{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T15:54:21Z","timestamp":1743090861957,"version":"3.40.3"},"publisher-location":"Cham","reference-count":22,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319608150"},{"type":"electronic","value":"9783319608167"}],"license":[{"start":{"date-parts":[[2017,1,1]],"date-time":"2017-01-01T00:00:00Z","timestamp":1483228800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017]]},"DOI":"10.1007\/978-3-319-60816-7_18","type":"book-chapter","created":{"date-parts":[[2017,6,20]],"date-time":"2017-06-20T01:42:40Z","timestamp":1497922960000},"page":"146-154","source":"Crossref","is-referenced-by-count":2,"title":["Reproducibility of Finding Enriched Gene Sets in Biological Data Analysis"],"prefix":"10.1007","author":[{"given":"Joanna","family":"Zyla","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Marczyk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanna","family":"Polanska","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,6,21]]},"reference":[{"issue":"D1","key":"18_CR1","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","volume":"44","author":"M Kanehisa","year":"2016","unstructured":"Kanehisa, M., et al.: KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44(D1), D457\u2013D462 (2016)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"18_CR2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner, M., et al.: Gene ontology: tool for the unification of biology. Nat. Genet. 25(1), 25\u201329 (2000)","journal-title":"Nat. Genet."},{"issue":"43","key":"18_CR3","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian, A., et al.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102(43), 15545\u201315550 (2005)","journal-title":"PNAS"},{"issue":"12","key":"18_CR4","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/nmeth.1267","volume":"5","author":"S Dongen Van","year":"2008","unstructured":"Van Dongen, S., Abreu-Goodger, C., Enright, A.J.: Detecting microRNA binding and siRNA off-target effects from expression data. Nat. Methods 5(12), 1023\u20131025 (2008)","journal-title":"Nat. Methods"},{"issue":"1","key":"18_CR5","doi-asserted-by":"crossref","first-page":"e97","DOI":"10.1371\/journal.pone.0000097","volume":"1","author":"R Laaksonen","year":"2006","unstructured":"Laaksonen, R., et al.: A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS ONE 1(1), e97 (2006)","journal-title":"PLoS ONE"},{"issue":"9","key":"18_CR6","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1093\/bioinformatics\/bth088","volume":"20","author":"T Bei\u00dfbarth","year":"2004","unstructured":"Bei\u00dfbarth, T., Speed, T.P.: GOstat: find statistically overrepresented Gene ontologies within a group of genes. Bioinformatics 20(9), 1464\u20131465 (2004)","journal-title":"Bioinformatics"},{"issue":"11","key":"18_CR7","doi-asserted-by":"crossref","first-page":"e79217","DOI":"10.1371\/journal.pone.0079217","volume":"8","author":"AL Tarca","year":"2013","unstructured":"Tarca, A.L., Bhatti, G., Romero, R.: A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PLoS ONE 8(11), e79217 (2013)","journal-title":"PLoS ONE"},{"issue":"2","key":"18_CR8","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1093\/bib\/bbv049","volume":"17","author":"MK Jaakkola","year":"2016","unstructured":"Jaakkola, M.K., Elo, L.L.: Empirical comparison of structure-based pathway methods. Brief. Bioinform. 17(2), 336\u2013345 (2016)","journal-title":"Brief. Bioinform."},{"issue":"1","key":"18_CR9","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1186\/s12859-017-1674-0","volume":"18","author":"J Zyla","year":"2017","unstructured":"Zyla, J., Marczyk, M., Weiner, J., Polanska, J.: Ranking metrics in gene set enrichment analysis: do they matter?. BMC Bioinform.  18(1), 256 (2017)","journal-title":"BMC Bioinform."},{"issue":"1","key":"18_CR10","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","volume":"30","author":"R Edgar","year":"2002","unstructured":"Edgar, R., Domrachev, M., Lash, A.E.: Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30(1), 207\u2013210 (2002)","journal-title":"Nucleic Acids Res."},{"key":"18_CR11","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.2307\/2533862","volume":"54","author":"W Baumgartner","year":"1998","unstructured":"Baumgartner, W., Wei\u00df, P., Schindler, H.: A nonparametric test for the general two-sample problem. Biometrics 54, 1129\u20131135 (1998)","journal-title":"Biometrics"},{"issue":"1","key":"18_CR12","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","volume":"14","author":"S H\u00e4nzelmann","year":"2013","unstructured":"H\u00e4nzelmann, S., Castelo, R., Guinney, J.: GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 14(1), 7 (2013)","journal-title":"BMC Bioinform."