{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T17:10:54Z","timestamp":1761844254150},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1243,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt386","type":"journal-article","created":{"date-parts":[[2013,5,11]],"date-time":"2013-05-11T03:30:30Z","timestamp":1368243030000},"page":"W89-W97","source":"Crossref","is-referenced-by-count":44,"title":["Graphite Web: web tool for gene set analysis exploiting pathway topology"],"prefix":"10.1093","volume":"41","author":[{"given":"Gabriele","family":"Sales","sequence":"first","affiliation":[]},{"given":"Enrica","family":"Calura","sequence":"additional","affiliation":[]},{"given":"Paolo","family":"Martini","sequence":"additional","affiliation":[]},{"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2013,5,10]]},"reference":[{"key":"key\n\t\t\t\t20171013120744_gkt386-B1","doi-asserted-by":"crossref","first-page":"W505","DOI":"10.1093\/nar\/gks445","article-title":"SteinerNet: a web server for integrating \u2018omic\u2019 data to discover hidden components of response pathways","volume":"40","author":"Tuncbag","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B2","doi-asserted-by":"crossref","first-page":"W424","DOI":"10.1093\/nar\/gkr359","article-title":"ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data","volume":"39","author":"Lan","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B3","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.4161\/epi.6.12.18176","article-title":"EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans","volume":"6","author":"Wang","year":"2011","journal-title":"Epigenetics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B4","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1186\/1471-2164-13-282","article-title":"NetWalker: a contextual network analysis tool for functional genomics","volume":"13","author":"Komurov","year":"2012","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B5","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/bioinformatics\/btn577","article-title":"A novel signaling pathway impact analysis","volume":"25","author":"Tarca","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B6","doi-asserted-by":"crossref","first-page":"13544","DOI":"10.1073\/pnas.0506577102","article-title":"Discovering statistically significant pathways in expression profiling studies","volume":"102","author":"Tian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B7","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/bioinformatics\/btg382","article-title":"A global test for groups of genes: testing association with a clinical outcome","volume":"20","author":"Goeman","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B8","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/ng1180","article-title":"PGC-1\u03b1-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes","volume":"34","author":"Mootha","year":"2003","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B9","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","author":"Subramanian","year":"2005","journal-title":"PNAS"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B10","doi-asserted-by":"crossref","first-page":"e19","DOI":"10.1093\/nar\/gks866","article-title":"Along signal paths: an empirical gene set approach exploiting pathway topology","volume":"41","author":"Martini","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B11","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1055","article-title":"Calculating the statistical significance of changes in pathway activity from gene expression data","volume":"3","author":"Rahnenf\u00fchrer","year":"2004","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B12","doi-asserted-by":"crossref","first-page":"P10","DOI":"10.1186\/1471-2105-11-S4-P10","article-title":"WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit","volume":"11","author":"Duncan","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B13","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1186\/1471-2105-9-552","article-title":"GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments","volume":"9","author":"Keller","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B14","doi-asserted-by":"crossref","first-page":"P3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: Database for annotation, visualization, and integrated discovery","volume":"4","author":"Dennis","year":"2003","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B15","doi-asserted-by":"crossref","first-page":"W210","DOI":"10.1093\/nar\/gkq388","article-title":"Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling","volume":"38","author":"Medina","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B16","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","article-title":"Analyzing gene expression data in terms of gene sets: methodological issues","volume":"23","author":"Goeman","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B17","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1471-2105-13-20","article-title":"graphite - a Bioconductor package to convert pathway topology to gene network","volume":"13","author":"Sales","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B18","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/1752-0509-4-121","article-title":"Gene set analysis exploiting the topology of a pathway","volume":"4","author":"Massa","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B19","doi-asserted-by":"crossref","first-page":"D355","DOI":"10.1093\/nar\/gkp896","article-title":"KEGG for representation and analysis of molecular networks involving diseases and drugs","volume":"38","author":"Kanehisa","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B20","doi-asserted-by":"crossref","first-page":"R39","DOI":"10.1186\/gb-2007-8-3-r39","article-title":"Reactome: a knowledge base of biologic pathways and processes","volume":"8","author":"Vastrik","year":"2007","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B21","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1093\/bioinformatics\/btq430","article-title":"Cytoscape Web: an interactive web-based network browser","volume":"26","author":"Lopes","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B22","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1093\/bib\/bbn001","article-title":"Gene-set approach for expression pattern analysis","volume":"9","author":"Nam","year":"2008","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B23","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1093\/bib\/bbr049","article-title":"Gene set enrichment analysis: performance evaluation and usage guidelines","volume":"13","author":"Hung","year":"2012","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B24","article-title":"The limitations of simple gene set enrichment analysis assuming gene independence","author":"Tamayo","year":"2012","journal-title":"Stat. Methods Med. Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B25","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1177\/0962280209351908","article-title":"Gene set enrichment analysis made simple","volume":"18","author":"Irizarry","year":"2009","journal-title":"Stat. Methods Med. Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B26","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1471-2105-10-47","article-title":"A general modular framework for gene set enrichment analysis","volume":"10","author":"Ackermann","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B27","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1093\/bib\/bbn042","article-title":"Gene-set analysis and reduction","volume":"10","author":"Dinu","year":"2009","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B28","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1093\/bioinformatics\/btf877","article-title":"Identifying differentially expressed genes using false discovery rate controlling procedures","volume":"19","author":"Reiner","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B29","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B30","doi-asserted-by":"crossref","first-page":"R14","DOI":"10.1186\/gb-2010-11-2-r14","article-title":"Gene ontology analysis for RNA-seq: accounting for selection bias","volume":"11","author":"Young","year":"2010","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B31","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1186\/1471-2105-8-242","article-title":"Improving gene set analysis of microarray data by SAM-GS","volume":"8","author":"Dinu","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B32","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1186\/1471-2105-5-193","article-title":"Comparing functional annotation analyses with Catmap","volume":"5","author":"Breslin","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B33","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","article-title":"Significance analysis of functional categories in gene expression studies: a structured permutation approach","volume":"21","author":"Barry","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B34","doi-asserted-by":"crossref","first-page":"W206","DOI":"10.1093\/nar\/gkm327","article-title":"Onto-Tools: new additions and improvements in 2006","volume":"35","author":"Khatri","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B35","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1214\/aos\/1013699998","article-title":"The control of the false discovery rate in multiple testing under dependency","volume":"29","author":"Benjamini","year":"2001","journal-title":"Annals of Statistics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B36","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-3242-6","volume-title":"Generalized Linear Models","author":"McCullagh","year":"1989"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B37","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B38","doi-asserted-by":"crossref","first-page":"Article3","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical bayes methods for assessing differential expression in microarray experiments","volume":"3","author":"Smyth","year":"2004","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B39","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1111\/j.1349-7006.1997.tb00461.x","article-title":"Expressions of cell cycle regulators in human colorectal cancer cell lines","volume":"88","author":"Tominaga","year":"1997","journal-title":"Jpn. J. Cancer Res."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B40","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1515\/BC.2004.053","article-title":"Colon cancer: genomics and apoptotic events","volume":"385","author":"Rupnarain","year":"2004","journal-title":"Biol. Chem."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B41","doi-asserted-by":"crossref","first-page":"7233","DOI":"10.3748\/wjg.v12.i45.7233","article-title":"Colon cancer and the immune system: the role of tumor invading T cells","volume":"12","author":"Waldner","year":"2006","journal-title":"World J. Gastroenterol."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B42","first-page":"21","article-title":"Reduced expression of TLR4 is associated with the metastatic status of human colorectal cancer","volume":"20","author":"Simiantonaki","year":"2007","journal-title":"Int. J. Mol. Med."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B43","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.cell.2004.07.002","article-title":"Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis","volume":"118","author":"Rakoff-Nahoum","year":"2004","journal-title":"Cell"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B44","doi-asserted-by":"crossref","first-page":"2974","DOI":"10.1002\/ijc.26314","article-title":"Toll-like receptor genes and their association with colon and rectal cancer development and prognosis","volume":"130","author":"Slattery","year":"2012","journal-title":"Int. J. Cancer"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B45","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1593\/neo.07971","article-title":"Inhibition of JAK1, 2\/STAT3 signaling induces apoptosis, cell cycle arrest, and reduces tumor cell invasion in colorectal cancer cells","volume":"10","author":"Xiong","year":"2008","journal-title":"Neoplasia"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B46","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.ctrv.2012.07.003","article-title":"Does interleukin-6 link explain the link between tumour necrosis, local and systemic inflammatory responses and outcome in patients with colorectal cancer?","volume":"39","author":"Guthrie","year":"2013","journal-title":"Cancer Treat. Rev."},{"key":"key\n\t\t\t\t20171013120744_gkt386-B47","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1093\/carcin\/bgp236","article-title":"Role of Notch signaling in colorectal cancer","volume":"30","author":"Qiao","year":"2009","journal-title":"Carcinogenesis"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B48","doi-asserted-by":"crossref","first-page":"4075","DOI":"10.1038\/onc.2011.122","article-title":"Hypoxia-induced Jagged2 promotes breast cancer metastasis and self-renewal of cancer stem-like cells","volume":"30","author":"Xing","year":"2011","journal-title":"Oncogene"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B49","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1002\/ijc.24032","article-title":"HIF-1\u03b1 and HIF-2\u03b1 have divergent roles in colon cancer","volume":"124","author":"Imamura","year":"2009","journal-title":"Int. J. Cancer"},{"key":"key\n\t\t\t\t20171013120744_gkt386-B50","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/S1470-2045(05)70168-6","article-title":"The MAPK signalling pathways and colorectal cancer","volume":"6","author":"Fang","year":"2005","journal-title":"Lancet Oncol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W89\/3836897\/gkt386.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,16]],"date-time":"2022-02-16T19:24:51Z","timestamp":1645039491000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W89\/1098410\/Graphite-Web-web-tool-for-gene-set-analysis"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,10]]},"references-count":50,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,5,10]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt386","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,5,10]]}}}