 400 | 397 408 HMDB0000068 Epinephrine Epinephrine Adrb3 Beta-3 adrenergic receptor https://en.wikipedia.org/wiki/Adrenergic_receptor Receptor 401 | 398 409 HMDB0001852 all-trans-Retinoic acid all-trans-Retinoic acid Rara Retinoic acid receptor alpha 20615454 Nuclear Receptor 402 | 399 410 HMDB0001085 Leukotriene B4 Leukotriene B4 Ppara Peroxisome proliferator-activated receptor alpha 20615454 Nuclear Receptor 403 | 400 411 HMDB0001547 Corticosterone Corticosterone Nr3c1 Glucocorticoid receptor 20615454 Nuclear Receptor 404 | 401 412 HMDB0000518 Chenodeoxycholic acid Chenodeoxycholic acid Nr1h4 Bile acid receptor 20615454 Nuclear Receptor 405 | 402 413 HMDB0006247 25-Hydroxycholesterol 25-Hydroxycholesterol Nr1h3 Oxysterols receptor LXR-alpha 20615454 Nuclear Receptor 406 | 403 414 HMDB0000121 Folic acid Folic acid Slc19a1 Reduced folate transporter 28284395 Transporter 407 | 404 415 HMDB0000235 Thiamine Thiamine Slc19a3 Thiamine transporter 2 28284395 Transporter 408 | 405 416 HMDB0000190 L-Lactic acid Lactate Slc16a1 Monocarboxylate transporter 1 32144120; 22428047 Transporter 409 | 406 417 HMDB0000077 Dehydroepiandrosterone Dehydroepiandrosterone Ar Androgen receptor 21303972; 24861263; 12647261 Nuclear Receptor 410 | 407 418 HMDB0000586 Potassium Potassium Abcc8 ATP-binding cassette sub-family C member 8 https://en.wikipedia.org/wiki/ABCC8; 23226049; 24399968; 22050960; 24700710 Transporter 411 | 408 420 HMDB0006111 12-HETE 12-HETE Gpr31b 12-(S)-hydroxy-5,8,10,14-eicosatetraenoic acid receptor 32918516 Receptor 412 | 409 421 HMDB0000757 Glycogen Glycogen Stbd1 Starch-binding domain-containing protein 1 20810658; 21893048; 32927708; 24837458 Receptor 413 | 410 423 HMDB0000715 Kynurenic acid Kynurenic acid Gpr35 G-protein coupled receptor 35 22523636; 23123095; 30141532; 29414686; 16754668 Receptor 414 | 411 424 HMDB0004385 Lipoxin A4 Lipoxin A4 Esr1 Estrogen receptor 24587003 Receptor 415 | 412 425 HMDB0000588 Sodium Sodium Slc5a1 Sodium/glucose cotransporter 1 Recon2 Transporter 416 | 413 426 HMDB0000588 Sodium Sodium Slc5a5 Sodium/iodide cotransporter Recon2 Transporter 417 | 414 427 HMDB0000588 Sodium Sodium Slc5a3 Sodium/myo-inositol cotransporter Recon2 Transporter 418 | 415 428 HMDB0000719 L-Homoserine L-homoserine Slc43a1 Large neutral amino acids transporter small subunit 3 Recon2 Transporter 419 | 416 429 HMDB0000492 Chloride ion Chloride Slc17a1 Sodium-dependent phosphate transport protein 1 Recon2 Transporter 420 | 417 430 HMDB0003229 Palmitoleic acid Hexadecenoate (n-C16:1) Slc27a2 Long-chain fatty acid transport protein 2 Recon2 Transporter 421 | 418 431 HMDB0012238 Iodide iodide Slc5a8 Sodium-coupled monocarboxylate transporter 1 Recon2 Transporter 422 | 419 432 HMDB0002003 Tetracosanoic acid lignocerate Slc27a2 Long-chain fatty acid transport protein 2 Recon2 Transporter 423 | 420 433 HMDB0001893 alpha-Tocopherol (+)-alpha-tocopherol Scarb1 Scavenger receptor class B member 1 Recon2 Transporter 424 | 421 434 HMDB0001893 alpha-Tocopherol (+)-alpha-tocopherol Npc1l1 NPC1-like intracellular cholesterol transporter 1 Recon2 Transporter 425 | 422 435 HMDB0000573 Elaidic acid elaidate Slc27a2 Long-chain fatty acid transport protein 2 Recon2 Transporter 426 | 423 436 HMDB0002086 Adenosylcobalamin Adenosylcobalamin Cubn Cubilin Recon2 Transporter 427 | 424 437 HMDB0002086 Adenosylcobalamin Adenosylcobalamin Amn Protein amnionless [Cleaved into: Soluble protein amnionless] Recon2 Transporter 428 | 425 438 HMDB0000630 Cytosine cytosine Slc29a2 Equilibrative nucleoside transporter 2 Recon2 Transporter 429 | 426 439 HMDB0006543 Debrisoquine debrisoquine Slc22a2 Solute carrier family 22 member 2 Recon2 Transporter 430 | 427 440 HMDB0011733 Glycyl-glycine Glycyl-glycine Slc15a1 Solute carrier family 15 member 1 Recon2 Transporter 431 | 428 441 HMDB0000295 Uridine 5'-diphosphate Uridine 5'-diphosphate P2ry6 P2Y purinoceptor 6 24335194 Receptor 432 | 429 442 HMDB0000801 Phytanic acid Phytanic acid Ppara Peroxisome proliferator-activated receptor alpha 11923221 Nuclear Receptor 433 | 430 443 HMDB0000801 Phytanic acid Phytanic acid Pparg Peroxisome proliferator-activated receptor gamma 11923221 Nuclear Receptor 434 | 431 444 HMDB0005079 15-Deoxy-d-12,14-PGJ2 15-Deoxy-d-12,14-PGJ2 Pparg Peroxisome proliferator-activated receptor gamma 20615454 Nuclear Receptor 435 | -------------------------------------------------------------------------------- /data/scFEA/Human_M168_information.symbols.csv: -------------------------------------------------------------------------------- 1 | "","Module_id","Compound_IN_name","Compound_IN_ID","Compound_OUT_name","Compound_OUT_ID","Supermodule_id" 2 | "M_1",1,"Glucose","C00267","G6P","C00668",1 3 | "M_2",2,"G6P","C00668","G3P","C00118",1 4 | "M_3",3,"G3P","C00118","3PD","C00197",1 5 | "M_4",4,"3PD","C00197","Pyruvate","C00022",1 6 | "M_5",5,"Pyruvate","C00022","Acetyl-Coa","C00024",1 7 | "M_6",6,"Pyruvate","C00022","Lactate","C00256",1 8 | "M_7",7,"Acetyl-CoA+Oxaloacetate","C00024+C00036","Citrate","C00158",1 9 | "M_8",8,"Citrate","C00158","2OG","C00026",1 10 | "M_9",9,"2OG","C00026","Succinyl-CoA","C00091",1 11 | "M_10",10,"Succinyl-CoA","C00091","Succinate","C00042",1 12 | "M_11",11,"Succinate","C00042","Fumarate","C00122",1 13 | "M_12",12,"Fumarate","C00122","Malate","C00149",1 14 | "M_13",13,"Malate","C00149","Oxaloacetate","C00036",1 15 | "M_14",14,"Pyruvate","C00022","Oxaloacetate","C00036",1 16 | "M_15",15,"3PD","C00197","Serine","C00065",2 17 | "M_16",16,"Serine","C00065","Pyruvate","C00022",2 18 | "M_17",17,"Serine","C00065","Cysteine","C00097",2 19 | "M_18",18,"Serine","C00065","Glycine","C00037",2 20 | "M_19",19,"Glycine","C00037","Creatine","C00300",2 21 | "M_20",20,"Glycine","C00037","Glyoxylate","C00048",2 22 | "M_21",21,"Choline","C00114","Glycine","C00037",2 23 | "M_22",22,"Glycine","C00037","Glycine-OUT","C00000",2 24 | "M_23",23,"Glycine","C00037","Glutathione","C00051",2 25 | "M_24",24,"Glutathione","C00051","Glycine + Cysteine","C00037+C00097",2 26 | "M_25",25,"Glutathione","C00051","glutamate","C00025",2 27 | "M_26",26,"Glutamate + Cysteine","C00025+C00097","Glutathione","C00051",2 28 | "M_27",27,"Serine","C00065","2-Aminoacrylate","C02218",2 29 | "M_28",28,"Serine","C00065","Methionine","C00073",2 30 | "M_29",29,"Cysteine","C00097","Pyruvate","C00022",2 31 | "M_30",30,"Methionine","C00073","Cysteine","C00097",2 32 | "M_31",31,"Methionine","C00073","Methionine-OUT","C00000",2 33 | "M_32",32,"Threonine","C00188","Propanoyl-CoA","C00100",2 34 | "M_33",33,"G3P","C00118","PRPP","C00119",3 35 | "M_34",34,"Acetyl-CoA","C00024","Fatty Acid","CC0001",4 36 | "M_35",35,"Fatty Acid","CC0001","Acetyl-CoA","C00024",4 37 | "M_36",36,"Aspartate","C00049","Pyrimidine","CC0002",5 38 | "M_37",37,"Aspartate","C00049","Aspartate-OUT","C00000",5 39 | "M_38",38,"Aspartate","C00049","Asparagine","C00152",5 40 | "M_39",39,"Aspartate","C00049","Fumarate","C00122",5 41 | "M_40",40,"Aspartate","C00049","Oxaloacetate","C00036",5 42 | "M_41",41,"Aspartate","C00049","B-Alanine","C00099",6 43 | "M_42",42,"Spermine","C00750","B-Alanine","C00099",6 44 | "M_43",43,"Histidine","C00135","B-Alanine","C00099",6 45 | "M_44",44,"B-Alanine","C00099","Acetyl-CoA","C00024",6 46 | "M_45",45,"Pyrimidine","CC0002","B-Alanine","C00099",6 47 | "M_46",46,"Propanoyl-CoA","C00100","Succinate","C00042",7 48 | "M_47",47,"Propanoyl-CoA","C00100","Acetyl-CoA","C00024",7 49 | "M_48",48,"Glutamate","C00025","Glutamine","C00064",8 50 | "M_49",49,"Glutamate","C00025","GABA","C00334",8 51 | "M_50",50,"GABA","C00334","Succinate","C00042",8 52 | "M_51",51,"Glutamate","C00025","2OG","C00026",8 53 | "M_52",52,"Histidine","C00135","glutamate","C00025",8 54 | "M_53",53,"Leucine","C00123","Acetyl-CoA","C00024",9 55 | "M_54",54,"Valine","C00183","Succinyl-CoA","C00091",9 56 | "M_55",55,"Isoleucine","C00407","Succinyl-CoA","C00091",9 57 | "M_56",56,"Isoleucine","C00407","Acetyl-CoA","C00024",9 58 | "M_57",57,"Tyrosine","C00082","Fumarate","C00122",9 59 | "M_58",58,"Tyrosine","C00082","Tyrosine-OUT","C00000",9 60 | "M_59",59,"Phenylalanine","C00079","Tyrosine","C00082",9 61 | "M_60",60,"lysine","C00047","Acetyl-CoA","C00024",9 62 | "M_61",61,"Putrescine","C00134","GABA","C00334",10 63 | "M_62",62,"Ornithine","C00077","Putrescine","C00134",10 64 | "M_63",63,"Arginine","C00062","Ornithine","C00077",10 65 | "M_64",64,"Arginine","C00062","Putrescine","C00134",10 