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Inst"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"3186","DOI":"10.1038\/onc.2011.36","article-title":"Identification of PUMA as an estrogen target gene that mediates the apoptotic response to tamoxifen in human breast cancer cells and predicts patient outcome and tamoxifen responsiveness in breast cancer","volume":"30","author":"CG Roberts","year":"2011","journal-title":"Oncogene"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1038\/cdd.2014.81","article-title":"Getting TRAIL back on track for cancer therapy","volume":"21","author":"J Lemke","year":"2014","journal-title":"Cell Death Differ"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1756-9966-29-10","article-title":"Distinct expression patterns of the E3 ligase SIAH-1 and its partner Kid\/KIF22 in normal tissues and in the breast tumoral processes","volume":"29","author":"H Bruzzoni-Giovanelli","year":"2010","journal-title":"J Exp Clin Cancer Res"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1158\/0008-5472.CAN-12-4348","article-title":"Siah: A promising anticancer target","author":"CSF Wong","year":"2013","journal-title":"Cancer Research"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"273","DOI":"10.2217\/fon.12.8","article-title":"Endocrine resistance in breast cancer: molecular pathways and rational development of targeted therapies","volume":"8","author":"RP Roop","year":"2012","journal-title":"Futur Oncol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1158\/1078-0432.CCR-10-2180","article-title":"Gene expression signature-based prognostic risk score in gastric cancer","volume":"17","author":"JY Cho","year":"2011","journal-title":"Clin Cancer Res"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1111\/cas.12356","article-title":"Context-dependent activation of Wnt signaling by tumor suppressor RUNX3 in gastric cancer cells","volume":"105","author":"X Ju","year":"2014","journal-title":"Cancer Sci"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s13073-015-0131-9","article-title":"The Sweden Cancerome Analysis Network\u2014Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine","volume":"7","author":"LH Saal","year":"2015","journal-title":"Genome Med"},{"key":"ref100","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0078644","article-title":"Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells","volume":"9","author":"S Zhao","year":"2014","journal-title":"PLoS One"},{"key":"ref101","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0052127","article-title":"Pathway Correlation Profile of Gene-Gene Co-Expression for Identifying Pathway Perturbation","volume":"7","author":"AN Tegge","year":"2012","journal-title":"PLoS One"},{"key":"ref102","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0087075","article-title":"Loss of connectivity in cancer co-expression networks","volume":"9","author":"R Anglani","year":"2014","journal-title":"PLoS One"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"19","DOI":"10.46582\/jsrm.0901005","article-title":"Regulated expression of CXCR4 constitutive active mutants revealed the up-modulated chemotaxis and up-regulation of genes crucial for CXCR4 mediated homing and engraftment of hematopoietic stem\/progenitor cells","volume":"9","author":"M Sharma","year":"2013","journal-title":"J Stem Cells Regen Med"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"2386","DOI":"10.1182\/blood.V124.21.2386.2386","article-title":"Adhesion Signaling States in AML","volume":"124","author":"CW Hu","year":"2014","journal-title":"Blood"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"e1002826","DOI":"10.1371\/journal.pcbi.1002826","article-title":"Chapter 1: Biomedical knowledge integration","volume":"8","author":"PRO Payne","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"e79217","DOI":"10.1371\/journal.pone.0079217","article-title":"A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity","volume":"8","author":"AL Tarca","year":"2013","journal-title":"PLoS One"},{"key":"ref107","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","author":"H Maciejewski","year":"2013","journal-title":"Brief Bioinform"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1186\/s12859-014-0390-2","article-title":"Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework","volume":"15","author":"L Yang","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"ref109","doi-asserted-by":"crossref","unstructured":"Koumakis L, Potamias G, Marias K, Tsiknakis M. An algorithmic approach for the effect of transcription factor binding sites over functional gene regulatory networks. Bioinformatics and Bioengineering (BIBE), 2015 IEEE 15th International Conference on. 2015. pp. 1\u20136.","DOI":"10.1109\/BIBE.2015.7367662"},{"key":"ref110","first-page":"1","author":"AJ Hartemink","year":"2001"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1126\/science.278.5338.680","article-title":"Exploring the metabolic and genetic control of gene expression on a genomic scale","volume":"278","author":"JL