{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T01:53:14Z","timestamp":1774489994411,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T00:00:00Z","timestamp":1510099200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,4]]},"DOI":"10.1093\/nar\/gkx1040","type":"journal-article","created":{"date-parts":[[2017,11,3]],"date-time":"2017-11-03T20:11:30Z","timestamp":1509739890000},"page":"D668-D676","source":"Crossref","is-referenced-by-count":25,"title":["PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology"],"prefix":"10.1093","volume":"46","author":[{"given":"Zongliang","family":"Yue","sequence":"first","affiliation":[]},{"given":"Qi","family":"Zheng","sequence":"additional","affiliation":[]},{"given":"Michael T","family":"Neylon","sequence":"additional","affiliation":[]},{"given":"Minjae","family":"Yoo","sequence":"additional","affiliation":[]},{"given":"Jimin","family":"Shin","sequence":"additional","affiliation":[]},{"given":"Zhiying","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Aik Choon","family":"Tan","sequence":"additional","affiliation":[]},{"given":"Jake Y","family":"Chen","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2017,11,8]]},"reference":[{"key":"key\n\t\t\t\t20180103185722_B1","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.1069492","article-title":"Systems biology: a brief overview","volume":"295","year":"2002","journal-title":"Science"},{"key":"key\n\t\t\t\t20180103185722_B2","doi-asserted-by":"crossref","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: current approaches and outstanding challenges","volume":"8","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20180103185722_B3","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/nrg3552","article-title":"Integrative approaches for finding modular structure in biological networks","volume":"14","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180103185722_B4","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ng1180","article-title":"PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes","volume":"34","year":"2003","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180103185722_B5","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20180103185722_B6","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-1-4939-0512-6_9","article-title":"A description of the Molecular Signatures Database (MSigDB) Web site","volume":"1150","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20180103185722_B7","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185722_B8","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","year":"2015","journal-title":"Cell Syst."},{"key":"key\n\t\t\t\t20180103185722_B9","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1093\/bib\/bbt002","article-title":"Gene set analysis methods: statistical models and methodological differences","volume":"15","year":"2014","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20180103185722_B10","doi-asserted-by":"crossref","first-page":"D1060","DOI":"10.1093\/nar\/gkr901","article-title":"GeneSigDB: a manually curated database and resource for analysis of gene expression signatures","volume":"40","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B11","doi-asserted-by":"crossref","first-page":"i250","DOI":"10.1093\/bioinformatics\/btv265","article-title":"PAGER: constructing PAGs and new PAG-PAG relationships for network biology","volume":"31","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185722_B12","doi-asserted-by":"crossref","first-page":"44232","DOI":"10.1038\/srep44232","article-title":"Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue","volume":"7","year":"2017","journal-title":"Sci. Rep."},{"key":"key\n\t\t\t\t20180103185722_B13","doi-asserted-by":"crossref","first-page":"1898","DOI":"10.1111\/ajt.12283","article-title":"Gene set enrichment analysis identifies key innate immune pathways in primary graft dysfunction after lung transplantation","volume":"13","year":"2013","journal-title":"Am. J. Transplant."},{"key":"key\n\t\t\t\t20180103185722_B14","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/srep00464","article-title":"Gene set enrichment analysis identifies LIF as a negative regulator of human Th2 cell differentiation","volume":"2","year":"2012","journal-title":"Sci. Rep."},{"key":"key\n\t\t\t\t20180103185722_B15","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1477-7827-7-94","article-title":"A cross-study gene set enrichment analysis identifies critical pathways in endometriosis","volume":"7","year":"2009","journal-title":"Reprod. Biol. Endocrinol."},{"key":"key\n\t\t\t\t20180103185722_B16","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s12864-017-3512-1","article-title":"HAPPI-2: a comprehensive and high-quality map of human annotated and predicted protein interactions","volume":"18","year":"2017","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180103185722_B17","first-page":"367","article-title":"Mining Alzheimer disease relevant proteins from integrated protein interactome data","year":"2006","journal-title":"Pac. Symp. Biocomput."