66 | "M_65",65,"Argininosuccinate","C03406","Arginine + Fumarate","C00062+C00122",10 67 | "M_66",66,"Citruline + Aspartate","C00327+C00049","Argininosuccinate","C03406",10 68 | "M_67",67,"Ornithine","C00077","Proline","C00148",10 69 | "M_68",68,"Proline","C00148","Glyoxylate + pyruvate","C00048+C00022",10 70 | "M_69",69,"Putresine","C00134","Spermine","C00750",11 71 | "M_70",70,"Methionine","C00073","Spermine","C00750",11 72 | "M_71",71,"Glucose_in","C00000","Glucose","C00267",12 73 | "M_72",72,"Acetyl-CoA_in","C00000","Acetyl-CoA","C00024",12 74 | "M_73",73,"Citrate_in","C00000","Citrate","C00158",12 75 | "M_74",74,"2OG_in","C00000","2OG","C00026",12 76 | "M_75",75,"Succinate_in","C00000","Succinate","C00042",12 77 | "M_76",76,"Malate_in","C00000","Malate","C00149",12 78 | "M_77",77,"Oxaloacetate_in","C00000","Oxaloacetate","C00036",12 79 | "M_78",78,"Lactate","C00256","Lactate_out","C00000",12 80 | "M_79",79,"serine_in","C00000","serine","C00065",12 81 | "M_80",80,"Cysteine_in","C00000","Cysteine","C00097",12 82 | "M_81",81,"Glycine_in","C00000","Glycine","C00037",12 83 | "M_83",83,"Choline_in","C00000","Choline","C00114",12 84 | "M_84",84,"Threonine_in","C00000","Threonine","C00188",12 85 | "M_85",85,"Aspartate_in","C00000","Aspartate","C00049",12 86 | "M_87",87,"Pyrimidine_in","C00000","Pyrimidine","CC0002",12 87 | "M_88",88,"Histidine_in","C00000","Histidine","C00135",12 88 | "M_89",89,"B-Alanine_in","C00000","B-Alanine","C00099",12 89 | "M_90",90,"Propanoyl-CoA_in","C00000","Propanoyl-CoA","C00100",12 90 | "M_91",91,"glutamate_in","C00000","glutamate","C00025",12 91 | "M_92",92,"Glutamine_in","C00000","Glutamine","C00064",12 92 | "M_93",93,"GABA_in","C00000","GABA","C00334",12 93 | "M_94",94,"Tyrosine_in","C00000","Tyrosine","C00082",12 94 | "M_95",95,"phenylalanine_in","C00000","phenylalanine","C00079",12 95 | "M_96",96,"Valine_in","C00000","Valine","C00183",12 96 | "M_97",97,"Isoleucine_in","C00000","Isoleucine","C00407",12 97 | "M_98",98,"Leucine_in","C00000","Leucine","C00123",12 98 | "M_99",99,"Lysine_in","C00000","Lysine","C00047",12 99 | "M_100",100,"Arginine","C00000","Arginine","C00062",12 100 | "M_101",101,"Citrulline_in","C00000","Citrulline","C00327",12 101 | "M_102",102,"Ornithine_in","C00000","Ornithine","C00077",12 102 | "M_103",103,"Proline_in","C00000","Proline","C00148",12 103 | "M_105",105,"Fatty Acid_in","C00000","Fatty Acid","CC0001",12 104 | "M_106",106,"Glucose","C00267","Glucose-6-phosphate","C00668",13 105 | "M_107",107,"Glucose-6-phosphate","C00668","UDP-N-acetylglucosamine","C00043",13 106 | "M_108",108,"Glucose-6-phosphate","C00668","Glucose-1-phosphate","C00103",13 107 | "M_109",109,"Glucose-1-phosphate","C00103","UDP-glucuronic acid","C00167",13 108 | "M_110",110,"UDP-glucuronic acid+UDP-N-acetylglucosamine","C00167+C00043","Hyaluronic acid","C00518",13 109 | "M_111",111,"Glucose-1-phosphate","C00103","Glycogen","C00182",14 110 | "M_112",112,"UDP-N-acetylglucosamine","C00043","CMP-N-acetylneuraminate","C00128",15 111 | "M_113",113,"Acetyl-CoA","C00024","(E,E)-Farnesyl-PP","C00448",16 112 | "M_114",114,"(E,E)-Farnesyl-PP","C00448","Geranylgeranyl-PP","C00353",16 113 | "M_115",115,"(E,E)-Farnesyl-PP","C00448","Farnesal","C03461",16 114 | "M_116",116,"(E,E)-Farnesyl-PP","C00448","Ubiquinone","C00399",16 115 | "M_117",117,"(E,E)-Farnesyl-PP","C00448","Dolichyl phosphate","C00110",16 116 | "M_118",118,"Dolichyl phosphate","C00110","Dolichyl phosphate D-mannose","C03862",16 117 | "M_119",119,"Dolichyl phosphate","C00110","(GlcNAc)4 (Man)3 (Asn)1","G00015",16 118 | "M_120",120,"(Glc)3 (GlcNAc)2 (Man)9 (PP-Dol)1+Protein asparagine","G00008+C03021","(Glc)3 (GlcNAc)2 (Man)9 (Asn)1","G00009",16 119 | "M_121",121,"(Glc)3 (GlcNAc)2 (Man)9 (Asn)1","G00009","(GlcNAc)4 (Man)3 (Asn)1","G00015",16 120 | "M_122",122,"(GlcNAc)4 (Man)3 (Asn)1","G00015","(Gal)2 (GlcNAc)4 (LFuc)1 (Man)3 (Neu5Ac)2 (Asn)1","G00018",16 121 | "M_123",123,"(GlcNAc)4 (Man)3 (Asn)1","G00015","(GlcNAc)7 (Man)3 (Asn)1","G00022",16 122 | "M_124",124,"(GlcNAc)4 (Man)3 (Asn)1","G00015","(GlcNAc)5 (Man)3 (Asn)1","G00019",16 123 | "M_125",125,"Dolichyl phosphate D-mannose+Protein serine","C03862+C02189","(Gal)1 (GlcNAc)1 (Man)1 (Ser/Thr)1","G13084",17 124 | "M_126",126,"(Gal)1 (GlcNAc)1 (Man)1 (Ser/Thr)1","G13084","(Gal)1 (GlcNAc)1 (Man)1 (Neu5Ac)1 (Ser/Thr)1","G13085",17 125 | "M_127",127,"(Gal)1 (GlcNAc)1 (Man)1 (Ser/Thr)1","G13084","(Gal)1 (GlcA)1 (GlcNAc)1 (Man)1 (S)1 (Ser/Thr)1","G13088",17 126 | "M_128",128,"(Gal)1 (GlcNAc)1 (Man)1 (Ser/Thr)1","G13084","(Gal)1 (GlcNAc)1 (LFuc)1 (Man)1 (Ser/Thr)1","G13100",17 127 | "M_129",129,"Protein serine","C02189","(Gal)2 (GlcA)1 (Xyl)1 (Ser)1","G00157",18 128 | "M_130",130,"(Gal)2 (GlcA)1 (Xyl)1 (Ser)1","G00157","Chondroitin","C00401",18 129 | "M_131",131,"Chondroitin","C00401","Dermatan","C01490",18 130 | "M_132",132,"(Gal)2 (GlcA)1 (Xyl)1 (Ser)1","G00157","(Gal)2 (GlcA)2 (GlcNAc)2 (Xyl)1 (Ser)1","G00164",19 131 | "M_133",133,"PRPP+Glutamine","C00119+C00064","IMP","C00130",20 132 | "M_134",134,"5-Phosphoribosylamine","C03090","AICAR","C04677",20 133 | "M_135",135,"AICAR","C04677","IMP","C00130",20 134 | "M_136",136,"IMP","C00130","AMP","C00020",20 135 | "M_137",137,"IMP","C00130","XMP","C00655",20 136 | "M_138",138,"AMP","C00020","Deoxyadenosine","C00559",20 137 | "M_139",139,"AMP","C00020","Adenine","C00147",20 138 | "M_140",140,"ADP","C00008","Deoxyadenosine","C00559",20 139 | "M_141",141,"Deoxyadenosine","C00559","Adenine","C00147",20 140 | "M_142",142,"Deoxyadenosine","C00559","Hypoxanthine","C00262",20 141 | "M_143",143,"IMP","C00130","Hypoxanthine","C00262",20 142 | "M_144",144,"Hypoxanthine","C00262","Xanthine","C00385",20 143 | "M_145",145,"XMP","C00655","Xanthine","C00385",20 144 | "M_146",146,"Xanthine","C00385","Uric acid","C00366",20 145 | "M_147",147,"Xanthine","C00385","Guanine","C00242",20 146 | "M_148",148,"XMP","C00655","Guanine","C00242",20 147 | "M_149",149,"GMP","C00144","Guanine","C00242",20 148 | "M_150",150,"PRPP","C00119","UMP","C00105",21 149 | "M_151",151,"Orotidylic acid","C01103","UMP","C00105",21 150 | "M_152",152,"UMP","C00105","B-Alanine","C00099",21 151 | "M_153",153,"UMP","C00105","CDP","C00112",21 152 | "M_154",154,"Uracil","C00106","B-Alanine","C00099",21 153 | "M_155",155,"UTP","C00075","CDP","C00112",21 154 | "M_156",156,"CDP","C00112","Cytidine","C00475",21 155 | "M_157",157,"CDP","C00112","dCDP","C00705",21 156 | "M_158",158,"dCDP","C00705","Deoxycytidine","C00881",21 157 | "M_159",159,"dCMP","C00239","Deoxycytidine","C00881",21 158 | "M_160",160,"dCDP","C00705","dUMP","C00365",21 159 | "M_161",161,"dCDP","C00705","dCTP","C00458",21 160 | "M_162",162,"dUMP","C00365","Deoxyuridine","C00526",21 161 | "M_163",163,"dUMP","C00365","dTMP","C00364",21 162 | "M_164",164,"dTMP","C00364","Succinyl-CoA","C00091",21 163 | "M_165",165,"dTMP","C00364","dTTP","C00459",21 164 | "M_166",166,"Thymine","C00178","Succinyl-CoA","C00091",21 165 | "M_167",167,"(E,E)-Farnesyl-PP","C00448","Cholesterol","C00187",22 166 | "M_168",168,"Cholesterol","C00187","Chenodeoxycholate","C02528",22 167 | "M_169",169,"Cholesterol","C00187"," Steroid_hormone","CC0003",22 168 | "M_170",170,"XMP","C00655","GMP","C00144",20 169 | "M_171",171,"dCDP","C00705","dCMP","C00239",21 170 | -------------------------------------------------------------------------------- /images/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/images/.DS_Store -------------------------------------------------------------------------------- /images/Mebocost_update.png: 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-------------------------------------------------------------------------------- 1 | [common] 2 | hmdb_info_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/mebocost_db/common/metabolite_annotation_HMDB_summary.tsv 3 | scfea_info_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/scFEA/Human_M168_information.symbols.csv 4 | compass_rxt_ann_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/Compass/rxn_md.csv 5 | compass_met_ann_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/Compass/met_md.csv 6 | 7 | [human] 8 | met_enzyme_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/mebocost_db/human/metabolite_associated_gene_reaction_HMDB_summary.tsv 9 | met_sensor_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/mebocost_db/human/met_sen_October-25-2022_14-52-47.tsv 