{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T02:54:41Z","timestamp":1773284081820,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T00:00:00Z","timestamp":1570406400000},"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\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA118100"],"award-info":[{"award-number":["P30CA118100"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Somatic mutation and gene expression dysregulation are considered two major tumorigenesis factors. While independent investigations of either factor pervade, studies of associations between somatic mutations and gene expression changes have been sporadic and nonsystematic. Utilizing genomic data collected from 11\u00a0315 subjects of 33 distinct cancer types, we constructed MutEx, a pan-cancer integrative genomic database. This database records the relationships among gene expression, somatic mutation and survival data for cancer patients. MutEx can be used to swiftly explore the relationship between these genomic\/clinic features within and across cancer types and, more importantly, search for corroborating evidence for hypothesis inception. Our database also incorporated Gene Ontology and several pathway databases to enhance functional annotation, and elastic net and a gene expression composite score to aid in survival analysis. To demonstrate the usability of MutEx, we provide several application examples, including top somatic mutations associated with the most extensive expression dysregulation in breast cancer, differential mutational burden downstream of DNA mismatch repair gene mutations and composite gene expression score-based survival difference in breast cancer. MutEx can be accessed at http:\/\/www.innovebioinfo.com\/Databases\/Mutationdb_About.php.<\/jats:p>","DOI":"10.1093\/bib\/bbz084","type":"journal-article","created":{"date-parts":[[2019,6,18]],"date-time":"2019-06-18T19:13:33Z","timestamp":1560885213000},"page":"1479-1486","source":"Crossref","is-referenced-by-count":12,"title":["MutEx: a multifaceted gateway for exploring integrative pan-cancer genomic data"],"prefix":"10.1093","volume":"21","author":[{"given":"Jie","family":"Ping","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center, Nashville, USA, 37232"}]},{"given":"Olufunmilola","family":"Oyebamiji","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA, 87109"}]},{"given":"Hui","family":"Yu","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA, 87109"}]},{"given":"Scott","family":"Ness","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA, 87109"}]},{"given":"Jeremy","family":"Chien","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA, 87109"}]},{"given":"Fei","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Vanderbilt University Medical Center, Nashville, USA, 37232"}]},{"given":"Huining","family":"Kang","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA, 87109"}]},{"given":"David","family":"Samuels","sequence":"additional","affiliation":[{"name":"Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, USA, 37232"}]},{"given":"Sergey","family":"Ivanov","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Vanderbilt University, Nashville, USA, 37232"}]},{"given":"Danqian","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China"}]},{"given":"Ying-yong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5252-3960","authenticated-orcid":false,"given":"Yan","family":"Guo","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA, 87109"}]}],"member":"286","published-online":{"date-parts":[[2019,10,7]]},"reference":[{"key":"2020080709263807200_ref1","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/embor.2013.92","article-title":"Cancer heterogeneity\u2014a multifaceted view","volume":"14","author":"Melo","year":"2013","journal-title":"EMBO Rep"},{"key":"2020080709263807200_ref2","doi-asserted-by":"crossref","DOI":"10.1126\/science.aan2507","article-title":"A pathology atlas of the human cancer transcriptome","volume":"357","author":"Uhlen","year":"2017","journal-title":"Science"},{"key":"2020080709263807200_ref3","first-page":"1896","article-title":"From genome to function by studying eQTLs","volume":"2014","author":"Westra","year":"1842","journal-title":"Biochim Biophys Acta"},{"key":"2020080709263807200_ref4","doi-asserted-by":"crossref","first-page":"30595","DOI":"10.1038\/srep30595","article-title":"eSNPO: an eQTL-based SNP ontology and SNP functional enrichment analysis platform","volume":"6","author":"Li","year":"2016","journal-title":"Sci Rep"},{"key":"2020080709263807200_ref5","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2020080709263807200_ref6","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/978-1-4939-0512-6_3","article-title":"edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology","volume":"1150","author":"Nikolayeva","year":"2014","journal-title":"Methods Mol Biol"},{"key":"2020080709263807200_ref7","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1111\/j.1467-9868.2007.00577.x","article-title":"Regression coefficient and autoregressive order shrinkage and selection via the lasso","volume":"69","author":"Wang","year":"2007","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"2020080709263807200_ref8","doi-asserted-by":"crossref","first-page":"986048","DOI":"10.1155\/2014\/986048","article-title":"Advanced heat map and clustering analysis using heatmap3","volume":"2014","author":"Zhao","year":"2014","journal-title":"Biomed Res