},{"issue":"1","key":"18_CR13","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1186\/1471-2105-6-225","volume":"6","author":"J Tomfohr","year":"2005","unstructured":"Tomfohr, J., Lu, J., Kepler, T.B.: Pathway level analysis of gene expression using singular value decomposition. BMC Bioinform. 6(1), 225 (2005)","journal-title":"BMC Bioinform."},{"key":"18_CR14","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/1471-2105-13-136","volume":"13","author":"AL Tarca","year":"2012","unstructured":"Tarca, A.L., Draghici, S., Bhatti, G., Romero, R.: Down-weighting overlapping genes improves gene set analysis. BMC Bioinform. 13, 136 (2012)","journal-title":"BMC Bioinform."},{"issue":"4","key":"18_CR15","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1093\/bib\/bbt002","volume":"15","author":"H Maciejewski","year":"2014","unstructured":"Maciejewski, H.: Gene set analysis methods: statistical models and methodological differences. Brief. Bioinform. 15(4), 504\u2013518 (2014)","journal-title":"Brief. Bioinform."},{"issue":"9","key":"18_CR16","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.1007\/s11095-008-9661-9","volume":"25","author":"P Anand","year":"2008","unstructured":"Anand, P., et al.: Cancer is a preventable disease that requires major lifestyle changes. Pharm. Res. 25(9), 2097\u20132116 (2008)","journal-title":"Pharm. Res."},{"issue":"7","key":"18_CR17","doi-asserted-by":"crossref","first-page":"e101717","DOI":"10.1371\/journal.pone.0101717","volume":"9","author":"L Micallef","year":"2014","unstructured":"Micallef, L., Rodgers, P.: euler APE: drawing area-proportional 3-Venn diagrams using ellipses. PLoS ONE 9(7), e101717 (2014)","journal-title":"PLoS ONE"},{"issue":"2","key":"18_CR18","doi-asserted-by":"crossref","first-page":"117","DOI":"10.18632\/oncoscience.13","volume":"1","author":"A Zaravinos","year":"2014","unstructured":"Zaravinos, A., et al.: Altered metabolic pathways in clear cell renal cell carcinoma: a meta-analysis and validation study focused on the deregulated genes and their associated networks. Oncoscience 1(2), 117 (2014)","journal-title":"Oncoscience"},{"issue":"3","key":"18_CR19","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1007\/s11255-013-0511-2","volume":"46","author":"H Huang","year":"2014","unstructured":"Huang, H., et al.: Key pathways and genes controlling the development and progression of clear cell renal cell carcinoma (ccRCC) based on gene set enrichment analysis. Int. Urol. Nephrol. 46(3), 539\u2013553 (2014)","journal-title":"Int. Urol. Nephrol."},{"issue":"5","key":"18_CR20","doi-asserted-by":"crossref","first-page":"e10696","DOI":"10.1371\/journal.pone.0010696","volume":"5","author":"HW Tun","year":"2010","unstructured":"Tun, H.W., et al.: Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PLoS ONE 5(5), e10696 (2010)","journal-title":"PLoS ONE"},{"issue":"5","key":"18_CR21","first-page":"7029","volume":"8","author":"H Zheng","year":"2015","unstructured":"Zheng, H., Guo, X., Tian, Q., Li, H., Zhu, Y.: Distinct role of Tim-3 in systemic lupus erythematosus and clear cell renal cell carcinoma. Int. J. Clin. Exp. Med. 8(5), 7029 (2015)","journal-title":"Int. J. Clin. Exp. Med."},{"issue":"19","key":"18_CR22","doi-asserted-by":"crossref","first-page":"5703","DOI":"10.1158\/1078-0432.CCR-07-0603","volume":"13","author":"T Morikawa","year":"2007","unstructured":"Morikawa, T., et al.: Identification of Toll-like receptor 3 as a potential therapeutic target in clear cell renal cell carcinoma. Clin. Cancer Res. 13(19), 5703\u20135709 (2007)","journal-title":"Clin. Cancer Res."}],"container-title":["Advances in Intelligent Systems and Computing","11th International Conference on Practical Applications of Computational Biology &amp; Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-60816-7_18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,7,20]],"date-time":"2017-07-20T22:21:46Z","timestamp":1500589306000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-60816-7_18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017]]},"ISBN":["9783319608150","9783319608167"],"references-count":22,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-60816-7_18","relation":{},"ISSN":["2194-5357","2194-5365"],"issn-type":[{"type":"print","value":"2194-5357"},{"type":"electronic","value":"2194-5365"}],"subject":[],"published":{"date-parts":[[2017]]}}}