10 | 11 | [mouse] 12 | met_enzyme_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/mebocost_db/mouse/metabolite_associated_gene_reaction_HMDB_summary_mouse.tsv 13 | met_sensor_path = /Users/rongbinzheng/Documents/BCH/ChenLab/Metabolism/MEBOCOST_Verisons/v1.0.4/MEBOCOST/data/mebocost_db/mouse/mouse_met_sen_October-25-2022_14-52-47.tsv 14 | 15 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | configparser 2 | scanpy~=1.10.1 3 | adjustText~=1.1.1 4 | matplotlib~=3.8.4 5 | networkx~=3.3 6 | scikit-learn~=1.4.2 7 | scipy~=1.13.0 8 | seaborn~=0.13.2 9 | statsmodels~=0.14.2 10 | pandas~=2.2.2 11 | numpy~=1.26.4 12 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """lisa: a bioinformatics software 2 | epigenome analysis to rank TFs from gene set 3 | """ 4 | import os 5 | import setuptools 6 | import configparser 7 | 8 | def _make_config(conf_path, workdir=os.getcwd()): 9 | """ 10 | read config file 11 | """ 12 | #read config 13 | cf = configparser.ConfigParser() 14 | cf.read(conf_path) 15 | config = cf._sections 16 | # remove the annotation: 17 | for firstLevel in config.keys(): 18 | for secondLevel in config[firstLevel]: 19 | if '#' in config[firstLevel][secondLevel]: 20 | path = config[firstLevel][secondLevel][:config[firstLevel][secondLevel].index('#')-1].rstrip() 21 | config[firstLevel][secondLevel] = os.path.join(workdir, path) 22 | else: 23 | path = config[firstLevel][secondLevel] 24 | config[firstLevel][secondLevel] = os.path.join(workdir, path) 25 | ## re-write 26 | cf_new = configparser.ConfigParser() 27 | for firstLevel in config.keys(): 28 | cf_new.add_section(firstLevel) 29 | for secondLevel in config[firstLevel]: 30 | cf_new.set(firstLevel, secondLevel, config[firstLevel][secondLevel]) 31 | with open('mebocost.conf', 'w') as f: 32 | cf.write(f) 33 | return(config) 34 | 35 | ## setup 36 | def main(): 37 | setuptools.setup(name="mebocost", 38 | version="1.0.4", 39 | description="a python-based method to predict metabolite mediated cell-cell communication", 40 | author='Rongbin Zheng, Kaifu Chen', 41 | author_email='Rongbin.Zheng@childrens.harvard.edu', 42 | url='https://openwetware.org/wiki/Chenlab', 43 | # scripts=glob('mebocost/*'), 44 | zip_safe=True, 45 | package_dir={"": "src"}, 46 | packages=setuptools.find_packages(where="src"), 47 | classifiers=[ 48 | 'Environment::Console', 49 | 'Operating System:: POSIX', 50 | "Programming Language :: Python :: 3.12", 51 | "Topic :: Scientific/Engineering :: Bio-Informatics"], 52 | keywords='Metabolism', 53 | license='OTHER' 54 | ) 55 | if __name__ == '__main__': 56 | ## change mebocost.conf to absolute path 57 | _make_config(conf_path = './src/mebocost.conf') 58 | ## setup 59 | main() 60 | -------------------------------------------------------------------------------- /src/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/src/.DS_Store -------------------------------------------------------------------------------- /src/mebocost.conf: -------------------------------------------------------------------------------- 1 | [common] 2 | hmdb_info_path = data/mebocost_db/common/metabolite_annotation_HMDB_summary.tsv 3 | scfea_info_path = data/scFEA/Human_M168_information.symbols.csv 4 | compass_rxt_ann_path = data/Compass/rxn_md.csv 5 | compass_met_ann_path = data/Compass/met_md.csv 6 | 7 | [human] 8 | met_enzyme_path = data/mebocost_db/human/metabolite_associated_gene_reaction_HMDB_summary.tsv 9 | met_sensor_path = data/mebocost_db/human/met_sen_October-25-2022_14-52-47.tsv 10 | 11 | [mouse] 12 | met_enzyme_path = data/mebocost_db/mouse/metabolite_associated_gene_reaction_HMDB_summary_mouse.tsv 13 | met_sensor_path = data/mebocost_db/mouse/mouse_met_sen_October-25-2022_14-52-47.tsv -------------------------------------------------------------------------------- /src/mebocost/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/src/mebocost/.DS_Store -------------------------------------------------------------------------------- /src/mebocost/MetEstimator.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | # ================================ 4 | # @auther: Rongbin Zheng 5 | # @email: Rongbin.Zheng@childrens.harvard.edu 6 | # @date: May 2024 7 | # ================================ 8 | 9 | import os,sys 10 | import pandas as pd 11 | import numpy as np 12 | import json 13 | import pickle as pk 14 | import collections 15 | import scanpy as sc 16 | from scipy.stats.mstats import gmean 17 | from datetime import datetime 18 | from scipy import sparse 19 | 20 | 21 | """ 22 | aggregate metabolite enzyme level from single cell, three ways can be used: 23 | 1) scFEA, a published software, analyzed cell-wise flux and metabolite balance 24 | 2) Compass, a published software, predicted cell-wise reaction flux, uptake, and secretion 25 | 3) estimate aggregate metabolite enzyme level using expression of enzymes related to metabolic reactions 26 | """ 27 | 28 | def info(string): 29 | """ 30 | print information 31 | """ 32 | today = datetime.today().strftime("%B %d, %Y") 33 | now = datetime.now().strftime("%H:%M:%S") 34 | current_time = today + ' ' + now 35 | print("[{}]: {}".format(current_time, string)) 36 | 37 | 38 | 39 | ## scFEA-flux 40 | def _scFEA_flux_est_(scFEA_pred, scFEA_info, hmdb_info): 41 | """ 42 | This function can summarize metabolite relative flux taking scFEA flux rate result as input 43 | 44 | Params 45 | ------ 46 | scFEA_pred 47 | a data frame, rows are cells, columns are metabolite modules in scFEA 48 | scFEA_info 49 | a data frame, the metabolite annotation file, can be found in scFEA database in github at https://github.com/changwn/scFEA/blob/master/data/Human_M168_information.symbols.csv 50 | hmdb_info 51 | a data frame, summarized metabolite annotation information, here needs metabolite HMDB id and KEGG compund id in the columns named as HMDB_ID and Kegg_ID, respectively 52 | 53 | Returns 54 | ------ 55 | Returns a data frame, the columns are cells, rows are metabolite HMDB id, value indicates the estimated metabolite abundance 56 | 57 | """ 58 | ## the scFEA flux result predicts flux rate in module (reaction) 59 | ## prepare scFEA in and out module 60 | met_m_out = pd.Series() 61 | met_m_in = pd.Series() 62 | for i, line in scFEA_info.iterrows(): 63 | m_out = line['Compound_OUT_ID'].split('+') 64 | m_in = line['Compound_IN_ID'].split('+') 65 | for m in m_out: ## out module 66 | if m in met_m_out: 67 | met_m_out[m] += '; '+i 68 | else: 69 | met_m_out[m] = i 70 | for m in m_in: ## in module 71 | if m in met_m_in: 72 | met_m_in[m] += '; '+i 73 | else: 74 | met_m_in[m] = i 75 | ## summarized module flux to metabolite level 76 | met_summ = {} 77 | ma = list(set(met_m_in.index.tolist()) & set(met_m_out.index.tolist())) ## all modules for iterate 78 | for m in ma: 79 | m_out = list(set(met_m_out[m].split('; ')) & set(scFEA_pred.columns.tolist())) ## interect with scFEA result 80 | m_in = list(set(met_m_in[m].split('; ')) & set(scFEA_pred.columns.tolist())) 81 | m_level = pd.Series() 82 | if m_out: 83 | m_level = scFEA_pred[m_out].T.sum() 84 | if m_in: 85 | m_level -= scFEA_pred[m_in].T.sum() 86 | if len(m_level) != 0: 87 | met_summ[m] = m_level 88 | met_summ = pd.DataFrame(met_summ) ## the estimated metabolite matrix, cell x met (kegg_id) 89 | ## we use hmdb id as accession, so match to that 90 | kegg_id_hmdb = {} 91 | for k, h in hmdb_info[['HMDB_ID', 'Kegg_ID']].values.tolist(): 92 | kegg_id_hmdb[k] = h 93 | ## rename met_summ matrix by hmdb id 94 | met_summ = met_summ.loc[:,met_summ.columns.isin(kegg_id_hmdb.keys())].T 95 | # met_summ.columns = [kegg_id_hmdb.get(x) for x in met_summ.columns.tolist()()] 96 | ## transpose 97 | indexer = [kegg_id_hmdb.get(x) for x in met_summ.columns.tolist()()] 98 | columns = met_summ.columns 99 | met_summ = sparse.csc_matrix(met_summ) 100 | return(met_summ, indexer, columns) 101 | 102 | ## scFEA-balance 103 | def _scFEA_balance_est_(scFEA_pred, scFEA_info, hmdb_info): 104 | """ 105 | scFEA predicts metabolite balance result, usually the rows are cells, columns are metabolite name, 106 | this function can match the metabolite name to HMDB id which is the unique accession here 107 | 108 | Params 109 | ----- 110 | scFEA_pred 111 | a data frame, rows are cells, columns are metabolite names in scFEA 112 | scFEA_info 113 | a data frame, the metabolite annotation file, can be found in scFEA database in github at