{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T14:55:05Z","timestamp":1771512905649,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,8,16]],"date-time":"2017-08-16T00:00:00Z","timestamp":1502841600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61571169"],"award-info":[{"award-number":["61571169"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,18]]},"DOI":"10.1093\/bib\/bbx091","type":"journal-article","created":{"date-parts":[[2017,7,9]],"date-time":"2017-07-09T07:07:02Z","timestamp":1499584022000},"page":"168-177","source":"Crossref","is-referenced-by-count":40,"title":["Pathway enrichment analysis approach based on topological structure and updated annotation of pathway"],"prefix":"10.1093","volume":"20","author":[{"given":"Qian","family":"Yang","sequence":"first","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enyu","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shunheng","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dianming","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haizhou","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qianqian","family":"Meng","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People\u2019s Republic of China"},{"name":"College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, People\u2019s Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,8,16]]},"reference":[{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B1","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1534\/g3.113.009688","article-title":"Fine mapping reveals that promotion susceptibility locus 1 (Psl1) is a compound locus with multiple genes that modify susceptibility to skin tumor development","volume":"4","author":"Angel","year":"2014","journal-title":"G3"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B2","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1089\/omi.2014.0121","article-title":"A systematic gene-gene and gene-environment interaction analysis of DNA repair genes XRCC1, XRCC2, XRCC3, XRCC4, and oral cancer risk","volume":"19","author":"Yang","year":"2015","journal-title":"OMICS"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B3","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1002\/cbf.3009","article-title":"Differential gene expression of the key signalling pathway in para-carcinoma, carcinoma and relapse human pancreatic cancer","volume":"32","author":"Chang","year":"2014","journal-title":"Cell Biochem Funct"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B4","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\t2019020107393162000_bbx091-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","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B6","doi-asserted-by":"crossref","first-page":"e87017.","DOI":"10.1371\/journal.pone.0087017","article-title":"Association between APOC1 polymorphism and Alzheimer's disease: a case-control study and meta-analysis","volume":"9","author":"Zhou","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B7","first-page":"17","article-title":"The emerging role of the Hippo pathway in lung cancers: clinical implications","author":"Das","year":"2016","journal-title":"Curr Drug Targets"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B8","first-page":"592","article-title":"Identifying hub genes and dysregulated pathways in hepatocellular carcinoma","volume":"19","author":"Jin","year":"2015","journal-title":"Eur Rev Med Pharmacol Sci"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B9","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1093\/bioinformatics\/bth234","article-title":"Gene co-expression network topology provides a framework for molecular characterization of cellular state","volume":"20","author":"Carter","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B10","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1093\/abbs\/gmt144","article-title":"Tumor suppressor p53 and its gain-of-function mutants in cancer","volume":"46","author":"Liu","year":"2014","journal-title":"Acta Biochim Biophys Sin"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B11","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.ajhg.2013.05.021","article-title":"Gain-of-function mutations in RIT1 cause Noonan syndrome, a RAS\/MAPK pathway syndrome","volume":"93","author":"Aoki","year":"2013","journal-title":"Am J Hum Genet"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B12","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1093\/bioinformatics\/btt008","article-title":"CePa: an R package for finding significant pathways weighted by multiple network centralities","volume":"29","author":"Gu","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B13","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\t2019020107393162000_bbx091-B14","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/nmeth.3963","article-title":"Impact of outdated gene annotations on pathway enrichment analysis","volume":"13","author":"Wadi","year":"2016","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B15","doi-asserted-by":"crossref","first-page":"2441","DOI":"10.1039\/C4MB00287C","article-title":"KEGG-PATH: Kyoto encyclopedia of genes and genomes-based pathway analysis using a path analysis model","volume":"10","author":"Du","year":"2014","journal-title":"Mol Biosyst"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B16","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/978-1-4939-3578-9_5","article-title":"The gene expression omnibus database","volume":"1418","author":"Clough","year":"2016","journal-title":"Methods Mol Biol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B17","first-page":"219","article-title":"Cancer genome atlas pan-cancer analysis project [in Chinese]","volume":"18","author":"Zhang","year":"2015","journal-title":"Zhongguo Fei Ai Za Zhi"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B18","doi-asserted-by":"crossref","first-page":"e131","DOI":"10.1093\/nar\/gkp667","article-title":"SubpathwayMiner: a software package for flexible identification of pathways","volume":"37","author":"Li","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B19","doi-asserted-by":"crossref","first-page":"R80.","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B20","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\t2019020107393162000_bbx091-B21","doi-asserted-by":"crossref","first-page":"413.","DOI":"10.1186\/1471-2105-12-413","article-title":"Impact of the spotted microarray preprocessing method on fold-change compression and variance stability","volume":"12","author":"Ambroise","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B22","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/srep00282","article-title":"Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses","volume":"2","author":"Jiang","year":"2012","journal-title":"Sci