{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T23:44:01Z","timestamp":1767915841570,"version":"3.49.0"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,5,6]],"date-time":"2019-05-06T00:00:00Z","timestamp":1557100800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,5,6]],"date-time":"2019-05-06T00:00:00Z","timestamp":1557100800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000913","name":"James S. McDonnell Foundation","doi-asserted-by":"crossref","award":["220020394"],"award-info":[{"award-number":["220020394"]}],"id":[{"id":"10.13039\/100000913","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"crossref","award":["R01HL128173"],"award-info":[{"award-number":["R01HL128173"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fishel Fellowship in Cancer Research"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-2829-y","type":"journal-article","created":{"date-parts":[[2019,5,6]],"date-time":"2019-05-06T15:03:28Z","timestamp":1557155008000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["GeneSurrounder: network-based identification of disease genes in expression data"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7644-1166","authenticated-orcid":false,"given":"Sahil D.","family":"Shah","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosemary","family":"Braun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,5,6]]},"reference":[{"issue":"7","key":"2829_CR1","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","volume":"43","author":"Matthew E. Ritchie","year":"2015","unstructured":"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43(7):e47.","journal-title":"Nucleic Acids Research"},{"key":"2829_CR2","doi-asserted-by":"crossref","unstructured":"Manoli T, Gretz N, Gr\u00f6ne HJ, Kenzelmann M, Eils R, Brors B. Group testing for pathway analysis improves comparability of different microarray datasets. 2006; 22(20):2500.","DOI":"10.1093\/bioinformatics\/btl424"},{"issue":"2","key":"2829_CR3","doi-asserted-by":"publisher","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","volume":"8","author":"Purvesh Khatri","year":"2012","unstructured":"Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012; 8(2):1002375. https:\/\/doi.org\/10.1371\/journal.pcbi.1002375 .","journal-title":"PLoS Computational Biology"},{"key":"2829_CR4","unstructured":"Braun R, Shah S. Network methods for pathway analysis of gene expression data. 2014. arXiv [q-bio.QM]. arXiv. http:\/\/arxiv.org\/abs\/1411.1993."},{"issue":"Database","key":"2829_CR5","doi-asserted-by":"publisher","first-page":"D480","DOI":"10.1093\/nar\/gkm882","volume":"36","author":"M. Kanehisa","year":"2007","unstructured":"Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008; 36(SUPPL. 1):480\u20134. https:\/\/doi.org\/10.1093\/nar\/gkm882 .","journal-title":"Nucleic Acids Research"},{"issue":"43","key":"2829_CR6","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A. Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette Ma, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005; 102(43):15545\u201350. https:\/\/doi.org\/10.1073\/pnas.0506580102 .","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"2829_CR7","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1093\/bioinformatics\/btn577","volume":"25","author":"AL Tarca","year":"2009","unstructured":"Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim J-S, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics. 2009; 25(1):75\u201382.","journal-title":"Bioinformatics"},{"issue":"5","key":"2829_CR8","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1093\/bioinformatics\/btt008","volume":"29","author":"Z Gu","year":"2013","unstructured":"Gu Z, Wang J. CePa: an R package for finding significant pathways weighted by multiple network centralities. Bioinformatics. 2013; 29(5):658\u201360.","journal-title":"Bioinformatics"},{"key":"2829_CR9","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/1752-0509-6-56","volume":"6","author":"Z Gu","year":"2012","unstructured":"Gu Z, Liu J, Cao K, Zhang J, Wang J. Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC Syst Biol. 2012; 6:56.","journal-title":"BMC Syst Biol"},{"key":"2829_CR10","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","volume":"18","author":"T Ideker","year":"2002","unstructured":"Ideker T, Ozier O, Schwikowski B, Siegel A. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002; 18:233\u201340.","journal-title":"Bioinformatics"},{"issue":"3","key":"2829_CR11","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1089\/cmb.2010.0265","volume":"18","author":"F Vandin","year":"2011","unstructured":"Vandin F, Upfal E, Raphael BJ. Algorithms for detecting significantly mutated pathways in cancer. J Comput Biol. 2011; 18(3):507\u201322.","journal-title":"J Comput Biol"},{"issue":"9","key":"2829_CR12","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1093\/bioinformatics\/btr136","volume":"27","author":"H Ma","year":"2011","unstructured":"Ma H, Schadt EE, Kaplan LM, Zhao H. COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics. 2011; 27(9):1290\u20138.","journal-title":"Bioinformatics"},{"issue":"Suppl 6","key":"2829_CR13","first-page":"15","volume":"13","author":"B Jiang","year":"2014","unstructured":"Jiang B, Gribskov M. Assessment of subnetwork detection methods for breast cancer. Cancer Inform. 2014; 13(Suppl 6):15.","journal-title":"Cancer Inform"},{"issue":"5","key":"2829_CR14","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/nbt1203","volume":"24","author":"S Aerts","year":"2006","unstructured":"Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent L-C, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006; 24(5):537\u201344.","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2829_CR15","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1016\/j.ajhg.2008.02.013","volume":"82","author":"S K\u00f6hler","year":"2008","unstructured":"K\u00f6hler S, Bauer S, Horn D, Robinson PN. Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet. 2008; 82(4):949\u201358.","journal-title":"Am J Hum Genet"},{"issue":"5","key":"2829_CR16","doi-asserted-by":"publisher","first-page":"e5526","DOI":"10.1371\/journal.pone.0005526","volume":"4","author":"Daniela Nitsch","year":"2009","unstructured":"Nitsch D, Tranchevent L-C, Thienpont B, Thorrez L, Van Esch H, Devriendt K, Moreau Y. Network analysis of differential expression for the identification of disease-causing genes. PLoS ONE. 2009; 4(5):5526. https:\/\/doi.org\/10.1371\/journal.pone.0005526 .","journal-title":"PLoS ONE"},{"key":"2829_CR17","doi-asserted-by":"crossref","unstructured":"Shafi A, Donato M, Draghici S. A systems biology approach for the identification of significantly perturbed genes. In: Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (BCB \u201915). New York: ACM: 2015. p. 423\u201332. http:\/\/doi.org\/10.1145\/2808719.2808763 .","DOI":"10.1145\/2808719.2808763"},{"key":"2829_CR18","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1186\/1471-2105-14-365","volume":"14","author":"C Wu","year":"2013","unstructured":"Wu C, Zhu J, Zhang X. Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. BMC Bioinformatics. 2013; 14:365.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"2829_CR19","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1093\/bioinformatics\/btw676","volume":"33","author":"F Gwinner","year":"2017","unstructured":"Gwinner F, Boulday G, Vandiedonck C, Arnould M, Cardoso C, Nikolayeva I, Guitart-Pla O, Denis CV, Christophe OD, Beghain J, Tournier-Lasserve E, Schwikowski B. Network-based analysis of omics data: The LEAN method. Bioinformatics. 2017; 33(5):701\u20139.","journal-title":"Bioinformatics"},{"key":"2829_CR20","volume-title":"Statistical methods for research workers, 4th edition","author":"RA Fisher","year":"1932","unstructured":"Fisher RA. Statistical methods for research workers, 4th edition. London: Oliver and Boyd; 1932."},{"issue":"1","key":"2829_CR21","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1751-0473-3-15","volume":"3","author":"A Camargo","year":"2008","unstructured":"Camargo A, Azuaje F, Wang H, Zheng H. Permutation\u2013based statistical tests for multiple hypotheses. Source Code Biol Med. 2008; 3(1):15.","journal-title":"Source Code Biol Med"},{"key":"2829_CR22","doi-asserted-by":"crossref","unstructured":"Dudoit S, Shaffer JP, Boldrick JC. Multiple hypothesis testing in microarray experiments. U.C. Berkeley Division of Biostatistics Working Paper Series. 2002:71\u2013103. https:\/\/biostats.bepress.com\/ucbbiostat\/paper110\/ .","DOI":"10.1214\/ss\/1056397487"},{"key":"2829_CR23","doi-asserted-by":"publisher","unstructured":"Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L. curatedOvarianData: Clinically annotated data for the ovarian cancer transcriptome. Database. 2013; 2013:1\u201310. https:\/\/doi.org\/10.1093\/database\/bat013 .","DOI":"10.1093\/database\/bat013"},{"issue":"4","key":"2829_CR24","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1093\/bioinformatics\/btu684","volume":"31","author":"G Yu","year":"2015","unstructured":"Yu G, Wang L-G, Yan G-R, He Q-Y. DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2015; 31(4):608\u20139.","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"2829_CR25","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1093\/nar\/gkr972","volume":"40","author":"LM Schriml","year":"2012","unstructured":"Schriml LM, Arze C, Nadendla S, Chang Y-WW, Mazaitis M, Felix V, Feng G, Kibbe WA. Disease ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012; 40(Database issue):940\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"2829_CR26","doi-asserted-by":"publisher","first-page":"2417","DOI":"10.1158\/1078-0432.CCR-08-1276","volume":"15","author":"AA Kulkarni","year":"2009","unstructured":"Kulkarni AA, Kingsbury SR, Tudzarova S, Hong H-K, Loddo M, Rashid M, Rodriguez-Acebes S, Prevost AT, Ledermann JA, Stoeber K, Williams GH. Cdc7 kinase is a predictor of survival and a novel therapeutic target in epithelial ovarian carcinoma. Clin Cancer Res. 2009; 15(7):2417\u201325.","journal-title":"Clin Cancer Res"},{"key":"2829_CR27","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1755-8794-2-71","volume":"2","author":"NJ Bowen","year":"2009","unstructured":"Bowen NJ, Walker LD, Matyunina LV, Logani S, Totten KA, Benigno BB, McDonald JF. Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells. BMC Med Genomics. 2009; 2:71.","journal-title":"BMC Med Genomics"},{"issue":"9","key":"2829_CR28","doi-asserted-by":"publisher","first-page":"920","DOI":"10.1593\/neo.08216","volume":"10","author":"D Bonte","year":"2008","unstructured":"Bonte D, Lindvall C, Liu H, Dykema K, Furge K, Weinreich M. Cdc7-Dbf4 kinase overexpression in multiple cancers and tumor cell lines is correlated with p53 inactivation. Neoplasia. 2008; 10(9):920\u201331.","journal-title":"Neoplasia"},{"issue":"5","key":"2829_CR29","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1158\/1078-0432.CCR-11-2271","volume":"18","author":"M Riester","year":"2012","unstructured":"Riester M, Taylor JM, Feifer A, Koppie T, Rosenberg JE, Downey RJ, Bochner BH, Michor F. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clin Cancer Res. 2012; 18(5):1323\u201333.","journal-title":"Clin Cancer Res"},{"issue":"11","key":"2829_CR30","doi-asserted-by":"publisher","first-page":"1470","DOI":"10.1093\/bioinformatics\/btp167","volume":"25","author":"Jitao David Zhang","year":"2009","unstructured":"Zhang JD, Wiemann S. KEGGgraph: A graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics. 2009; 25(11):1470\u20131. https:\/\/doi.org\/10.1093\/bioinformatics\/btp167 .","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2829-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2829-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2829-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T08:33:29Z","timestamp":1694853209000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2829-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,6]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2829"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2829-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,6]]},"assertion":[{"value":"21 June 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 April 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 May 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"229"}}