Int"},{"key":"2020080709263807200_ref9","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature12213","article-title":"Mutational heterogeneity in cancer and the search for new cancer-associated genes","volume":"499","author":"Lawrence","year":"2013","journal-title":"Nature"},{"key":"2020080709263807200_ref10","doi-asserted-by":"crossref","first-page":"4692","DOI":"10.1038\/s41388-018-0273-5","article-title":"KMT2C mediates the estrogen dependence of breast cancer through regulation of ER alpha enhancer function","volume":"37","author":"Gala","year":"2018","journal-title":"Oncogene"},{"key":"2020080709263807200_ref11","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1158\/1541-7786.MCR-09-0484","article-title":"Crosstalk of EDA-A2\/XEDAR in the p53 signaling pathway","volume":"8","author":"Tanikawa","year":"2010","journal-title":"Mol Cancer Res"},{"key":"2020080709263807200_ref12","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1097\/PAT.0b013e32835d0efb","article-title":"Tumours associated with BAP1 mutations","volume":"45","author":"Murali","year":"2013","journal-title":"Pathology"},{"key":"2020080709263807200_ref13","doi-asserted-by":"crossref","first-page":"ra90","DOI":"10.1126\/scisignal.aac6757","article-title":"The E3 ligase RNF43 inhibits Wnt signaling downstream of mutated beta-catenin by sequestering TCF4 to the nuclear membrane","volume":"8","author":"Loregger","year":"2015","journal-title":"Sci Signal"},{"key":"2020080709263807200_ref14","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/onc.2017.313","article-title":"Functional significance and therapeutic implication of ring-type E3 ligases in colorectal cancer","volume":"37","author":"Liu","year":"2018","journal-title":"Oncogene"},{"key":"2020080709263807200_ref15","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1038\/ng.3127","article-title":"RNF43 is frequently mutated in colorectal and endometrial cancers","volume":"46","author":"Giannakis","year":"2014","journal-title":"Nat Genet"},{"key":"2020080709263807200_ref16","doi-asserted-by":"crossref","first-page":"12649","DOI":"10.1073\/pnas.1307218110","article-title":"Inactivating mutations of RNF43 confer Wnt dependency in pancreatic ductal adenocarcinoma","volume":"110","author":"Jiang","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020080709263807200_ref17","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/0092-8674(93)90500-P","article-title":"WAF1, a potential mediator of p53 tumor suppression","volume":"75","author":"el-Deiry","year":"1993","journal-title":"Cell"},{"key":"2020080709263807200_ref18","first-page":"2782","article-title":"Impact of p53 knockout and topotecan treatment on gene expression profiles in human colon carcinoma cells: a pharmacogenomic study","volume":"63","author":"Daoud","year":"2003","journal-title":"Cancer Res"},{"key":"2020080709263807200_ref19","doi-asserted-by":"crossref","first-page":"4333","DOI":"10.1038\/onc.2011.594","article-title":"Identification of phosphorylase kinase as a novel therapeutic target through high-throughput screening for anti-angiogenesis compounds in zebrafish","volume":"31","author":"Camus","year":"2012","journal-title":"Oncogene"},{"key":"2020080709263807200_ref20","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1016\/j.cmet.2012.10.017","article-title":"Glucose utilization via glycogen phosphorylase sustains proliferation and prevents premature senescence in cancer cells","volume":"16","author":"Favaro","year":"2012","journal-title":"Cell Metab"},{"key":"2020080709263807200_ref21","first-page":"558","article-title":"Long non-coding RNAs and complex diseases: from experimental results to computational models","volume":"18","author":"Chen","year":"2017","journal-title":"Brief Bioinform"},{"key":"2020080709263807200_ref22","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1093\/bib\/bbx130","article-title":"MicroRNAs and complex diseases: from experimental results to computational models","volume":"20","author":"Chen","year":"2019","journal-title":"Brief Bioinform"},{"key":"2020080709263807200_ref23","doi-asserted-by":"crossref","first-page":"4256","DOI":"10.1093\/bioinformatics\/bty503","article-title":"Predicting miRNA-disease association based on inductive matrix completion","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2020080709263807200_ref24","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006418","article-title":"MDHGI: matrix decomposition and heterogeneous graph inference for miRNA-disease association prediction","volume":"14","author":"Chen","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2020080709263807200_ref25","doi-asserted-by":"crossref","first-page":"2617","DOI":"10.1093\/bioinformatics\/btt426","article-title":"Novel human lncRNA-disease association inference based on lncRNA expression profiles","volume":"29","author":"Chen","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/21\/4\/1479\/33585530\/bbz084.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/21\/4\/1479\/33585530\/bbz084.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,17]],"date-time":"2023-09-17T15:16:00Z","timestamp":1694963760000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/21\/4\/1479\/5581642"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,7]]},"references-count":25,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,10,7]]},"published-print":{"date-parts":[[2020,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbz084","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7]]},"published":{"date-parts":[[2019,10,7]]}}}