Rep"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B23","doi-asserted-by":"crossref","first-page":"20131057","DOI":"10.1098\/rsif.2013.1057","article-title":"Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease","volume":"11","author":"Meng","year":"2014","journal-title":"J R Soc Interface"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B24","doi-asserted-by":"crossref","first-page":"34427","DOI":"10.1074\/jbc.M302659200","article-title":"The Notch ligands, Jagged and Delta, are sequentially processed by alpha-secretase and presenilin\/gamma-secretase and release signaling fragments","volume":"278","author":"LaVoie","year":"2003","journal-title":"J Biol Chem"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B25","doi-asserted-by":"crossref","first-page":"baq020.","DOI":"10.1093\/database\/baq020","article-title":"GeneCards version 3: the human gene integrator","volume":"2010","author":"Safran","year":"2010","journal-title":"Database"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B26","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1207\/s15327914nc4701_10","article-title":"Mechanism of activation of caspase cascade during beta-carotene-induced apoptosis in human tumor cells","volume":"47","author":"Palozza","year":"2003","journal-title":"Nutr Cancer"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B27","doi-asserted-by":"crossref","first-page":"G490","DOI":"10.1152\/ajpgi.90393.2008","article-title":"KLF4 gene expression is inhibited by the notch signaling pathway that controls goblet cell differentiation in mouse gastrointestinal tract","volume":"296","author":"Zheng","year":"2009","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B28","doi-asserted-by":"crossref","first-page":"219","DOI":"10.3816\/CCC.2010.n.032","article-title":"The insulin-like growth factor signaling pathway as a target for treatment of colorectal carcinoma","volume":"9","author":"Ewing","year":"2010","journal-title":"Clin Colorectal Cancer"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B29","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1039\/C5MB00253B","article-title":"HOXC10 up-regulation contributes to human thyroid cancer and indicates poor survival outcome","volume":"11","author":"Feng","year":"2015","journal-title":"Mol BioSyst"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B30","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1590\/S0004-27302010000400010","article-title":"Expression of SMAD proteins, TGF-beta\/activin signaling mediators, in human thyroid tissues","volume":"54","author":"Matsuo","year":"2010","journal-title":"Arq Bras Endocrinol Metabol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B31","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.ygyno.2012.05.012","article-title":"Improved risk assessment of endometrial cancer by combined analysis of MSI, PI3K\u2013AKT, Wnt\/\u03b2-catenin and P53 pathway activation","volume":"126","author":"Nout","year":"2012","journal-title":"Gynecol Oncol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B32","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.mce.2016.01.019","article-title":"Up-regulation of genes involved in the insulin signalling pathway (IGF1, PTEN and IGFBP1) in the endometrium may link polycystic ovarian syndrome and endometrial cancer","volume":"424","author":"Shafiee","year":"2016","journal-title":"Mol Cell Endocrinol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B33","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.18632\/oncotarget.3066","article-title":"MicroRNA 196B regulates FAS-mediated apoptosis in colorectal cancer cells","volume":"6","author":"Mo","year":"2015","journal-title":"Oncotarget"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B34","doi-asserted-by":"crossref","first-page":"e116252.","DOI":"10.1371\/journal.pone.0116252","article-title":"Activation of the RhoB signaling pathway by thyroid hormone receptor beta in thyroid cancer cells","volume":"9","author":"Ichijo","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B35","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1158\/0008-5472.CAN-06-0981","article-title":"RET\/papillary thyroid carcinoma oncogenic signaling through the Rap1 small GTPase","volume":"67","author":"De Falco","year":"2007","journal-title":"Cancer Res"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B36","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/modpathol.3800579","article-title":"Phosphorylated KDR expression in endometrial cancer cells relates to HIF1alpha\/VEGF pathway and unfavourable prognosis","volume":"19","author":"Giatromanolaki","year":"2006","journal-title":"Mod Pathol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B37","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1007\/s00432-011-1103-0","article-title":"Roles of genetic variants in the PI3K and RAS\/RAF pathways in susceptibility to endometrial cancer and clinical outcomes","volume":"138","author":"Wang","year":"2011","journal-title":"J Cancer Res Clin Oncol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B38","doi-asserted-by":"crossref","first-page":"D488","DOI":"10.1093\/nar\/gkv1024","article-title":"WikiPathways: capturing the full diversity of pathway knowledge","volume":"44","author":"Kutmon","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B39","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\t2019020107393162000_bbx091-B40","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1161\/01.ATV.0000066134.79956.58","article-title":"High density lipoprotein-induced angiogenesis requires the activation of Ras\/MAP kinase in human coronary artery endothelial cells","volume":"23","author":"Miura","year":"2003","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B41","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1089\/ars.2011.4373","article-title":"p53-PGC-1alpha pathway mediates oxidative mitochondrial damage and cardiomyocyte necrosis induced by monoamine oxidase-A upregulation: role in chronic left ventricular dysfunction in mice","volume":"18","author":"Villeneuve","year":"2013","journal-title":"Antioxid Redox Signal"},{"key":"key\n\t\t\t\t2019020107393162000_bbx091-B42","doi-asserted-by":"crossref","first-page":"419.","DOI":"10.1186\/1471-2105-11-419","article-title":"TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs","volume":"11","author":"Lu","year":"2010","journal-title":"BMC Bioinformatics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/20\/1\/168\/27689764\/bbx091.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,29]],"date-time":"2019-09-29T01:32:32Z","timestamp":1569720752000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/20\/1\/168\/4083289"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,16]]},"references-count":42,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,8,16]]},"published-print":{"date-parts":[[2019,1,18]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbx091","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1]]},"published":{"date-parts":[[2017,8,16]]}}}