https://github.com/changwn/scFEA/blob/master/data/Human_M168_information.symbols.csv 114 | hmdb_info 115 | a data frame, summarized metabolite annotation information, here needs metabolite HMDB id and KEGG compund id in the columns named as HMDB_ID and Kegg_ID, respectively 116 | 117 | Return 118 | ----- 119 | Returns a data frame, columns are cells, rows are metabolite HMDB id 120 | 121 | """ 122 | ## metabolite name to kegg compound id in scFEA info 123 | met_to_kegg = {} 124 | for i, line in scFEA_info.iterrows(): 125 | metabolite = line['Compound_OUT_name'].split(' + ') 126 | kegg_id = line['Compound_OUT_ID'].split('+') 127 | for x in range(len(kegg_id)): 128 | met_to_kegg[metabolite[x].strip().upper()] = kegg_id[x] 129 | ## kegg compound id to HMDB id 130 | kegg_id_hmdb = {} 131 | for k, h in hmdb_info[['HMDB_ID', 'Kegg_ID']].values.tolist(): 132 | kegg_id_hmdb[k] = h 133 | ## rename column name for scFEA pred to kegg id 134 | scFEA_pred.columns = scFEA_pred.columns.str.upper() 135 | scFEA_pred = scFEA_pred.loc[:,scFEA_pred.columns.isin(met_to_kegg.keys())] 136 | scFEA_pred.columns = [met_to_kegg.get(x) for x in scFEA_pred.columns.tolist()] 137 | ## renamce kegg id to hmdb id 138 | scFEA_pred = scFEA_pred.loc[:, scFEA_pred.columns.isin(kegg_id_hmdb.keys())].T 139 | # scFEA_pred.columns = [kegg_id_hmdb.get(x) for x in scFEA_pred.columns.tolist()()] 140 | ## transpose 141 | indexer = [kegg_id_hmdb.get(x) for x in scFEA_pred.columns.tolist()()] 142 | columns = scFEA_pred.columns 143 | scFEA_pred = sparse.csc_matrix(scFEA_pred) 144 | return(scFEA_pred) 145 | 146 | ## Compass-reaction 147 | def _compass_react_est_(compass_pred, compass_react_ann, compass_met_ann, hmdb_info): 148 | """ 149 | Compass predicts metabolic reaction flux, usually rows are reactions (pos and neg), columns are cells 150 | this function can estimate metabolite relative abundance based on the reaction happening predicted by Compass 151 | 152 | Params 153 | ----- 154 | compass_pred 155 | a data frame, output from Compass software, rows are reactions, columns are cells 156 | compass_react_ann 157 | a data frame, containing reaction annotation of Compass used, can be found at https://github.com/YosefLab/Compass/blob/master/compass/Resources/Recon2_export/rxn_md.csv 158 | compass_met_ann 159 | a data frame, containing metabolite annotation of Compass used, can be found at https://github.com/YosefLab/Compass/blob/master/compass/Resources/Recon2_export/met_md.csv 160 | hmdb_info 161 | a data frame, summarized metabolite annotation information, here needs metabolite HMDB primary id and secondary id in the columns named as HMDB_ID and Secondary_HMDB_ID, respectively 162 | 163 | Return 164 | ----- 165 | Returns a data frame, columns are cells, rows are metabolite HMDB id 166 | """ 167 | ## Compass reaction predicts flux for reaction happening in positive or negative (reverse) 168 | ## separate pos and neg flux, the met level could be the difference between pos and neg 169 | compass_pred_pos = compass_pred.loc[compass_pred.index.str.endswith('_pos'),:] 170 | compass_pred_pos.index = compass_pred.index.str.replace('_pos', '') 171 | compass_pred_neg = compass_pred.loc[compass_pred.index.str.endswith('_neg'),:] 172 | compass_pred_neg.index = compass_pred.index.str.replace('_neg', '') 173 | 174 | ## get in and out met based on reaction formula in compass 175 | compass_met_re_in = {} 176 | compass_met_re_out = {} 177 | for i, line in compass_react_ann.iterrows(): 178 | in_ms = line['rxn_formula'].split(' --> ')[0].split(' + ') 179 | in_ms = list(set([j.split(' [')[0].split(' * ')[-1].strip() for j in in_ms])) 180 | out_ms = line['rxn_formula'].split(' --> ')[-1].replace('\nNo genes', '').split(' + ') 181 | out_ms = list(set([j.split(' [')[0].split(' * ')[-1].strip() for j in out_ms])) 182 | for m in in_ms: 183 | if m in compass_met_re_in: 184 | compass_met_re_in[m] += '; '+i 185 | else: 186 | compass_met_re_in[m] = i 187 | for m in out_ms: 188 | if m in compass_met_re_out: 189 | compass_met_re_out[m] += '; '+i 190 | else: 191 | compass_met_re_out[m] = i 192 | ## estimate met level from reaction 193 | ## four situiations for a met in reaction direction 194 | ## cases: in-pos, in-neg, out-pos, out-neg 195 | ## wights: -1, +1, +1, -1 196 | met_all = list(set(list(compass_met_re_in.keys())+list(compass_met_re_out.keys()))) 197 | met_from_react = {} 198 | for m in met_all: 199 | ## reaction of in met 200 | m_in_r = compass_met_re_in[m].split('; ') if m in compass_met_re_in else [] 201 | ## positive flux for in met 202 | m_in_r_pos = list(set(m_in_r) & set(compass_pred_pos.index.tolist())) 203 | m_in_r_neg = list(set(m_in_r) & set(compass_pred_neg.index.tolist())) 204 | ## reaction of out met 205 | m_out_r = compass_met_re_out[m].split('; ') if m in compass_met_re_out else [] 206 | ## positive flux of out met 207 | m_out_r_pos = list(set(m_out_r) & set(compass_pred_pos.index.tolist())) 208 | m_out_r_neg = list(set(m_out_r) & set(compass_pred_neg.index.tolist())) 209 | ## 210 | met_level = pd.Series() 211 | if m_out_r_pos: 212 | met_level = compass_pred_pos.loc[m_out_r_pos,:].sum() ## +1 for out-pos 213 | if m_in_r_neg: 214 | met_level += compass_pred_neg.loc[m_in_r_neg,:].sum() ## +1 for in-neg 215 | if m_in_r_pos: 216 | met_level -= compass_pred_pos.loc[m_in_r_pos,:].sum() ## -1 for in-pos 217 | if m_out_r_neg: 218 | met_level -= compass_pred_neg.loc[m_out_r_neg,:].sum() ## -1 for out-neg 219 | if len(met_level) != 0: 220 | met_from_react[m] = met_level 221 | met_from_react = pd.DataFrame(met_from_react) ## the estimated met matrix, rows are cells, columns are met 222 | ## rename metabolite name to HMDB id 223 | compass_met_ann = pd.merge(compass_met_ann, hmdb_info, left_on = 'hmdbID', right_on = 'Secondary_HMDB_ID', how = 'left') 224 | met_to_hmdbid = {} 225 | for i, line in compass_met_ann[['metName', 'HMDB_ID']].dropna().iterrows(): 226 | met, hmdbid = line['metName'], line['HMDB_ID'] 227 | met_to_hmdbid[met] = hmdbid 228 | ## rename 229 | met_from_react = met_from_react.loc[:, met_from_react.columns.isin(met_to_hmdbid.keys())].T 230 | # met_from_react.columns = [met_to_hmdbid.get(x) for x in met_from_react.columns.tolist()] 231 | ## transpose 232 | indexer = [met_to_hmdbid.get(x) for x in met_from_react.columns.tolist()] 233 | columns = met_from_react.columns 234 | met_from_react = sparse.csc_matrix(met_from_react) 235 | return(met_from_react) 236 | 237 | ## compass-uptake or compass-secretion 238 | def _compass_uptake_secrete_est_(compass_pred, compass_met_ann, hmdb_info): 239 | """ 240 | Compass software predicts uptake and secretion flux as well as reaction, such estimation can be directly used 241 | usually, it is a matrix that rows are metabolites, columns are cells 242 | 243 | Params 244 | ----- 245 | compass_pred 246 | a data frame, output from Compass software (uptake or secretion), rows are metabolite, columns are cells 247 | compass_met_ann 248 | a data frame, containing metabolite annotation of Compass used, can be found at https://github.com/YosefLab/Compass/blob/master/compass/Resources/Recon2_export/met_md.csv 249 | hmdb_info 250 | a data frame, summarized metabolite annotation information, here needs compass metabolite id and HMDB id in the columns named as met and HMDB_ID, respectively 251 | 252 | Return 253 | ----- 254 | Returns a data frame, columns are cells, rows are metabolite HMDB id 255 | """ 256 | ## rename metabolite name to HMDB id, compass_pred columns are metId in compass 257 | compass_met_ann = pd.merge(compass_met_ann, hmdb_info, left_on = 'hmdbID', right_on = 'Secondary_HMDB_ID', how = 'left') 258 | met_to_hmdbid = {} 259 | for i, line in compass_met_ann[['met', 'HMDB_ID']].dropna().iterrows(): 260 | met, hmdbid = line['met'], line['HMDB_ID'] 261 | met_to_hmdbid[met] = hmdbid 262 | ## rename 263 | compass_pred = compass_pred.loc[compass_pred.index.isin(met_to_hmdbid.keys()),:].T 264 | # compass_pred.index = [met_to_hmdbid.get(x) for x in compass_pred.index.tolist()] 265 | ## transpose 266 | indexer = [met_to_hmdbid.get(x) for x in compass_pred.index.tolist()] 267 | columns = compass_pred.columns 268 | compass_pred = sparse.csc_matrix(compass_pred) ## rows are met, columns are cells 269 | return(compass_pred) 270 | 271 | # estimate from enzyme gene expression 272 | def _met_est_input_dataframe_(exp_mat, mIdList, met_gene, method): 273 | """ 274 | expression matrix is a data frame 275 | """ 276 | met_from_gene = pd.DataFrame() 277 | with_exp_gene_m = [] ## only met-enzyme gene in the matrix can be estimated 278 | for mId in mIdList: 279 | ## genes for the reaction of producing the metabolite 280 | gene_pos = met_gene[(met_gene['HMDB_ID'] == mId) & (met_gene['direction'] == 'product')]['gene_name'].tolist() 281 | gene_pos = list(set(gene_pos) & set(exp_mat.index.tolist())) 282 | ## genes for the reaction of taking the metabolite as substrate 283 | gene_neg = met_gene[(met_gene['HMDB_ID'] == mId) & (met_gene['direction'] == 'substrate')]['gene_name'].tolist() 284 | gene_neg = list(set(gene_neg) & set(exp_mat.index.tolist())) if gene_neg else [] 285 | ## estimate by aggerating gene_pos and gene_neg 286 | ## only estimate when there are genes of positive reactons 287 | if len(gene_pos) != 0: 288 | with_exp_gene_m.append(mId) 289 | ## if neg genes, do subraction from pos genes 290 | if not gene_neg: 291 | if method == 'mean': 292 | m_from_enzyme = exp_mat.loc[exp_mat.index.isin(gene_pos),:].mean() 293 | elif method == 'median': 294 | m_from_enzyme = exp_mat.loc[exp_mat.index.isin(gene_pos),:].median() 295 | elif method == 'max': 296 | m_from_enzyme = exp_mat.loc[exp_mat.index.isin(gene_pos),:].max() 297 | elif method == 'gmean': 298 | m_from_enzyme = exp_mat.loc[exp_mat.index.isin(gene_pos),:].apply(lambda col: gmean(col)) 299 | else: 300 | raise KeyError('method error') 301 | else: 302 | if method == 'mean': 303 | pos = exp_mat.loc[exp_mat.index.isin(gene_pos),:].mean() 304 | neg = exp_mat.loc[exp_mat.index.isin(gene_neg),:].mean() 305 | elif method == 'median': 306 | pos = exp_mat.loc[exp_mat.index.isin(gene_pos),:].median() 307 | neg = exp_mat.loc[exp_mat.index.isin(gene_neg),:].median() 308 | elif method == 'max': 309 | pos = exp_mat.loc[exp_mat.index.isin(gene_pos),:].max() 310 | neg = exp_mat.loc[exp_mat.index.isin(gene_neg),:].max() 311 | elif method == 'gmean': 312 | pos = exp_mat.loc[exp_mat.index.isin(gene_pos),:].apply(lambda col: gmean(col)) 313 | neg = exp_mat.loc[exp_mat.index.isin(gene_neg),:].apply(lambda col: gmean(col)) 314 | else: 315 | raise KeyError('method error') 316 | m_from_enzyme = pos - neg 317 | met_from_gene = pd.concat([met_from_gene, 318 | m_from_enzyme], axis = 1) 319 | met_from_gene.columns = with_exp_gene_m 320 | ## tranpose 321 | met_from_gene = met_from_gene.T ## rows = metabolite (HMDB ID), columns = cells 322 | return(met_from_gene) 323 | 324 | def met_est_input_adata_(adata, mIdList, met_gene, method): 325 | """ 326 | expression data in scanpy adata object 327 | """ 328 | ## check the adata object 329 | ngene = len(adata.var_names) 330 | ncell = len(adata.obs_names) 331 | # info('We are receiving expression data with {n1} genes and {n2} cells.'.format(n1 = ngene, n2 = ncell)) 332 | # if ngene < 10000: 333 | # info('scanpy object contains less than 10000 genes, please make sure you are using raw.to_adata()') 334 | ## estimating for each met 335 | met_from_gene = pd.DataFrame() 336 | with_exp_gene_m = [] 337 | for mId in mIdList: 338 | ## genes for the reaction of producing the metabolite 339 | gene_pos = met_gene[(met_gene['HMDB_ID'] == mId) & (met_gene['direction'] == 'product')]['gene_name'].tolist() 340 | gene_pos = list(set(gene_pos) & 341 | set(adata.var_names.tolist())) 342 | ## genes for the reaction of taking the metabolite as substrate 343 | gene_neg = met_gene[(met_gene['HMDB_ID'] == mId) & (met_gene['direction'] == 'substrate')]['gene_name'].tolist() 344 | gene_neg = list(set(gene_neg) & set(adata.var_names.tolist())) if gene_neg else [] 345 | ## estimate by aggerating gene_pos and gene_neg 346 | ## only estimate when there are genes of positive reactons 347 | if len(gene_pos) != 0: 348 | with_exp_gene_m.append(mId) 349 | ## gene pos matrix 350 | pos_g_index = np.where(adata.var_names.isin(gene_pos)) 351 | pos_exp = pd.DataFrame(adata.T[pos_g_index].X.toarray(), 352 | index = adata.var_names[pos_g_index].tolist(), 353 | columns = adata.obs_names.tolist()) 354 | 355 | ## if neg genes, do subraction from pos genes 356 | if not gene_neg: 357 | if method == 'mean': 358 | m_from_enzyme = pos_exp.mean() 359 | elif method == 'median': 360 | m_from_enzyme = pos_exp.median() 361 | elif method == 'max': 362 | m_from_enzyme = pos_exp.max() 363 | elif method == 'gmean': 364 | m_from_enzyme = pos_exp.apply(lambda col: gmean(col)) 365 | else: 366 | continue 367 | else: 368 | ## gene neg matrix 369 | neg_g_index = np.where(adata.var_names.isin(gene_neg)) 370 | neg_exp = pd.DataFrame(adata.T[neg_g_index].X.toarray(), 371 | index = adata.var_names[neg_g_index].tolist(), 372 | columns = adata.obs_names.tolist()) 373 | if method == 'mean': 374 | pos = pos_exp.mean() 375 | neg = neg_exp.mean() 376 | elif method == 'median': 377 | pos = pos_exp.median() 378 | neg = neg_exp.median() 379 | elif method == 'max': 380 | pos = pos_exp.max() 381 | neg = neg_exp.max() 382 | elif method == 'gmean': 383 | pos = pos_exp.apply(lambda col: gmean(col)) 384 | neg = neg_exp.apply(lambda col: gmean(col), axis = 1) 385 | else: 386 | raise ValueError('method should be one of [mean, gmean, median, max]') 387 | m_from_enzyme = pos - neg 388 | met_from_gene = pd.concat([met_from_gene, 389 | m_from_enzyme], axis = 1) 390 | met_from_gene.columns = with_exp_gene_m 391 | ## tranpose 392 | met_from_gene = met_from_gene.T ## rows = metabolite (HMDB ID), columns = cells 393 | return(met_from_gene) 394 | 395 | 396 | def _met_from_enzyme_dataframe_adata_(exp_mat=None, adata=None, mIdList=[], met_gene=pd.DataFrame, method = 'mean'): 397 | """ 398 | This function takes expression of metabolic reaction related genes (enzyme) as input, and estimate the relative abundance of metabolite in cells, 399 | the idea is that the metabolite accumulation can be a reaction happening balance between the one of taking the metabolite as substrates and the one of producing it. 400 | 401 | Params 402 | ----- 403 | exp_mat 404 | a data frame, single cell expression matrix, rows are genes, columns are cells 405 | 'exp_mat' is exclusive parameter to 'adata' 406 | adata 407 | a scanpy adata object, the expression will be extracted from the adata to estimate metabolite level 408 | 'adata' is exclusive parameter to 'exp_mat' 409 | mIdList 410 | a list of the HMDB ID, the given HMDB ID will be estimated if there are associated genes available, such as: 411 | ['HMDB0000017', 'HMDB0000026', 'HMDB0000033', ...] 412 | met_gene 413 | a data frame, containing the curated metabolite related genes, the data frame at least includes three columns representing HMDB ID, gene, and direction (product or substrate) 414 | for example: 415 | HMDB0003944 ACOX1[Unknown] product 416 | HMDB0003944 ACOX3[Unknown] product 417 | HMDB0003944 ACADSB[Unknown] product 418 | HMDB0003944 MECR[Unknown] substrate 419 | HMDB0006529 PECR[Enzyme] substrate 420 | .... 421 | method 422 | the way to aggerate expression of metabolite related multiple genes or enzymes, should be one of [mean, gmean, median, max], 423 | mean for taking arithmetic mean, gmean for taking geomatrix mean, median for taking median value, max for taking maximum value across the genes. 424 | By default, we set mean which is arithmetic mean. 425 | 426 | 427 | Return 428 | ----- 429 | Returns a data frame, columns are cells, rows are metabolite HMDB id 430 | 431 | """ 432 | ## metabolite related genes to data frame 433 | met_gene_new = [] 434 | for i, line in met_gene.iterrows(): 435 | genes = line['gene'].split('; ') 436 | for g in genes: 437 | tmp = line.copy() 438 | tmp['gene'] = g 439 | met_gene_new.append(tmp) 440 | met_gene = pd.DataFrame(met_gene_new) ## each row is the related gene annotation for metabolite 441 | met_gene['gene_name'] = met_gene['gene'].apply(lambda x: x.split('[')[0]) 442 | if len(mIdList) == 0: 443 | mIdList = met_gene['HMDB_ID'].unique().tolist() 444 | ## check input and load right estimator 445 | if (type(exp_mat) == type(pd.DataFrame())) and (type(adata) == type(None)): 446 | info('Receiving input from a data frame') 447 | met_from_gene = _met_est_input_dataframe_(exp_mat = exp_mat, mIdList = mIdList, met_gene = met_gene, method = method) 448 | 449 | elif (type(exp_mat) == type(None)) and (type(adata) != type(None)): 450 | info('Receiving input from a scanpy adata object') 451 | try: 452 | cells = adata.obs_names 453 | genes = adata.var_names 454 | except: 455 | raise ValueError('adata prolem! cannot extract adata.obs_names or adata.var_names, may be it is not a scanpy object.') 