DeRisi","year":"1997","journal-title":"Science"},{"key":"ref112","first-page":"24","article-title":"Assessment of discretization techniques for relevant pattern discovery from gene expression data","author":"RG Pensa","year":"2004","journal-title":"Proc ACM BIOKDD"},{"key":"ref113","first-page":"1","article-title":"Discretization of gene expression data revised","author":"CA Gallo","year":"2015","journal-title":"Brief Bioinform"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1002\/(SICI)1098-111X(200001)15:1<61::AID-INT4>3.0.CO;2-O","article-title":"Entropy and MDL discretization of continuous variables for Bayesian belief networks","volume":"15","author":"EJ Clarke","year":"2000","journal-title":"Int J Intell Syst"},{"key":"ref115","unstructured":"Fayyad UM, Irani KB. Multi-Interval Discretization of Continuos-Valued Attributes for Classification Learning. Proceedings of the International Joint Conference on Uncertainty in AI. 1993. pp. 1022\u20131027."},{"key":"ref116","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1093\/bioinformatics\/18.5.725","article-title":"Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns","volume":"18","author":"J Li","year":"2002","journal-title":"Bioinformatics"},{"key":"ref117","first-page":"194","article-title":"Supervised and unsupervised discretization of continuous features","volume":"54","author":"J Dougherty","year":"1995","journal-title":"Mach Learn Proc Twelfth Int Conf"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1023\/A:1022611825350","article-title":"Boolean Feature Discovery in Empirical Learning","volume":"5","author":"G Pagallo","year":"1990","journal-title":"Mach Learn"},{"key":"ref119","doi-asserted-by":"crossref","unstructured":"Potamias G, Koumakis L, Moustakis V. Gene Selection via Discretized Gene-Expression Profiles and Greedy Feature-Elimination. Methods and Applications of Artificial Intelligence, Third Helenic Conference on AI, {SETN} 2004, Samos, Greece, May 5\u20138, 2004, Proceedings. 2004. pp. 256\u2013266.","DOI":"10.1007\/978-3-540-24674-9_27"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/BF00116251","article-title":"Induction of decision trees","volume":"1","author":"JR Quinlan","year":"1986","journal-title":"Mach Learn"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"2039","DOI":"10.1109\/18.930936","article-title":"Binomial and Poisson distributions as maximum entropy distributions","volume":"47","author":"P Harremo\u00ebs","year":"2001","journal-title":"IEEE Trans Inf Theory"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"S Anders","year":"2010","journal-title":"Genome Biol"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"7589","DOI":"10.1158\/0008-5472.CAN-06-2020","article-title":"Loss of p63 leads to increased cell migration and up-regulation of genes involved in invasion and metastasis","volume":"66","author":"CE Barbieri","year":"2006","journal-title":"Cancer Res"},{"key":"ref124","first-page":"83","article-title":"Modern Formal Methods and Applications SE\u20145","author":"A Richard","year":"2006"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1016\/S0140-6736(05)67424-7","article-title":"Genetic association studies","volume":"366","author":"HJ Cordell","year":"2005","journal-title":"Lancet"},{"key":"ref126","doi-asserted-by":"crossref","first-page":"R70","DOI":"10.1186\/gb-2003-4-10-r70","article-title":"Identifying biological themes within lists of genes with EASE","volume":"4","author":"D a Hosack","year":"2003","journal-title":"Genome Biol"},{"key":"ref127","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":"Y Benjamini","year":"2001","journal-title":"Ann Stat"},{"key":"ref128","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1093\/bioinformatics\/btg227","article-title":"The effect of replication on gene expression microarray experiments","volume":"19","author":"P Pavlidis","year":"2003","journal-title":"Bioinformatics"},{"key":"ref129","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1093\/bioinformatics\/18.9.1184","article-title":"Determination of minimum sample size and discriminatory expression patterns in microarray data","volume":"18","author":"D Hwang","year":"2002","journal-title":"Bioinformatics"},{"key":"ref130","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nrg1749","article-title":"Microarray data analysis: from disarray to consolidation and consensus","volume":"7","author":"DB Allison","year":"2006","journal-title":"Nat Rev Genet"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005187","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,13]],"date-time":"2022-07-13T02:29:10Z","timestamp":1657679350000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005187"}},"subtitle":[],"editor":[{"given":"Rachel","family":"Karchin","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,11,10]]},"references-count":130,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2016,11,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005187","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,11,10]]}}}