├── .gitignore ├── 01 Introduction to Multimodal Networks.ipynb ├── 02 Data Representation in Mambo.ipynb ├── 03 Workflow for Constructing a Multimodal Network.ipynb ├── 04 Creating Mode Tables.ipynb ├── 05 Creating Link Tables.ipynb ├── 06 Constructing a Multimodal Network from Mode and Link Tables.ipynb ├── 07 Loading a Multimodal Network.ipynb ├── 08 Performing Analytics on a Multimodal Network.ipynb ├── 09 Giga-Scale Multimodal Biological Network.ipynb ├── 10 Supplementary - Filtering a Giga-Scale Multimodal Biological Network.ipynb ├── README.md ├── datasets ├── cancer_example │ ├── chemical-chemical │ │ └── drugbank_parsed_chemical_chemical.tsv │ ├── chemical-protein │ │ └── drugbank_parsed_chemical_protein.tsv │ ├── chemical │ │ ├── drugbank_parsed.tsv │ │ └── mapped_chemicals.tsv │ ├── disease-chemical │ │ └── ctd_disease_chem_parsed.tsv │ ├── disease-disease │ │ └── doid_disease_disease_parsed.tsv │ ├── disease-function │ │ └── ctd_disease_func_parsed.tsv │ ├── disease-protein │ │ └── ctd_disease_protein_parsed.tsv │ ├── disease │ │ ├── ctd_mesh_parsed.tsv │ │ ├── ctd_omim_parsed.tsv │ │ ├── do_mesh_equiv.tsv │ │ ├── do_omim_equiv.tsv │ │ ├── do_parsed.tsv │ │ ├── mapped_diseases.tsv │ │ └── omim_parsed.tsv │ ├── function-function │ │ └── go_parsed.tsv │ ├── function │ │ └── go_nodes.tsv │ ├── gene-gene │ │ ├── filter_gene_gene.py │ │ └── genemania_data │ │ │ ├── Co-expression.Agnelli-Neri-2007.txt │ │ │ ├── Co-expression.Agnelli-Neri-2009.txt │ │ │ ├── Co-expression.Alizadeh-Staudt-2000.txt │ │ │ ├── Co-expression.Alter-Stephan-2011.txt │ │ │ ├── Co-expression.Ariazi-Jordan-2011.txt │ │ │ ├── Co-expression.Arijs-Rutgeerts-2009.txt │ │ │ ├── Co-expression.Bahr-Bowler-2013.txt │ │ │ ├── Co-expression.Balgobind-den_Boer-2011.txt │ │ │ ├── Co-expression.Barnes-Colbert-2009.txt │ │ │ ├── Co-expression.Barnes-Glass-2010.txt │ │ │ ├── Co-expression.Barretina-Singer-2010.txt │ │ │ ├── Co-expression.Baty-Brutsche-2006.txt │ │ │ ├── Co-expression.Beane-Spira-2007.txt │ │ │ ├── Co-expression.Berchtold-Cotman-2008.txt │ │ │ ├── Co-expression.Berkofsky-Fessler-Hilton-2009.txt │ │ │ ├── Co-expression.Bhojwani-Carroll-2006.txt │ │ │ ├── Co-expression.Bigler-Russell-2013.txt │ │ │ ├── Co-expression.Bild-Nevins-2006_A.txt │ │ │ ├── Co-expression.Bild-Nevins-2006_B.txt │ │ │ ├── Co-expression.Bild-Nevins-2006_C.txt │ │ │ ├── Co-expression.Bjornsdottir-O'Toole-2011.txt │ │ │ ├── Co-expression.Blader-Boothroyd-2001.txt │ │ │ ├── Co-expression.Boldrick-Relman-2002.txt │ │ │ ├── Co-expression.Bonome-Birrer-2008.txt │ │ │ ├── Co-expression.Bos-Massague-2009.txt │ │ │ ├── Co-expression.Botling-Micke-2013.txt │ │ │ ├── Co-expression.Broyl-Sonneveld-2010.txt │ │ │ ├── Co-expression.Burczynski-Dorner-2006.txt │ │ │ ├── Co-expression.Burington-Shaughnessy-2008.txt │ │ │ ├── Co-expression.Chang-Katzenellenbogen-2008.txt │ │ │ ├── Co-expression.Chapman-Golub-2011.txt │ │ │ ├── Co-expression.Chen-Brown-2002.txt │ │ │ ├── Co-expression.Chen-Yeatman-2010.txt │ │ │ ├── Co-expression.Chen-Zhao-2008.txt │ │ │ ├── Co-expression.Cheok-Evans-2003.txt │ │ │ ├── Co-expression.Chibon-Aurias-2010.txt │ │ │ ├── Co-expression.Chng-Fonseca-2007.txt │ │ │ ├── Co-expression.Chowdary-Mazumder-2006.txt │ │ │ ├── Co-expression.Chuang-Kipps-2012.txt │ │ │ ├── Co-expression.Clarke-Clynes-2013.txt │ │ │ ├── Co-expression.Cliff-Dockrell-2013.txt │ │ │ ├── Co-expression.Compagno-Pasqualucci-2009.txt │ │ │ ├── Co-expression.Corvol-Baranzini-2008.txt │ │ │ ├── Co-expression.Coustan-Smith-Campana-2011.txt │ │ │ ├── Co-expression.Creighton-Chang-2012.txt │ │ │ ├── Co-expression.Cuadras-Greenberg-2002.txt │ │ │ ├── Co-expression.D'Alfonso-Shin-2013.txt │ │ │ ├── Co-expression.Day-Maxwell-2011.txt │ │ │ ├── Co-expression.De_Jager-Oksenberg-2009.txt │ │ │ ├── Co-expression.Demmer-Papapanou-2008.txt │ │ │ ├── Co-expression.Den_Boer-Pieters-2009_A.txt │ │ │ ├── Co-expression.Den_Boer-Pieters-2009_B.txt │ │ │ ├── Co-expression.Der-Tsao-2014.txt │ │ │ ├── Co-expression.Desmedt-Sotiriou-2007.txt │ │ │ ├── Co-expression.Detweiler-Falkow-2001.txt │ │ │ ├── Co-expression.Dombroski-Spielman-2010.txt │ │ │ ├── Co-expression.Driscoll-Munshi-2010.txt │ │ │ ├── Co-expression.Einecke-Halloran-2010.txt │ │ │ ├── Co-expression.Elashoff-Topol-2011_A.txt │ │ │ ├── Co-expression.Elashoff-Topol-2011_B.txt │ │ │ ├── Co-expression.Elashoff-Topol-2011_C.txt │ │ │ ├── Co-expression.Ellis-Mardis-2012.txt │ │ │ ├── Co-expression.Filipits-Gnant-2011.txt │ │ │ ├── Co-expression.Finak-Park-2006.txt │ │ │ ├── Co-expression.Finak-Park-2008.txt │ │ │ ├── Co-expression.Folkersen-Paulsson-Berne-2012.txt │ │ │ ├── Co-expression.Fountzilas-Fountzilas-2013.txt │ │ │ ├── Co-expression.Freedman-Nevins-2011.txt │ │ │ ├── Co-expression.Fry-Samson-2008.txt │ │ │ ├── Co-expression.Gadd-Perlman-2012.txt │ │ │ ├── Co-expression.Gaedcke-Ghadimi-2010.txt │ │ │ ├── Co-expression.Garber-Petersen-2001.txt │ │ │ ├── Co-expression.Gibault-Aurias-2012.txt │ │ │ ├── Co-expression.Gobble-Singer-2011.txt │ │ │ ├── Co-expression.Gomez-Abad-Piris-2011.txt │ │ │ ├── Co-expression.Griffin-Glass-2009.txt │ │ │ ├── Co-expression.Grigoryev-Salomon-2010.txt │ │ │ ├── Co-expression.Gysin-McMahon-2012.txt │ │ │ ├── Co-expression.Haferlach-Falini-2009.txt │ │ │ ├── Co-expression.Hagg-Bjorkegren-2009.txt │ │ │ ├── Co-expression.Hanamura-Shaughnessy-2006.txt │ │ │ ├── Co-expression.Hannenhalli-Cappola-2006.txt │ │ │ ├── Co-expression.Harms-Bichakjian-2013.txt │ │ │ ├── Co-expression.Hatzis-Symmans-2011_A.txt │ │ │ ├── Co-expression.Hatzis-Symmans-2011_B.txt │ │ │ ├── Co-expression.Hatzis-Symmans-2011_C.txt │ │ │ ├── Co-expression.Haugen-Van_Houten-2010.txt │ │ │ ├── Co-expression.Hendrix-Cho-2006.txt │ │ │ ├── Co-expression.Hessel-Tilley-2014.txt │ │ │ ├── Co-expression.Heuck-Barlogie-2012.txt │ │ │ ├── Co-expression.Hinze-Grom-2010.txt │ │ │ ├── Co-expression.Hochstenbach-van_Delft-2012.txt │ │ │ ├── Co-expression.Holland-Grimbacher-2007.txt │ │ │ ├── Co-expression.Holleman-Evans-2004.txt │ │ │ ├── Co-expression.Homminga-Meijerink-2011.txt │ │ │ ├── Co-expression.Honda-Kaneko-2010.txt │ │ │ ├── Co-expression.Horak-Liu-2013.txt │ │ │ ├── Co-expression.Hou-Philipsen-2010.txt │ │ │ ├── Co-expression.Huang-Perlman-2009.txt │ │ │ ├── Co-expression.Hummel-Siebert-2006.txt │ │ │ ├── Co-expression.Innocenti-Brown-2011.txt │ │ │ ├── Co-expression.Ioannidis-Flano-2012.txt │ │ │ ├── Co-expression.Iqbal-Chan-2010.txt │ │ │ ├── Co-expression.Iwamoto-Kato-2005.txt │ │ │ ├── Co-expression.Iwamoto-Pusztai-2011.txt │ │ │ ├── Co-expression.Iyer-Brown-1999.txt │ │ │ ├── Co-expression.Jones-Libermann-2005.txt │ │ │ ├── Co-expression.Jorissen-Sieber-2008.txt │ │ │ ├── Co-expression.Jorissen-Sieber-2009.txt │ │ │ ├── Co-expression.Kabbarah-Chin-2010.txt │ │ │ ├── Co-expression.Kaiser-Aronow-2007.txt │ │ │ ├── Co-expression.Kang-Willman-2010.txt │ │ │ ├── Co-expression.Kannan-Zweidler-McKay-2011.txt │ │ │ ├── Co-expression.Kao-Huang-2011.txt │ │ │ ├── Co-expression.Karlovich-Caulfield-2009.txt │ │ │ ├── Co-expression.Kikuchi-Sugihara-2013.txt │ │ │ ├── Co-expression.Kim-Green-2011_A.txt │ │ │ ├── Co-expression.Kim-Green-2011_B.txt │ │ │ ├── Co-expression.Kim-Paik-2011.txt │ │ │ ├── Co-expression.Klein-Dugas-2009.txt │ │ │ ├── Co-expression.Kobayashi-DeLeo-2010.txt │ │ │ ├── Co-expression.Kogo-Mori-2011.txt │ │ │ ├── Co-expression.Kohlmann-Haferlach-2008_A.txt │ │ │ ├── Co-expression.Kohlmann-Haferlach-2008_B.txt │ │ │ ├── Co-expression.Kuehner-Speit-2013.txt │ │ │ ├── Co-expression.LaBreche-Huang-2011.txt │ │ │ ├── Co-expression.Landi-Jen-2008.txt │ │ │ ├── Co-expression.Lauwerys-Houssiau-2013.txt │ │ │ ├── Co-expression.Lee-Fine-2006.txt │ │ │ ├── Co-expression.Lee-Kim-2008.txt │ │ │ ├── Co-expression.Lee-MacDonald-2013.txt │ │ │ ├── Co-expression.Lenz-Staudt-2008.txt │ │ │ ├── Co-expression.Levy-Hessner-2012_A.txt │ │ │ ├── Co-expression.Levy-Hessner-2012_B.txt │ │ │ ├── Co-expression.Lewis-Ortel-2011.txt │ │ │ ├── Co-expression.Li-Bhatia-2011.txt │ │ │ ├── Co-expression.Li-Han-2009.txt │ │ │ ├── Co-expression.Li-Wang-2010_A.txt │ │ │ ├── Co-expression.Li-Wang-2010_B.txt │ │ │ ├── Co-expression.Liang-Stephan-2007.txt │ │ │ ├── Co-expression.Liu-Bratslavsky-2013.txt │ │ │ ├── Co-expression.Liu-Godbout-2011.txt │ │ │ ├── Co-expression.Liu-Hsieh-2012.txt │ │ │ ├── Co-expression.Lu-Chuang-2010.txt │ │ │ ├── Co-expression.Lu-Richardson-2008.txt │ │ │ ├── Co-expression.Lugthart-Evans-2005.txt │ │ │ ├── Co-expression.Maertzdorf-Kaufmann-2011.txt │ │ │ ├── Co-expression.Mallon-McKay-2013.txt │ │ │ ├── Co-expression.Marisa-Boige-2013.txt │ │ │ ├── Co-expression.Maser-DePinho-2007.txt │ │ │ ├── Co-expression.Mateescu-Mechta-Grigoriou-2011.txt │ │ │ ├── Co-expression.Matsuyama-Sugihara-2010.txt │ │ │ ├── Co-expression.Meier-Seiler-2009.txt │ │ │ ├── Co-expression.Meyer-Debatin-2011.txt │ │ │ ├── Co-expression.Micke-Botling-2011.txt │ │ │ ├── Co-expression.Miller-Dixon-2007.txt │ │ │ ├── Co-expression.Miller-Dixon-2012.txt │ │ │ ├── Co-expression.Mills-Haferlach-2009.txt │ │ │ ├── Co-expression.Minn-Massague-2005.txt │ │ │ ├── Co-expression.Miyake-Noguchi-2012.txt │ │ │ ├── Co-expression.Moffatt-Cookson-2007.txt │ │ │ ├── Co-expression.Mullighan-Downing-2009.txt │ │ │ ├── Co-expression.Naesens-Sarwal-2011.txt │ │ │ ├── Co-expression.Nair-Abecasis-2009.txt │ │ │ ├── Co-expression.Nakayama-Hasegawa-2007.txt │ │ │ ├── Co-expression.Newman-Radeke-2012.txt │ │ │ ├── Co-expression.Niu-Wang-2010.txt │ │ │ ├── Co-expression.Noble-Diehl-2008.txt │ │ │ ├── Co-expression.Noble-Diehl-2010.txt │ │ │ ├── Co-expression.Nookaew-Carlsson-2013.txt │ │ │ ├── Co-expression.Okayama-Yokota-2012.txt │ │ │ ├── Co-expression.Olmos-de_Bono-2012.txt │ │ │ ├── Co-expression.Ooi-Tan-2009.txt │ │ │ ├── Co-expression.Papapanou-Demmer-2009.txt │ │ │ ├── Co-expression.Payton-Ley-2009.txt │ │ │ ├── Co-expression.Pellagatti-Boultwood-2010.txt │ │ │ ├── Co-expression.Peng-Katze-2009.txt │ │ │ ├── Co-expression.Peri-Russo-2012.txt │ │ │ ├── Co-expression.Perou-Botstein-1999.txt │ │ │ ├── Co-expression.Perou-Botstein-2000.txt │ │ │ ├── Co-expression.Petruzziello-Pellegrini-Marsden-2012.txt │ │ │ ├── Co-expression.Pfister-Pommier-2009.txt │ │ │ ├── Co-expression.Popovici-Pusztai-2010_A.txt │ │ │ ├── Co-expression.Popovici-Pusztai-2010_B.txt │ │ │ ├── Co-expression.Postel-Vinay-Delattre-2012.txt │ │ │ ├── Co-expression.Potti-Nevins-2006.txt │ │ │ ├── Co-expression.Radtke-Downing-2009.txt │ │ │ ├── Co-expression.Raman-Crystal-2009.txt │ │ │ ├── Co-expression.Ramaswamy-Golub-2001.txt │ │ │ ├── Co-expression.Raponi-Beer-2006.txt │ │ │ ├── Co-expression.Raue-Trappe-2012.txt │ │ │ ├── Co-expression.Reeve-Halloran-2013.txt │ │ │ ├── Co-expression.Rieger-Chu-2004.txt │ │ │ ├── Co-expression.Rosenwald-Staudt-2001.txt │ │ │ ├── Co-expression.Ross-Brown-2000.txt │ │ │ ├── Co-expression.Ross-Perou-2001.txt │ │ │ ├── Co-expression.Roth-Zlotnik-2006.txt │ │ │ ├── Co-expression.Rotunno-Landi-2011.txt │ │ │ ├── Co-expression.Rousseaux-Khochbin-2013.txt │ │ │ ├── Co-expression.Sabatier-Bertucci-2011_A.txt │ │ │ ├── Co-expression.Sabatier-Bertucci-2011_B.txt │ │ │ ├── Co-expression.Salaverria-Siebert-2011.txt │ │ │ ├── Co-expression.Savola-Vakkila-2011.txt │ │ │ ├── Co-expression.Scatolini-Chiorino-2010.txt │ │ │ ├── Co-expression.Scherzer-Gullans-2007.txt │ │ │ ├── Co-expression.Schmidt-Gehrmann-2008.txt │ │ │ ├── Co-expression.Scott-Rimsza-2014.txt │ │ │ ├── Co-expression.Sears-Subramaniam-2009.txt │ │ │ ├── Co-expression.Seok-Tompkins-2013.txt │ │ │ ├── Co-expression.Shalhoub-Martin-2010.txt │ │ │ ├── Co-expression.Shaykhiev-Crystal-2011.txt │ │ │ ├── Co-expression.Shea-Musser-2010.txt │ │ │ ├── Co-expression.Sheffer-Domany-2009.txt │ │ │ ├── Co-expression.Singh-Celli-2011.txt │ │ │ ├── Co-expression.Sinnaeve-Granger-2009.txt │ │ │ ├── Co-expression.Skov-Hasselbalch-2011.txt │ │ │ ├── Co-expression.Skrzypczak-Ostrowsk-2010.txt │ │ │ ├── Co-expression.Smeets-Christiaens-2011.txt │ │ │ ├── Co-expression.Smirnov-Cheung-2009.txt │ │ │ ├── Co-expression.Smirnov-Cheung-2012.txt │ │ │ ├── Co-expression.Smith-Beauchamp-2010.txt │ │ │ ├── Co-expression.Sorich-Evans-2008.txt │ │ │ ├── Co-expression.Sotiriou-Delorenzi-2006.txt │ │ │ ├── Co-expression.Spira-Brody-2007.txt │ │ │ ├── Co-expression.Srlie-Brresen-Dale-2001.txt │ │ │ ├── Co-expression.Steidl-Gascoyne-2010.txt │ │ │ ├── Co-expression.Stinson-Dornan-2011.txt │ │ │ ├── Co-expression.Stirewalt-Radich-2008.txt │ │ │ ├── Co-expression.Stratford-Yeh-2010.txt │ │ │ ├── Co-expression.Strulovici-Barel-Crystal-2010.txt │ │ │ ├── Co-expression.Suarez-Farinas-Krueger-2012.txt │ │ │ ├── Co-expression.Sun-Fine-2006.txt │ │ │ ├── Co-expression.Sun-Troester-2013.txt │ │ │ ├── Co-expression.Swan-Spiller-2013.txt │ │ │ ├── Co-expression.Symmans-Pusztai-2010.txt │ │ │ ├── Co-expression.Tabchy-Pusztai-2010.txt │ │ │ ├── Co-expression.Tarca-Zechner-2013.txt │ │ │ ├── Co-expression.Taskesen-Dohner-2011.txt │ │ │ ├── Co-expression.Taylor-Belle-2007.txt │ │ │ ├── Co-expression.Taylor-Kwo-2008.txt │ │ │ ├── Co-expression.Tian-Shaughnessy-2003_A.txt │ │ │ ├── Co-expression.Tian-Shaughnessy-2003_B.txt │ │ │ ├── Co-expression.Tilley-Crystal-2011.txt │ │ │ ├── Co-expression.Toedter-Baribaud-2011.txt │ │ │ ├── Co-expression.Tomasson-Ley-2008.txt │ │ │ ├── Co-expression.Tomida-Takahashi-2009.txt │ │ │ ├── Co-expression.Tothill-Bowtell-2008_A.txt │ │ │ ├── Co-expression.Tothill-Bowtell-2008_B.txt │ │ │ ├── Co-expression.Tsukamoto-Sugihara-2011.txt │ │ │ ├── Co-expression.Vallat-Bahram-2013.txt │ │ │ ├── Co-expression.Verhaak-Valk-2009.txt │ │ │ ├── Co-expression.Wagner-Ashkenazi-2007.txt │ │ │ ├── Co-expression.Wang-Crystal-2011.txt │ │ │ ├── Co-expression.Wang-Foekens-2005.txt │ │ │ ├── Co-expression.Wang-Maris-2006.txt │ │ │ ├── Co-expression.Wang-McClelland-2010_A.txt │ │ │ ├── Co-expression.Wang-McClelland-2010_B.txt │ │ │ ├── Co-expression.Wardell-McDonnell-2012.txt │ │ │ ├── Co-expression.Warren-Tompkins-2009.txt │ │ │ ├── Co-expression.Watanabe-Muto-2011.txt │ │ │ ├── Co-expression.Watanabe-Nagawa-2007.txt │ │ │ ├── Co-expression.Whitfield-Botstein-2002.txt │ │ │ ├── Co-expression.Williams-DeVane-Edwards-2013.txt │ │ │ ├── Co-expression.Williams-Gascoyne-2010.txt │ │ │ ├── Co-expression.Winter-Larson-2007.txt │ │ │ ├── Co-expression.Wong-Aronow-2007.txt │ │ │ ├── Co-expression.Wong-Shanley-2009_A.txt │ │ │ ├── Co-expression.Wong-Shanley-2009_B.txt │ │ │ ├── Co-expression.Woodruff-Fahy-2007.txt │ │ │ ├── Co-expression.Woods-Ginsburg-2013.txt │ │ │ ├── Co-expression.Wouters-Delwel-2009.txt │ │ │ ├── Co-expression.Wu-Garvey-2007.txt │ │ │ ├── Co-expression.Wynn-Wong-2011.txt │ │ │ ├── Co-expression.Xiao-Tompkins-2011.txt │ │ │ ├── Co-expression.Xu-Shannon-2013.txt │ │ │ ├── Co-expression.Yang-Steele-2012.txt │ │ │ ├── Co-expression.Yao-Jallal-2008.txt │ │ │ ├── Co-expression.Yoshihara-Tanaka-2010.txt │ │ │ ├── Co-expression.Yu-Lee-2012.txt │ │ │ ├── Co-expression.Yu-Tan-2008.txt │ │ │ ├── Co-expression.Zaas-Ginsburg-2009.txt │ │ │ ├── Co-expression.Zangrando-Basso-2009.txt │ │ │ ├── Co-expression.Zhang-Foekens-2009.txt │ │ │ ├── Co-expression.Zhang-Mullighan-2012.txt │ │ │ ├── Co-expression.Zhou-O'Keefe-2010.txt │ │ │ ├── Co-expression.de_Cremoux-Spyratos-2011.txt │ │ │ ├── Co-expression.de_Sousa_E_Melo-Medema-2011.txt │ │ │ ├── Co-localization.Johnson-Shoemaker-2003.txt │ │ │ ├── Co-localization.Satoh-Yamamoto-2013.txt │ │ │ ├── Co-localization.Schadt-Shoemaker-2004.txt │ │ │ ├── Genetic_interactions.BIOGRID-SMALL-SCALE-STUDIES.txt │ │ │ ├── Genetic_interactions.IREF-SMALL-SCALE-STUDIES.txt │ │ │ ├── Genetic_interactions.Lin-Boeke-2012_A.txt │ │ │ ├── Genetic_interactions.Lin-Boeke-2012_B.txt │ │ │ ├── Genetic_interactions.Lin-Smith-2010.txt │ │ │ ├── Genetic_interactions.Toyoshima-Grandori-2012.txt │ │ │ ├── Genetic_interactions.Willingham-Muchowski-2003.txt │ │ │ ├── Pathway.PATHWAYCOMMONS-CELL_MAP.txt │ │ │ ├── Pathway.PATHWAYCOMMONS-HUMANCYC.txt │ │ │ ├── Pathway.PATHWAYCOMMONS-IMID.txt │ │ │ ├── Pathway.PATHWAYCOMMONS-NCI_NATURE.txt │ │ │ ├── Pathway.PATHWAYCOMMONS-REACTOME.txt │ │ │ ├── Pathway.Wu-Stein-2010.txt │ │ │ ├── Physical_interactions.Abu-Odeh-Aqeilan-2014.txt │ │ │ ├── Physical_interactions.Agrawal-Sedivy-2010.txt │ │ │ ├── Physical_interactions.Aichem-Groettrup-2012.txt │ │ │ ├── Physical_interactions.Albers-Koegl-2005.txt │ │ │ ├── Physical_interactions.Alexandru-Deshaies-2008.txt │ │ │ ├── Physical_interactions.Altun-Kessler-2011.txt │ │ │ ├── Physical_interactions.Andresen-Flores-Morales-2014.txt │ │ │ ├── Physical_interactions.Arbuckle-Grant-2010.txt │ │ │ ├── Physical_interactions.Arora-Mercola-2008.txt │ │ │ ├── Physical_interactions.BIOGRID-SMALL-SCALE-STUDIES.txt │ │ │ ├── Physical_interactions.Bandyopadhyay-Ideker-2010.txt │ │ │ ├── Physical_interactions.Bantscheff-Drewes-2011.txt │ │ │ ├── Physical_interactions.Barr-Knapp-2009.txt │ │ │ ├── Physical_interactions.Barrios-Rodiles-Wrana-2005.txt │ │ │ ├── Physical_interactions.Behrends-Harper-2010.txt │ │ │ ├── Physical_interactions.Behzadnia-Luhrmann-2007.txt │ │ │ ├── Physical_interactions.Bennett-Harper-2010.txt │ │ │ ├── Physical_interactions.Benzinger-Hermeking-2005.txt │ │ │ ├── Physical_interactions.Berggard-James-2006.txt │ │ │ ├── Physical_interactions.Bett-Hay-2013.txt │ │ │ ├── Physical_interactions.Blandin-Richard-2013.txt │ │ │ ├── Physical_interactions.Bouwmeester-Superti-Furga-2004.txt │ │ │ ├── Physical_interactions.Brajenovic-Drewes-2004.txt │ │ │ ├── Physical_interactions.Brehme-Superti-Furga-2009.txt │ │ │ ├── Physical_interactions.Bruderer-Hay-2011.txt │ │ │ ├── Physical_interactions.Byron-Humphries-2012.txt │ │ │ ├── Physical_interactions.Cai-Conaway-2007.txt │ │ │ ├── Physical_interactions.Camargo-Brandon-2007.txt │ │ │ ├── Physical_interactions.Cannavo-Jiricny-2007.txt │ │ │ ├── Physical_interactions.Cao-Chinnaiyan-2014.txt │ │ │ ├── Physical_interactions.Chen-Ge-2013.txt │ │ │ ├── Physical_interactions.Chen-Naus-2012.txt │ │ │ ├── Physical_interactions.Chen-Zhang-2013.txt │ │ │ ├── Physical_interactions.Cheng-Chen-2010.txt │ │ │ ├── Physical_interactions.Cloutier-Coulombe-2013.txt │ │ │ ├── Physical_interactions.Colland-Gauthier-2004.txt │ │ │ ├── Physical_interactions.Couzens-Gingras-2013.txt │ │ │ ├── Physical_interactions.Cox-Rizzino-2013.txt │ │ │ ├── Physical_interactions.Danielsen-Nielsen-2011.txt │ │ │ ├── Physical_interactions.Dyer-Sobral-2010.txt │ │ │ ├── Physical_interactions.Emanuele-Elledge-2011.txt │ │ │ ├── Physical_interactions.Ewing-Figeys-2007.txt │ │ │ ├── Physical_interactions.Fenner-Prehn-2010.txt │ │ │ ├── Physical_interactions.Foerster-Ritter-2013.txt │ │ │ ├── Physical_interactions.Foster-Marshall-2013.txt │ │ │ ├── Physical_interactions.Freibaum-Taylor-2010.txt │ │ │ ├── Physical_interactions.Gao-Reinberg-2012.txt │ │ │ ├── Physical_interactions.Gautier-Hall-2009.txt │ │ │ ├── Physical_interactions.Giannone-Liu-2010.txt │ │ │ ├── Physical_interactions.Glatter-Gstaiger-2009.txt │ │ │ ├── Physical_interactions.Gloeckner-Ueffing-2007.txt │ │ │ ├── Physical_interactions.Goehler-Wanker-2004.txt │ │ │ ├── Physical_interactions.Golebiowski-Hay-2009.txt │ │ │ ├── Physical_interactions.Goudreault-Gingras-2009.txt │ │ │ ├── Physical_interactions.Grant-2010.txt │ │ │ ├── Physical_interactions.Greco-Cristea-2011.txt │ │ │ ├── Physical_interactions.Havrylov-Redowicz-2009.txt │ │ │ ├── Physical_interactions.Havugimana-Emili-2012.txt │ │ │ ├── Physical_interactions.Hayes-Urbe-2012.txt │ │ │ ├── Physical_interactions.Hegele-Stelzl-2012_A.txt │ │ │ ├── Physical_interactions.Hegele-Stelzl-2012_B.txt │ │ │ ├── Physical_interactions.Humphries-Humphries-2009.txt │ │ │ ├── Physical_interactions.Hutchins-Peters-2010.txt │ │ │ ├── Physical_interactions.IREF-BIND.txt │ │ │ ├── Physical_interactions.IREF-BIOGRID.txt │ │ │ ├── Physical_interactions.IREF-DIP.txt │ │ │ ├── Physical_interactions.IREF-HPRD.txt │ │ │ ├── Physical_interactions.IREF-INNATEDB.txt │ │ │ ├── Physical_interactions.IREF-INTACT.txt │ │ │ ├── Physical_interactions.IREF-MATRIXDB.txt │ │ │ ├── Physical_interactions.IREF-MPPI.txt │ │ │ ├── Physical_interactions.IREF-OPHID.txt │ │ │ ├── Physical_interactions.IREF-PUBMED.txt │ │ │ ├── Physical_interactions.IREF-SMALL-SCALE-STUDIES.txt │ │ │ ├── Physical_interactions.Ingham-Pawson-2005.txt │ │ │ ├── Physical_interactions.Jager-Krogan-2012.txt │ │ │ ├── Physical_interactions.Jeronimo-Coulombe-2007.txt │ │ │ ├── Physical_interactions.Jin-Pawson-2004.txt │ │ │ ├── Physical_interactions.Jones-MacBeath-2006.txt │ │ │ ├── Physical_interactions.Joshi-Cristea-2013.txt │ │ │ ├── Physical_interactions.Kahle-Zoghbi-2011.txt │ │ │ ├── Physical_interactions.Kim-Gygi-2011.txt │ │ │ ├── Physical_interactions.Kneissl-Grummt-2003.txt │ │ │ ├── Physical_interactions.Koch-Hermeking-2007.txt │ │ │ ├── Physical_interactions.Kristensen-Foster-2012.txt │ │ │ ├── Physical_interactions.Lau-Ronai-2012.txt │ │ │ ├── Physical_interactions.Lee-Doedens-2011.txt │ │ │ ├── Physical_interactions.Lee-Songyang-2011.txt │ │ │ ├── Physical_interactions.Lehner-Sanderson-2004_A.txt │ │ │ ├── Physical_interactions.Lehner-Sanderson-2004_B.txt │ │ │ ├── Physical_interactions.Leng-Wang-2014.txt │ │ │ ├── Physical_interactions.Li-Dorf-2011_A.txt │ │ │ ├── Physical_interactions.Li-Dorf-2011_B.txt │ │ │ ├── Physical_interactions.Lim-Zoghbi-2006.txt │ │ │ ├── Physical_interactions.Liu-Wang-2012.txt │ │ │ ├── Physical_interactions.Loch-Strickler-2012.txt │ │ │ ├── Physical_interactions.Lopitz-Otsoa-Rodriguez-2012.txt │ │ │ ├── Physical_interactions.Lu-Zhang-2013.txt │ │ │ ├── Physical_interactions.Mak-Moffat-2010.txt │ │ │ ├── Physical_interactions.Malovannaya-Qin-2010.txt │ │ │ ├── Physical_interactions.Marechal-Zou-2014.txt │ │ │ ├── Physical_interactions.Markson-Sanderson-2009.txt │ │ │ ├── Physical_interactions.Matafora-Bachi-2009.txt │ │ │ ├── Physical_interactions.Matsumoto-Nakayama-2005.txt │ │ │ ├── Physical_interactions.McCracken-Blencowe-2005.txt │ │ │ ├── Physical_interactions.McFarland-Nussbaum-2008.txt │ │ │ ├── Physical_interactions.Meek-Piwnica-Worms-2004.txt │ │ │ ├── Physical_interactions.Meierhofer-Kaiser-2008.txt │ │ │ ├── Physical_interactions.Miyamoto-Sato-Yanagawa-2010.txt │ │ │ ├── Physical_interactions.Nakayama-Ohara-2002.txt │ │ │ ├── Physical_interactions.Nakayasu-Adkins-2013.txt │ │ │ ├── Physical_interactions.Napolitano-Meroni-2011.txt │ │ │ ├── Physical_interactions.Nathan-Goldberg-2013.txt │ │ │ ├── Physical_interactions.Neganova-Lako-2011.txt │ │ │ ├── Physical_interactions.Newman-Keating-2003.txt │ │ │ ├── Physical_interactions.Olah-Ovadi-2011.txt │ │ │ ├── Physical_interactions.Olma-Pintard-2009.txt │ │ │ ├── Physical_interactions.Oshikawa-Nakayama-2012.txt │ │ │ ├── Physical_interactions.Ouyang-Gill-2009.txt │ │ │ ├── Physical_interactions.Panigrahi-Pati-2012.txt │ │ │ ├── Physical_interactions.Perez-Hernandez-Yanez-Mo-2013.txt │ │ │ ├── Physical_interactions.Persaud-Rotin-2009.txt │ │ │ ├── Physical_interactions.Pichlmair-Superti-Furga-2011.txt │ │ │ ├── Physical_interactions.Pichlmair-Superti-Furga-2012.txt │ │ │ ├── Physical_interactions.Pilot-Storck-Goillot-2010.txt │ │ │ ├── Physical_interactions.Povlsen-Choudhary-2012.txt │ │ │ ├── Physical_interactions.Ramachandran-LaBaer-2004.txt │ │ │ ├── Physical_interactions.Ravasi-Hayashizaki-2010.txt │ │ │ ├── Physical_interactions.Reinke-Keating-2013.txt │ │ │ ├── Physical_interactions.Richter-Chrzanowska-Lightowlers-2010.txt │ │ │ ├── Physical_interactions.Roux-Burke-2012.txt │ │ │ ├── Physical_interactions.Rowbotham-Mermoud-2011.txt │ │ │ ├── Physical_interactions.Roy-Parent-2013.txt │ │ │ ├── Physical_interactions.Rual-Vidal-2005_A.txt │ │ │ ├── Physical_interactions.Rual-Vidal-2005_B.txt │ │ │ ├── Physical_interactions.San-Marina-Minden-2008.txt │ │ │ ├── Physical_interactions.Sang-Jackson-2011.txt │ │ │ ├── Physical_interactions.Sato-Conaway-2004.txt │ │ │ ├── Physical_interactions.Shi-Qin-2011.txt │ │ │ ├── Physical_interactions.Singh-Moore-2012.txt │ │ │ ├── Physical_interactions.Soler-Lopez-Aloy-2011.txt │ │ │ ├── Physical_interactions.Sowa-Harper-2009.txt │ │ │ ├── Physical_interactions.Stehling-Lill-2012.txt │ │ │ ├── Physical_interactions.Stelzl-Wanker-2005.txt │ │ │ ├── Physical_interactions.Suter-Wanker-2013.txt │ │ │ ├── Physical_interactions.Taipale-Lindquist-2012.txt │ │ │ ├── Physical_interactions.Takahashi-Conaway-2011.txt │ │ │ ├── Physical_interactions.Tarallo-Weisz-2011.txt │ │ │ ├── Physical_interactions.Tatham-Hay-2011.txt │ │ │ ├── Physical_interactions.Teixeira-Gomes-2010.txt │ │ │ ├── Physical_interactions.Thalappilly-Dusetti-2008.txt │ │ │ ├── Physical_interactions.Tsai-Cristea-2012.txt │ │ │ ├── Physical_interactions.Udeshi-Carr-2012.txt │ │ │ ├── Physical_interactions.Vandamme-Angrand-2011.txt │ │ │ ├── Physical_interactions.Vanderwerf-Bagby-2009.txt │ │ │ ├── Physical_interactions.Varjosalo-Gstaiger-2013_A.txt │ │ │ ├── Physical_interactions.Varjosalo-Gstaiger-2013_B.txt │ │ │ ├── Physical_interactions.Varjosalo-Superti-Furga-2013.txt │ │ │ ├── Physical_interactions.Venkatesan-Vidal-2009.txt │ │ │ ├── Physical_interactions.Vinayagam-Wanker-2011.txt │ │ │ ├── Physical_interactions.Wagner-Choudhary-2011.txt │ │ │ ├── Physical_interactions.Wallach-Kramer-2013.txt │ │ │ ├── Physical_interactions.Wang-Balch-2006.txt │ │ │ ├── Physical_interactions.Wang-He-2008.txt │ │ │ ├── Physical_interactions.Wang-Yang-2011.txt │ │ │ ├── Physical_interactions.Weimann-Stelzl-2013_A.txt │ │ │ ├── Physical_interactions.Weimann-Stelzl-2013_B.txt │ │ │ ├── Physical_interactions.Weinmann-Meister-2009.txt │ │ │ ├── Physical_interactions.Wilker-Yaffe-2007.txt │ │ │ ├── Physical_interactions.Wong-O'Bryan-2012.txt │ │ │ ├── Physical_interactions.Woods-Monteiro-2012.txt │ │ │ ├── Physical_interactions.Woodsmith-Sanderson-2012.txt │ │ │ ├── Physical_interactions.Wu-Li-2007.txt │ │ │ ├── Physical_interactions.Wu-Ma-2012.txt │ │ │ ├── Physical_interactions.Xiao-Lefkowitz-2007.txt │ │ │ ├── Physical_interactions.Xie-Cong-2013.txt │ │ │ ├── Physical_interactions.Xu-Jaffrey-2010.txt │ │ │ ├── Physical_interactions.Xu-Ye-2012.txt │ │ │ ├── Physical_interactions.Yang-Chen-2010.txt │ │ │ ├── Physical_interactions.Yatim-Benkirane-2012.txt │ │ │ ├── Physical_interactions.Yu-Chow-2013.txt │ │ │ ├── Physical_interactions.Yu-Vidal-2011.txt │ │ │ ├── Physical_interactions.Zanon-Pichler-2013.txt │ │ │ ├── Physical_interactions.Zhang-Zou-2011.txt │ │ │ ├── Physical_interactions.Zhao-Krug-2005.txt │ │ │ ├── Physical_interactions.Zhao-Yang-2011.txt │ │ │ ├── Physical_interactions.Zhou-Conrads-2004.txt │ │ │ ├── Physical_interactions.Zhou-Liang-2012.txt │ │ │ ├── Physical_interactions.de_Hoog-Mann-2004.txt │ │ │ ├── Physical_interactions.van_Wijk-Timmers-2009.txt │ │ │ ├── Predicted.I2D-BIND-Fly2Human.txt │ │ │ ├── Predicted.I2D-BIND-Mouse2Human.txt │ │ │ ├── Predicted.I2D-BIND-Rat2Human.txt │ │ │ ├── Predicted.I2D-BIND-Worm2Human.txt │ │ │ ├── Predicted.I2D-BIND-Yeast2Human.txt │ │ │ ├── Predicted.I2D-BioGRID-Fly2Human.txt │ │ │ ├── Predicted.I2D-BioGRID-Mouse2Human.txt │ │ │ ├── Predicted.I2D-BioGRID-Rat2Human.txt │ │ │ ├── Predicted.I2D-BioGRID-Worm2Human.txt │ │ │ ├── Predicted.I2D-BioGRID-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Chen-Pawson-2009-PiwiScreen-Mouse2Human.txt │ │ │ ├── Predicted.I2D-Formstecher-Daviet-2005-Embryo-Fly2Human.txt │ │ │ ├── Predicted.I2D-Giot-Rothbert-2003-Low-Fly2Human.txt │ │ │ ├── Predicted.I2D-INNATEDB-Mouse2Human.txt │ │ │ ├── Predicted.I2D-IntAct-Fly2Human.txt │ │ │ ├── Predicted.I2D-IntAct-Mouse2Human.txt │ │ │ ├── Predicted.I2D-IntAct-Rat2Human.txt │ │ │ ├── Predicted.I2D-IntAct-Worm2Human.txt │ │ │ ├── Predicted.I2D-IntAct-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Krogan-Greenblatt-2006-Core-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Krogan-Greenblatt-2006-NonCore-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Li-Vidal-2004-CORE-1-Worm2Human.txt │ │ │ ├── Predicted.I2D-Li-Vidal-2004-non-core-Worm2Human.txt │ │ │ ├── Predicted.I2D-MGI-Mouse2Human.txt │ │ │ ├── Predicted.I2D-MINT-Fly2Human.txt │ │ │ ├── Predicted.I2D-MINT-Mouse2Human.txt │ │ │ ├── Predicted.I2D-MINT-Rat2Human.txt │ │ │ ├── Predicted.I2D-MINT-Worm2Human.txt │ │ │ ├── Predicted.I2D-MINT-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Manual-Mouse2Human.txt │ │ │ ├── Predicted.I2D-Manual-Rat2Human.txt │ │ │ ├── Predicted.I2D-Ptacek-Snyder-2005-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Tarassov-PCA-Yeast2Human.txt │ │ │ ├── Predicted.I2D-Tewari-Vidal-2004-TGFb-Worm2Human.txt │ │ │ ├── Predicted.I2D-Wang-Orkin-2006-EScmplx-Mouse2Human.txt │ │ │ ├── Predicted.I2D-Wang-Orkin-2006-EScmplxlow-Mouse2Human.txt │ │ │ ├── Predicted.I2D-Yu-Vidal-2008-GoldStd-Yeast2Human.txt │ │ │ ├── Predicted.I2D-vonMering-Bork-2002-High-Yeast2Human.txt │ │ │ ├── Predicted.I2D-vonMering-Bork-2002-Low-Yeast2Human.txt │ │ │ ├── Predicted.I2D-vonMering-Bork-2002-Medium-Yeast2Human.txt │ │ │ ├── Predicted.Stuart-Kim-2003.txt │ │ │ └── Predicted.Wu-Stein-2010.txt │ ├── gene-protein │ │ └── ensembl_mapping.tsv │ ├── gene │ │ └── icgc_parsed.tsv │ ├── protein-function │ │ └── gene_association.goa_human │ ├── protein-protein │ │ └── string_data │ │ │ ├── coexpression-9606.tsv │ │ │ ├── combined_score-9606.tsv │ │ │ ├── cooccurence-9606.tsv │ │ │ ├── database-9606.tsv │ │ │ ├── experimental-9606.tsv │ │ │ ├── fusion-9606.tsv │ │ │ ├── neighborhood-9606.tsv │ │ │ └── textmining-9606.tsv │ └── protein │ │ ├── go_parsed.tsv │ │ ├── protein_mapping.tsv │ │ ├── string_parsed.tsv │ │ └── uniprot_ensembl.tsv └── protein_example │ ├── genemania │ └── README.txt │ ├── mappings │ └── string_genemania_mappings │ │ ├── 10090_gene_mapping.tsv │ │ ├── 10116_gene_mapping.tsv │ │ ├── 3702_gene_mapping.tsv │ │ ├── 4932_gene_mapping.tsv │ │ ├── 511145_gene_mapping.tsv │ 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