456 | met_from_gene = met_est_input_adata_(adata = adata, mIdList = mIdList, met_gene = met_gene, method = method) 457 | else: 458 | raise ValueError('please either provide expression matrix through exp_mat or adata!') 459 | 460 | return(met_from_gene) 461 | 462 | def _met_est_input_sparse_(exp_mat, indexer, columns, mIdList, met_gene, method): 463 | """ 464 | expression matrix is a data frame 465 | """ 466 | met_from_gene = np.empty(shape=(0,len(columns))) 467 | with_exp_gene_m = [] ## only met-enzyme gene in the matrix can be estimated 468 | for mId in mIdList: 469 | ## genes for the reaction of producing the metabolite 470 | gene_pos = met_gene[(met_gene['HMDB_ID'] == mId) & (met_gene['direction'] == 'product')]['gene_name'].tolist() 471 | gene_pos_loc = [i for i, g in enumerate(indexer) if g in gene_pos] 472 | ## genes for the reaction of taking the metabolite as substrate 473 | gene_neg = met_gene[(met_gene['HMDB_ID'] == mId) & (met_gene['direction'] == 'substrate')]['gene_name'].tolist() 474 | gene_neg_loc = [i for i, g in enumerate(indexer) if g in gene_neg] if gene_neg else [] 475 | ## estimate by aggerating gene_pos and gene_neg 476 | ## only estimate when there are genes of positive reactons 477 | if len(gene_pos_loc) != 0: 478 | with_exp_gene_m.append(mId) 479 | ## if neg genes, do subraction from pos genes 480 | if not gene_neg_loc: 481 | if method == 'mean': 482 | m_from_enzyme = exp_mat[gene_pos_loc].mean(axis = 0) 483 | else: 484 | raise KeyError('method error') 485 | else: 486 | if method == 'mean': 487 | pos = exp_mat[gene_pos_loc].mean(axis = 0) 488 | neg = exp_mat[gene_neg_loc].mean(axis = 0) 489 | else: 490 | raise KeyError('method error') 491 | m_from_enzyme = pos - neg 492 | met_from_gene = np.concatenate((met_from_gene, m_from_enzyme), axis = 0) 493 | 494 | met_from_gene = sparse.csc_matrix(met_from_gene) 495 | met_indexer = with_exp_gene_m 496 | met_columns = columns.copy() 497 | return(met_from_gene, met_indexer, met_columns) 498 | 499 | 500 | def _met_from_enzyme_est_(exp_mat, indexer, columns, mIdList=[], met_gene=pd.DataFrame, method = 'mean'): 501 | """ 502 | This function takes expression of metabolic reaction related genes (enzyme) as input, and estimate the relative abundance of metabolite in cells, 503 | the idea is that the metabolite accumulation can be a reaction happening balance between the one of taking the metabolite as substrates and the one of producing it. 504 | 505 | Params 506 | ----- 507 | exp_mat 508 | a data frame, single cell expression matrix, rows are genes, columns are cells 509 | 'exp_mat' is exclusive parameter to 'adata' 510 | adata 511 | a scanpy adata object, the expression will be extracted from the adata to estimate metabolite level 512 | 'adata' is exclusive parameter to 'exp_mat' 513 | mIdList 514 | a list of the HMDB ID, the given HMDB ID will be estimated if there are associated genes available, such as: 515 | ['HMDB0000017', 'HMDB0000026', 'HMDB0000033', ...] 516 | met_gene 517 | a data frame, containing the curated metabolite related genes, the data frame at least includes three columns representing HMDB ID, gene, and direction (product or substrate) 518 | for example: 519 | HMDB0003944 ACOX1[Unknown] product 520 | HMDB0003944 ACOX3[Unknown] product 521 | HMDB0003944 ACADSB[Unknown] product 522 | HMDB0003944 MECR[Unknown] substrate 523 | HMDB0006529 PECR[Enzyme] substrate 524 | .... 525 | method 526 | the way to aggerate expression of metabolite related multiple genes or enzymes, should be one of [mean, gmean, median, max], 527 | mean for taking arithmetic mean, gmean for taking geomatrix mean, median for taking median value, max for taking maximum value across the genes. 528 | By default, we set mean which is arithmetic mean. 529 | 530 | 531 | Return 532 | ----- 533 | Returns a data frame, columns are cells, rows are metabolite HMDB id 534 | 535 | """ 536 | ## metabolite related genes to data frame 537 | met_gene_new = [] 538 | for i, line in met_gene.iterrows(): 539 | genes = line['gene'].split('; ') 540 | for g in genes: 541 | tmp = line.copy() 542 | tmp['gene'] = g 543 | met_gene_new.append(tmp) 544 | met_gene = pd.DataFrame(met_gene_new) ## each row is the related gene annotation for metabolite 545 | met_gene['gene_name'] = met_gene['gene'].apply(lambda x: x.split('[')[0]) 546 | if len(mIdList) == 0: 547 | mIdList = met_gene['HMDB_ID'].unique().tolist() 548 | 549 | met_from_gene, met_indexer, met_columns = _met_est_input_sparse_(exp_mat = exp_mat, indexer = indexer, 550 | columns = columns, mIdList = mIdList, 551 | met_gene = met_gene, method = method) 552 | 553 | return(met_from_gene, met_indexer, met_columns) 554 | 555 | 556 | 557 | 558 | 559 | 560 | -------------------------------------------------------------------------------- /src/mebocost/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kaifuchenlab/MEBOCOST/cbd154ab03d46e040cf988f6115676fde3f57336/src/mebocost/__init__.py -------------------------------------------------------------------------------- /src/mebocost/crosstalk_calculator.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | # ================================ 4 | # @auther: Rongbin Zheng 5 | # @email: Rongbin.Zheng@childrens.harvard.edu 6 | # @date: May 2024 7 | # ================================ 8 | 9 | import os,sys 10 | import time 11 | import pickle as pk 12 | from datetime import datetime 13 | import numpy as np 14 | import pandas as pd 15 | import traceback 16 | from operator import itemgetter 17 | import statsmodels 18 | from statsmodels import api as sm 19 | import scipy 20 | from scipy import sparse 21 | import collections 22 | import multiprocessing 23 | 24 | """ 25 | main functions of metabolic cross talk 26 | 27 | """ 28 | 29 | 30 | def info(string): 31 | """ 32 | print information 33 | """ 34 | today = datetime.today().strftime("%B %d, %Y") 35 | now = datetime.now().strftime("%H:%M:%S") 36 | current_time = today + ' ' + now 37 | print("[{}]: {}".format(current_time, string)) 38 | 39 | 40 | class InferComm: 41 | """ 42 | class for infering communication 43 | input at least includes: 44 | expression data of metabolite sensor 45 | estimated metabolite level in cell-wise 46 | metabolite sensor inofrmation 47 | cell annotation used for grouping cells 48 | 49 | Params 50 | ----- 51 | exp_mat 52 | data frame, expression matrix, cells in row names, genes in column names 53 | met_mat 54 | data frame, metabolite abundance matrix, cells in row names, metabolite in column names 55 | cell_ann 56 | data frame, cell annotation information, cells in row names, columns are needed annotation such as cell_group, cell_type, cluster, 57 | by default, we automatically find "cell_type" and "cluster" columns to group cells and take the average sensor expression and metabolite abundance for them 58 | met_sensor 59 | data frame, metabolite sensor information, each row is a pair of metabolite and sensor, must include columns named HMDB_ID and Gene_name, 60 | we will model the communication for each pair of metabolite and sensor 61 | group_col 62 | a list, specify the column names in 'cell_ann' for grouping cells, by default 'cell_type' and 'cluster' will be used 63 | sensor_type 64 | a list, provide a list of sensor type that will be used in the communication modeling, must be one or more from ['receptor', 'transporter', 'interacting'], default is all the three 65 | 66 | """ 67 | def __init__(self, 68 | exp_mat, 69 | exp_mat_indexer, 70 | exp_mat_columns, 71 | met_mat, 72 | met_mat_indexer, 73 | met_mat_columns, 74 | cell_ann, 75 | met_sensor, 76 | avg_exp = None, 77 | avg_exp_indexer = None, 78 | avg_exp_columns = None, 79 | avg_met = None, 80 | avg_met_indexer = None, 81 | avg_met_columns = None, 82 | sensor_type=['Receptor', 'Transporter', 'Nuclear Receptor'], 83 | thread=None 84 | ): 85 | self.exp_mat = exp_mat 86 | self.exp_mat_indexer = exp_mat_indexer 87 | self.exp_mat_columns = exp_mat_columns 88 | 89 | self.met_mat = met_mat 90 | self.met_mat_indexer = met_mat_indexer 91 | self.met_mat_columns = met_mat_columns 92 | 93 | self.cell_ann = cell_ann 94 | 95 | self.avg_exp = avg_exp 96 | self.avg_exp_indexer = avg_exp_indexer 97 | self.avg_exp_columns = avg_exp_columns 98 | 99 | self.avg_met = avg_met 100 | self.avg_met_indexer = avg_met_indexer 101 | self.avg_met_columns = avg_met_columns 102 | 103 | ## focus on the given sensor types 104 | met_sensor = met_sensor[met_sensor['Annotation'].str.upper().isin([x.upper() for x in sensor_type])] 105 | ## only focus on met and gene in the data 106 | met_sensor = met_sensor[met_sensor['Gene_name'].isin(self.exp_mat_indexer) & 107 | met_sensor['HMDB_ID'].isin(self.met_mat_indexer)] 108 | info('Sensor type used %s'%met_sensor['Annotation'].unique().tolist()) 109 | self.met_sensor = met_sensor 110 | self.thread = thread 111 | 112 | 113 | def _get_shuffled_avg_exp_(self, i): 114 | """ 115 | get averaged expression of met and gene in each permutation 116 | given i is a index of permutation 117 | """ 118 | indexer = self.shuffle_index[i] 119 | cell_label_new = np.array(self.cell_ann['cell_group'].tolist())[indexer] ## shuffling the cell labels 120 | 121 | e_avg = np.empty(shape = (self.exp_mat.shape[0],0)) ## save exp data 122 | m_avg = np.empty(shape = (self.met_mat.shape[0],0)) ## save met data 123 | 124 | for x in self.group_names: 125 | cell_indexer = np.where(cell_label_new == x)[0] 126 | e_avg = np.concatenate((e_avg, self.exp_mat[:,cell_indexer].mean(axis = 1)), axis = 1) 127 | m_avg = np.concatenate((m_avg, self.met_mat[:,cell_indexer].mean(axis = 1)), axis = 1) 128 | 129 | e_avg = sparse.csr_matrix(e_avg) 130 | m_avg = sparse.csr_matrix(m_avg) 131 | return(i, e_avg, m_avg) 132 | 133 | 134 | def _shuffling_(self, group_names, n_shuffle = 1000, seed = 12345): 135 | """ 136 | permutation to generate random backgroud 137 | """ 138 | ## intersect cells in exp_mat, met_mat, and cell_ann 139 | common_cell = sorted(list(set(self.exp_mat_columns.tolist()) & 140 | set(self.met_mat_columns.tolist()) & 141 | set(self.cell_ann.index.tolist()))) 142 | ## cell ann 143 | self.cell_ann = self.cell_ann.loc[common_cell,:] 144 | ## exp 145 | cell_index = np.where(pd.Series(self.exp_mat_columns).isin(common_cell))[0] 146 | self.exp_mat = self.exp_mat[:,cell_index] 147 | self.exp_mat_columns = self.exp_mat_columns[cell_index] 148 | ## met 149 | cell_index = np.where(pd.Series(self.met_mat_columns).isin(common_cell))[0] 150 | self.met_mat = self.met_mat[:,cell_index] 151 | self.met_mat_columns = self.met_mat_columns[cell_index] 152 | 153 | ## get index of cells in shuffling 154 | np.random.seed(seed) ## set seed for reproducible shuffling 155 | self.shuffle_index = [np.random.choice(range(len(common_cell)), 156 | len(common_cell), 157 | replace = False) for i in range(n_shuffle)] 158 | 159 | ## cell group used to take mean 160 | cell_group = self.cell_ann.reindex(index = common_cell)[['cell_group']] 161 | ## exp mat for each shuffle 162 | info('take exp and met avg for shuffling') 163 | sensor_gene_loc = np.where(pd.Series(self.exp_mat_indexer).isin(self.met_sensor['Gene_name']))[0] 164 | sensor_gene = self.exp_mat_indexer[sensor_gene_loc] 165 | 166 | self.exp_mat = self.exp_mat[sensor_gene_loc,:] 167 | self.exp_mat_indexer = self.exp_mat_indexer[sensor_gene_loc] 168 | 169 | self.perm_exp_avg = collections.defaultdict() 170 | self.perm_met_avg = collections.defaultdict() 171 | 172 | pool = multiprocessing.Pool(self.thread) 173 | perm_col = pool.map(self._get_shuffled_avg_exp_, range(len(self.shuffle_index))) 174 | pool.close() 175 | ## into dict 176 | for i, e, m in perm_col: 177 | ## i is index of permute, e is exp shuffling, m is met shuffling 178 | self.perm_exp_avg[i] = e 179 | self.perm_met_avg[i] = m 180 | 181 | self.permute_exp_indexer = np.array(sensor_gene) 182 | self.permute_exp_columns = self.group_names 183 | 184 | self.permute_met_indexer = self.met_mat_indexer 185 | self.permute_met_columns = self.group_names 186 | 187 | 188 | def _commu_score_for_one_(self, 189 | avg_exp_sensor, 190 | avg_met_met, 191 | perm_exp_avg_sensor, 192 | perm_met_avg_met, 193 | norm = None, 194 | method = 'product' 195 | ): 196 | """ 197 | given a pair of sensor and metabolite 198 | calculate the communication score for eal data using ave_exp and avg_met object 199 | and calculate the backgroud of communication score using perm_exp_avg and perm_met_avg 200 | """ 201 | ## real data 202 | sx = avg_exp_sensor.copy() 203 | mx = avg_met_met.copy() 204 | 205 | ## caculating communication score by products in pairwise cell group 206 | info('Normalizing Cluster Mean and Calculating Communication Score') 207 | norm_func = lambda x: (x - np.min(x)) / (np.max(x) - np.min(x)) if np.max(x) != np.min(x) else np.array([0]*len(x)) 208 | if norm == 'min-max': 209 | sx = norm_func(sx) 210 | mx = norm_func(mx) 211 | 212 | prod_mat = collections.defaultdict() 213 | if method == 'product': 214 | for i in range(len(self.group_names)): 215 | v = mx[i] 216 | c = self.group_names[i] 217 | ## met in one cell groups multiply all cell groups for sensor, so do pairwise 218 | prod_mat[c] = np.multiply(v, sx) 219 | elif method == 'average': 220 | for i in range(len(self.group_names)): 221 | v = mx[i] 222 | c = self.group_names[i] 223 | prod_mat[c] = np.array([np.mean([x, v]) for x in sx.tolist()]) 224 | elif method == 'product_sqrt': 225 | for i in range(len(self.group_names)): 226 | v = mx[i] 227 | c = self.group_names[i] 228 | prod_mat[c] = np.nan_to_num(np.sqrt(np.multiply(v, sx))) 229 | else: 230 | raise KeyError('scoring problem!') 231 | 232 | prod_mat = pd.DataFrame.from_dict(prod_mat, orient = 'columns') ## column = sender 233 | prod_mat.index = self.group_names ## receiver 234 | ## reshape matrix 235 | prod_mat_values = prod_mat.unstack().reset_index() 236 | # prod_mat_values = prod_mat.where(np.triu(np.ones(prod_mat.shape)).astype(np.bool_)).unstack().reset_index().dropna() 237 | prod_mat_values.columns = ['Sender', 'Receiver', 'Commu_Score'] 238 | 239 | ## background using shuffling data 240 | background = [] 241 | if norm == 'min-max': 242 | ## norm by max-min normalization 243 | perm_exp_avg_sensor = {i: norm_func(perm_exp_avg_sensor[i]) for i in perm_exp_avg_sensor} 244 | perm_met_avg_met = {i: norm_func(perm_met_avg_met[i]) for i in perm_met_avg_met} 245 | 246 | if method == 'product': 247 | for i in range(len(perm_exp_avg_sensor)): 248 | e, m = perm_exp_avg_sensor[i], perm_met_avg_met[i] 249 | background.extend([[i, self.group_names[x]]+np.multiply(m[x], e).tolist() for x in range(len(self.group_names))]) 250 | elif method == 'average': 251 | for i in range(len(perm_exp_avg_sensor)): 252 | e, m = perm_exp_avg_sensor[i], perm_met_avg_met[i] 253 | background.extend([[i, self.group_names[x]]+[np.mean([m[x], e]) for i in e.tolist()] for x in range(len(self.group_names))]) 254 | elif method == 'product_sqrt': 255 | for i in range(len(perm_exp_avg_sensor)): 256 | e, m = perm_exp_avg_sensor[i], perm_met_avg_met[i] 257 | background.extend([[i, self.group_names[x]]+np.nan_to_num(np.sqrt(np.multiply(m[x], e))).tolist() for x in range(len(self.group_names))]) 258 | else: 259 | raise KeyError('scoring problem!') 260 | 261 | background_df = pd.DataFrame(background, 262 | columns = ['N_permut', 'Sender_']+self.group_names) 263 | 264 | return prod_mat_values, background_df 265 | 266 | 267 | def cummin(self, x): 268 | """A python implementation of the cummin function in R""" 269 | for i in range(1, len(x)): 270 | if x[i-1] < x[i]: 271 | x[i] = x[i-1] 272 | return x 273 | 274 | 275 | def bh_fdr(self, pval): 276 | """A python implementation of the Benjamani-Hochberg FDR method. 