},{"key":"key\n\t\t\t\t20180103185722_B18","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/ng0504-431","article-title":"The genetic association database","volume":"36","year":"2004","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180103185722_B19","doi-asserted-by":"crossref","first-page":"D1001","DOI":"10.1093\/nar\/gkt1229","article-title":"The NHGRI GWAS Catalog, a curated resource of SNP-trait associations","volume":"42","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B20","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1038\/nbt.2749","article-title":"Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data","volume":"31","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20180103185722_B21","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.immuni.2015.12.006","article-title":"Compendium of immune signatures identifies conserved and species-specific biology in response to inflammation","volume":"44","year":"2016","journal-title":"Immunity"},{"key":"key\n\t\t\t\t20180103185722_B22","doi-asserted-by":"crossref","first-page":"501","DOI":"10.2217\/pgs.10.15","article-title":"Pharmacogenomics and bioinformatics: PharmGKB","volume":"11","year":"2010","journal-title":"Pharmacogenomics"},{"key":"key\n\t\t\t\t20180103185722_B23","doi-asserted-by":"crossref","first-page":"3069","DOI":"10.1093\/bioinformatics\/btv313","article-title":"DSigDB: drug signatures database for gene set analysis","volume":"31","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185722_B24","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1471-2105-9-110","article-title":"SPIKE\u2013a database, visualization and analysis tool of cellular signaling pathways","volume":"9","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180103185722_B25","doi-asserted-by":"crossref","first-page":"e184","DOI":"10.1371\/journal.pbio.0060184","article-title":"WikiPathways: pathway editing for the people","volume":"6","year":"2008","journal-title":"PLoS Biol."},{"issue":"Suppl. 11","key":"key\n\t\t\t\t20180103185722_B26","first-page":"S5","article-title":"HPD: an online integrated human pathway database enabling systems biology studies","volume":"10","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180103185722_B27","doi-asserted-by":"crossref","first-page":"D691","DOI":"10.1093\/nar\/gkq1018","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B28","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1089\/152791601750294344","article-title":"BioCarta","volume":"2","year":"2001","journal-title":"Biotech. Softw. Internet Rep."},{"key":"key\n\t\t\t\t20180103185722_B29","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the Pathway Interaction Database","volume":"37","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B30","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/27.1.29","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"27","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B31","first-page":"D154","article-title":"miRBase: tools for microRNA genomics","volume":"36","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B32","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","year":"2015","journal-title":"Elife"},{"key":"key\n\t\t\t\t20180103185722_B33","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkv1258","article-title":"miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database","volume":"44","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B34","doi-asserted-by":"crossref","first-page":"E2341","DOI":"10.1002\/humu.22096","article-title":"NGS catalog: a database of next generation sequencing studies in humans","volume":"33","year":"2012","journal-title":"Hum. Mutat."},{"key":"key\n\t\t\t\t20180103185722_B35","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1089\/bio.2015.29031.hmm","article-title":"The Genotype-Tissue Expression (GTEx) Project","volume":"13","year":"2015","journal-title":"Biopreserv. Biobank"},{"key":"key\n\t\t\t\t20180103185722_B36","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene Ontology Consortium: going forward","volume":"43","author":"Gene Ontology, C.","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B37","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B38","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1093\/bioinformatics\/btu164","article-title":"Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles","volume":"30","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180103185722_B39","first-page":"918710","article-title":"GNormPlus: An Integrative approach for tagging genes, gene families, and protein domains","volume":"2015","year":"2015","journal-title":"Biomed. Res. Int."},{"key":"key\n\t\t\t\t20180103185722_B40","doi-asserted-by":"crossref","first-page":"D12","DOI":"10.1093\/nar\/gkw1071","article-title":"Database Resources of the National Center for Biotechnology Information","volume":"45","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180103185722_B41","doi-asserted-by":"crossref","first-page":"S377","DOI":"10.1097\/JTO.0b013e31826df0bc","article-title":"Targeting MEK for the treatment of non-small-cell lung cancer","volume":"7","year":"2012","journal-title":"J. Thorac. Oncol."},{"key":"key\n\t\t\t\t20180103185722_B42","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1634\/theoncologist.2016-0458","article-title":"Targeting BRAF-mutant non-small cell lung cancer: from molecular profiling to rationally designed therapy","volume":"22","year":"2017","journal-title":"Oncologist"},{"key":"key\n\t\t\t\t20180103185722_B43","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1093\/annonc\/mdv072","article-title":"A randomized phase II study of the MEK1\/MEK2 inhibitor trametinib (GSK1120212) compared with docetaxel in KRAS-mutant advanced non-small-cell lung cancer (NSCLC)dagger","volume":"26","year":"2015","journal-title":"Ann. Oncol."},{"key":"key\n\t\t\t\t20180103185722_B44","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/S1470-2045(12)70489-8","article-title":"Selumetinib plus docetaxel for KRAS-mutant advanced non-small-cell lung cancer: a randomised, multicentre, placebo-controlled, phase 2 study","volume":"14","year":"2013","journal-title":"Lancet Oncol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/D1\/D668\/23162136\/gkx1040.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,5]],"date-time":"2019-10-05T15:36:00Z","timestamp":1570289760000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/46\/D1\/D668\/4602868"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,8]]},"references-count":44,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2017,11,8]]},"published-print":{"date-parts":[[2018,1,4]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkx1040","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":[[2017,11,8]]}}}