{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T11:41:33Z","timestamp":1768477293950,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2017,11,20]],"date-time":"2017-11-20T00:00:00Z","timestamp":1511136000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,4]]},"DOI":"10.1093\/nar\/gkx1138","type":"journal-article","created":{"date-parts":[[2017,10,31]],"date-time":"2017-10-31T20:13:17Z","timestamp":1509480797000},"page":"D601-D607","source":"Crossref","is-referenced-by-count":43,"title":["FunCoup 4: new species, data, and visualization"],"prefix":"10.1093","volume":"46","author":[{"given":"Christoph","family":"Ogris","sequence":"first","affiliation":[]},{"given":"Dimitri","family":"Guala","sequence":"additional","affiliation":[]},{"given":"Mateusz","family":"Kaduk","sequence":"additional","affiliation":[]},{"given":"Erik L L","family":"Sonnhammer","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2017,11,20]]},"reference":[{"key":"key\n\t\t\t\t20180104212200_B1","doi-asserted-by":"crossref","first-page":"D449","DOI":"10.1093\/nar\/gkh086","article-title":"The Database of Interacting Proteins: 2004 update","volume":"32","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B2","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkt1115","article-title":"The MIntAct project\u2014IntAct as a common curation platform for 11 molecular interaction databases","volume":"42","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B3","first-page":"D991","article-title":"NCBI GEO: archive for functional genomics data sets\u2014update","volume":"41","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180104212200_B5","doi-asserted-by":"crossref","first-page":"D369","DOI":"10.1093\/nar\/gkw1102","article-title":"The BioGRID interaction database: 2017 update","volume":"45","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B6","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1089\/cmb.2006.13.810","article-title":"How scale-free are biological networks","volume":"13","year":"2006","journal-title":"J. Comput. Biol."},{"key":"key\n\t\t\t\t20180104212200_B7","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1093\/bfgp\/elr024","article-title":"Network-based methods for human disease gene prediction","volume":"10","year":"2011","journal-title":"Brief. Funct. Genomics"},{"key":"key\n\t\t\t\t20180104212200_B8","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/nbt825","article-title":"Global protein function prediction from protein-protein interaction networks","volume":"21","year":"2003","journal-title":"Nat. Biotech."},{"key":"key\n\t\t\t\t20180104212200_B9","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1186\/s12864-016-3176-2","article-title":"Large-scale gene co-expression network as a source of functional annotation for cattle genes","volume":"17","year":"2016","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180104212200_B10","doi-asserted-by":"crossref","first-page":"i130","DOI":"10.1093\/bioinformatics\/btu285","article-title":"Functional association networks as priors for gene regulatory network inference","volume":"30","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180104212200_B11","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1093\/nar\/gkw849","article-title":"A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation","volume":"45","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B12","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.1093\/bioinformatics\/btu344","article-title":"MaxLink: network-based prioritization of genes tightly linked to a disease seed set","volume":"30","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180104212200_B13","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.087528.108","article-title":"Global networks of functional coupling in eukaryotes from comprehensive data integration","volume":"19","year":"2009","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180104212200_B14","doi-asserted-by":"crossref","first-page":"D821","DOI":"10.1093\/nar\/gkr1062","article-title":"Comparative interactomics with Funcoup 2.0","volume":"40","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B15","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkt984","article-title":"FunCoup 3.0: database of genome-wide functional coupling networks","volume":"42","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B16","doi-asserted-by":"crossref","first-page":"D362","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: quality-controlled protein\u2013protein association networks, made broadly accessible","volume":"45","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B17","doi-asserted-by":"crossref","first-page":"W115","DOI":"10.1093\/nar\/gkt533","article-title":"GeneMANIA Prediction Server 2013 Update","volume":"41","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B18","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/ng.3259","article-title":"Understanding multicellular function and disease with human tissue-specific networks","volume":"47","year":"2015","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180104212200_B19","doi-asserted-by":"crossref","first-page":"D234","DOI":"10.1093\/nar\/gku1203","article-title":"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic","volume":"43","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B20","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/1479-7364-5-1-17","article-title":"What the papers say: Text mining for genomics and systems biology","volume":"5","year":"2010","journal-title":"Hum. Genomics"},{"key":"key\n\t\t\t\t20180104212200_B21","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt Consortium","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B22","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/1471-2105-9-405","article-title":"iRefIndex: A consolidated protein interaction database with provenance","volume":"9","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180104212200_B23","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","year":"2015","journal-title":"Science"},{"key":"key\n\t\t\t\t20180104212200_B24","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene Ontology Consortium: going forward","volume":"43","author":"Gene Ontology Consortium","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B25","doi-asserted-by":"crossref","first-page":"aaf1420","DOI":"10.1126\/science.aaf1420","article-title":"A global genetic interaction network maps a wiring diagram of cellular function","volume":"353","year":"2016","journal-title":"Science"},{"key":"key\n\t\t\t\t20180104212200_B26","doi-asserted-by":"crossref","first-page":"e1004120","DOI":"10.1371\/journal.pgen.1004120","article-title":"Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli","volume":"10","year":"2014","journal-title":"PLOS Genet."},{"key":"key\n\t\t\t\t20180104212200_B27","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1074\/mcp.O111.014704","article-title":"PaxDb, a database of protein abundance averages across all three domains of life","volume":"11","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"key\n\t\t\t\t20180104212200_B28","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B29","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","article-title":"Conservation of gene order: a fingerprint of proteins that physically interact","volume":"23","year":"1998","journal-title":"Trends Biochem. Sci."},{"key":"key\n\t\t\t\t20180104212200_B30","doi-asserted-by":"crossref","first-page":"3442","DOI":"10.1093\/nar\/28.18.3442","article-title":"STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene","volume":"28","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180104212200_B31","doi-asserted-by":"crossref","first-page":"D479","DOI":"10.1093\/nar\/gkn784","article-title":"OperonDB: a comprehensive database of predicted operons in microbial genomes","volume":"37","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180104212200_B32","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D3 - Data-Driven Documents","volume":"17","year":"2011","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"key\n\t\t\t\t20180104212200_B33","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1093\/bioinformatics\/btn213","article-title":"jSquid: a Java applet for graphical on-line network exploration","volume":"24","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180104212200_B34","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nature14877","article-title":"Panorama of ancient metazoan macromolecular complexes","volume":"525","year":"2015","journal-title":"Nature"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/D1\/D601\/23262428\/gkx1138.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:40:41Z","timestamp":1522680041000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/46\/D1\/D601\/4641901"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,20]]},"references-count":34,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2017,11,20]]},"published-print":{"date-parts":[[2018,1,4]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkx1138","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1,4]]},"published":{"date-parts":[[2017,11,20]]}}}