277 | This code should always give precisely the same answer as using 278 | p.adjust(pval, method="BH") in R. 279 | Parameters 280 | ---------- 281 | pval : list or array 282 | list/array of p-values 283 | Returns 284 | ------- 285 | pval_adj : np.array 286 | adjusted p-values according the benjamani-hochberg method 287 | """ 288 | pval_array = np.array(pval) 289 | sorted_order = np.argsort(pval_array) 290 | original_order = np.argsort(sorted_order) 291 | pval_array = pval_array[sorted_order] 292 | 293 | # calculate the needed alpha 294 | n = float(len(pval)) 295 | pval_adj = np.zeros(int(n)) 296 | i = np.arange(1, int(n)+1, dtype=float)[::-1] # largest to smallest 297 | pval_adj = np.minimum(1, self.cummin(n/i * pval_array[::-1]))[::-1] 298 | return pval_adj[original_order] 299 | 300 | def _fdr_(self, 301 | pvalue_res, 302 | testing_method = ['ztest', 'ttest', 'ranksum_test', 'permutation_test']): 303 | """ 304 | calculate FDR correction 305 | """ 306 | pvalue_res = pvalue_res.fillna(1) ## if NA 307 | for method in testing_method: 308 | fdr = self.bh_fdr(pvalue_res[method+'_pval']) 309 | pvalue_res[method+'_fdr'] = fdr 310 | del fdr 311 | return(pvalue_res) 312 | 313 | 314 | def _testing_(self, real_score, bg_values, method = 'ztest'): 315 | """ 316 | run hypothesis testing 317 | real_score: the observed value 318 | bg_value: a array-like or list of background value 319 | """ 320 | stat, pval = 0, 1 321 | if method == 'ztest': 322 | stat, pval = sm.stats.ztest(bg_values, 323 | value = real_score, 324 | alternative = "smaller") 325 | elif method == 'ttest': 326 | stat, pval, df = sm.stats.ttest_ind(x1 = bg_values, 327 | x2 = [real_score], 328 | alternative = "smaller") 329 | elif method == 'ranksum_test': 330 | stat, pval = scipy.stats.ranksums(x = bg_values, y = [real_score], alternative='less') 331 | # elif method == 'sign_test': 332 | # stat, pval = statsmodels.stats.descriptivestats.sign_test(bg_values, real_score) 333 | elif method == 'permutation_test': 334 | bg_larger = 0 335 | for i in bg_values: 336 | if i > real_score: 337 | bg_larger += 1 338 | stat, pval = bg_larger, bg_larger / len(bg_values) 339 | else: 340 | info('+++ unknown testing') 341 | return(stat, pval) 342 | 343 | def _signif_test_(self, commu_mat, background_df): 344 | """ 345 | different statistical testing was used to evaluate the significance of observed communication score in background 346 | --------- 347 | """ 348 | info('Calculating P-value') 349 | testing_method = ['ztest', 'ttest', 'ranksum_test', 'permutation_test'] 350 | pvalue_res = [] 351 | for n, iteract in commu_mat.sort_values('Commu_Score', ascending = False).iterrows(): 352 | sender, receiver, real_score = iteract.tolist() 353 | bg_values = background_df[background_df['Sender_']==sender][receiver] 354 | ## z test to be used to compare population means to a sample's 355 | ## null hypothesis: mean of background is far more samller than observation 356 | testing_res = iteract.copy() 357 | testing_res['bg_mean'] = bg_values.mean() 358 | testing_res['bg_std'] = bg_values.std() 359 | # if testing_res['bg_mean'] != 0: 360 | # testing_res['Norm_Commu_Score'] = testing_res['Commu_Score'] / testing_res['bg_mean'] 361 | # else: 362 | # testing_res['Norm_Commu_Score'] = testing_res['Commu_Score'] 363 | ## hypothesis testing using more methods 364 | for method in testing_method: 365 | if testing_res['bg_std'] == 0 and testing_res['bg_mean'] == 0: 366 | ## sometimes, the gene is not expressed at all cells, so no need to do testing 367 | stat, pval = 0, 1 368 | else: 369 | stat, pval = self._testing_(real_score=real_score, bg_values=bg_values, method = method) 370 | testing_res[method+'_stat'] = stat 371 | testing_res[method+'_pval'] = pval 372 | pvalue_res.append(testing_res) 373 | del testing_res 374 | ## data frame and calculate fdr 375 | pvalue_res = pd.DataFrame(pvalue_res) 376 | # pvalue_res = self._fdr_(pvalue_res = pvalue_res, testing_method = testing_method) 377 | return(pvalue_res) 378 | 379 | def _excu_commu_(self, s_m): 380 | """ 381 | link function to self._commu_score_for_one_ and self._signif_test_ 382 | """ 383 | info('{}'.format(s_m)) 384 | sensor, met = s_m.split(' ~ ') 385 | sensor_loc = self.avg_exp_indexer.tolist().index(sensor) 386 | avg_exp_sensor = self.avg_exp[sensor_loc].toarray()[0] 387 | 388 | met_loc = self.avg_met_indexer.tolist().index(met) 389 | avg_met_met = self.avg_met[met_loc].toarray()[0] 390 | 391 | sensor_perm_loc = self.permute_exp_indexer.tolist().index(sensor) 392 | perm_exp_avg_sensor = {i:self.perm_exp_avg[i][sensor_perm_loc].toarray()[0] for i in self.perm_exp_avg} 393 | 394 | met_perm_loc = self.permute_met_indexer.tolist().index(met) 395 | perm_met_avg_met = {i:self.perm_met_avg[i][met_perm_loc].toarray()[0] for i in self.perm_met_avg} 396 | 397 | commu_mat, background_df = self._commu_score_for_one_( 398 | avg_exp_sensor = avg_exp_sensor, 399 | avg_met_met = avg_met_met, 400 | perm_exp_avg_sensor = perm_exp_avg_sensor, 401 | perm_met_avg_met = perm_met_avg_met 402 | ) 403 | pvalue_res = self._signif_test_(commu_mat = commu_mat, background_df = background_df) 404 | pvalue_res['Metabolite'] = met 405 | pvalue_res['Sensor'] = sensor 406 | 407 | return met+'~'+sensor, pvalue_res, background_df 408 | 409 | 410 | def _avg_exp_group_(self, group_names): 411 | ## avg exp by cell_group for met sensor 412 | avg_exp = np.empty(shape = (self.exp_mat.shape[0],0)) ## save exp data 413 | 414 | for x in group_names: 415 | cells = self.cell_ann[self.cell_ann['cell_group'] == x].index.tolist() 416 | cell_loc = [i for i, c in enumerate(self.exp_mat_columns) if c in cells] 417 | avg_exp = np.concatenate((avg_exp, self.exp_mat[:,cell_loc].mean(axis = 1)), axis = 1) 418 | self.avg_exp = sparse.csc_matrix(avg_exp) 419 | self.avg_exp_indexer = np.array(self.exp_mat_indexer) 420 | self.avg_exp_columns = np.array(group_names) 421 | 422 | def _avg_met_group_(self, group_names): 423 | """ 424 | take average of sensor expression and metabolite by cell groups 425 | """ 426 | ## avg met by cell_group for met 427 | avg_met = np.empty(shape = (self.met_mat.shape[0],0)) ## save exp data 428 | 429 | for x in group_names: 430 | cells = self.cell_ann[self.cell_ann['cell_group'] == x].index.tolist() 431 | cell_loc = [i for i, c in enumerate(self.met_mat_columns) if c in cells] 432 | avg_met = np.concatenate((avg_met, self.met_mat[:,cell_loc].mean(axis = 1)), axis = 1) 433 | self.avg_met = sparse.csc_matrix(avg_met) 434 | self.avg_met_indexer = np.array(self.met_mat_indexer) 435 | self.avg_met_columns = group_names 436 | 437 | 438 | def pred(self, n_shuffle = 1000, seed = 12345): 439 | """ 440 | handling commmunication score 441 | """ 442 | self.n_shuffle = n_shuffle 443 | self.seed = seed 444 | ## multiprocessing 445 | if self.thread is None: 446 | self.thread = 1 447 | 448 | info('Parameters: {shuffling: %s times, random seed: %s, thread: %s}'%(self.n_shuffle, self.seed, self.thread)) 449 | 450 | ## avg exp and met level in cell group for real data 451 | group_names = self.cell_ann['cell_group'].unique().tolist() 452 | self.group_names = group_names 453 | 454 | ## make sure the same order by giving group_names 455 | if self.avg_met is None or self.avg_met_columns is not self.group_names: 456 | self._avg_met_group_(group_names = self.group_names) 457 | if self.avg_exp is None or self.avg_exp_columns is not self.group_names: 458 | self._avg_exp_group_(group_names = self.group_names) 459 | 460 | ## report data shape 461 | info('met_sensor: (%s, %s)'%self.met_sensor.shape) 462 | info('avg_exp: (%s, %s) for (gene, cell) of needed'%self.avg_exp.shape) 463 | info('avg_met: (%s, %s) for (metabolite, cell) of needed'%self.avg_met.shape) 464 | 465 | ## do n times shuffling for generating backgroud 466 | ## return a dict, index will be time of shuffling, given each shuffling, it is a matrix, rows are cell_group, columns are genes 467 | info('shuffling %s times for generating backgroud' % self.n_shuffle) 468 | self._shuffling_(group_names=self.group_names, n_shuffle = self.n_shuffle, seed = self.seed) 469 | 470 | ## omputing commu score for each met and sensor 471 | commu_res = collections.defaultdict() ## collect communication scores for plot later 472 | commu_res_bg = collections.defaultdict() 473 | 474 | info('thread: %s'%self.thread) 475 | pool = multiprocessing.Pool(self.thread) 476 | ## all sensor and met pairs 477 | s_m_all = self.met_sensor['Gene_name'] + ' ~ ' + self.met_sensor['HMDB_ID'] 478 | res_col = pool.map(self._excu_commu_, s_m_all.tolist()) 479 | pool.close() 480 | ## into dict 481 | for k, c, b in res_col: 482 | ## k is met~sensor, c is commu, b is background 483 | commu_res[k] = c 484 | commu_res_bg[k] = b 485 | ## dataframe of commu_res 486 | commu_res_df = pd.DataFrame() 487 | for pair in commu_res: 488 | commu_res_df = pd.concat([commu_res_df, commu_res[pair]]) 489 | ## do fdr correction 490 | testing_method = ['ztest', 'ttest', 'ranksum_test', 'permutation_test'] 491 | commu_res_df = self._fdr_(pvalue_res = commu_res_df, testing_method = testing_method) 492 | commu_res_df = commu_res_df.sort_values('permutation_test_fdr') 493 | return commu_res_df, commu_res_bg ## dict, keys are pair of met and sensor 494 | 495 | 496 | 497 | 498 | 499 | 500 | 501 | --------------------------------------------------------------------------------