{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:09:16Z","timestamp":1761059356086,"version":"3.37.3"},"reference-count":26,"publisher":"Wiley","license":[{"start":{"date-parts":[[2012,6,28]],"date-time":"2012-06-28T00:00:00Z","timestamp":1340841600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Young Investigators Award of the Prostate Cancer Foundation, USA"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Advances in Bioinformatics"],"published-print":{"date-parts":[[2012,6,28]]},"abstract":"<jats:p>Gene alterations are a major component of the landscape of tumor genomes. To assess the significance of these alterations in the development of prostate cancer, it is necessary to identify these alterations and analyze them from systems biology perspective. Here, we present a new method (EigFusion) for predicting outlier genes with potential gene rearrangement. EigFusion demonstrated excellent performance in identifying outlier genes with potential rearrangement by testing it to synthetic and real data to evaluate performance. EigFusion was able to identify previously unrecognized genes such as <jats:italic>FABP5 <\/jats:italic> and <jats:italic> KCNH8<\/jats:italic> and confirmed their association with primary and metastatic prostate samples while confirmed the metastatic specificity for other genes such as <jats:italic>PAH, TOP2A,<\/jats:italic> and <jats:italic>SPINK1<\/jats:italic>. We performed protein network based approaches to analyze the network context of potential rearranged genes. Functional gene rearrangement Modules are constructed by integrating functional protein networks. Rearranged genes showed to be highly connected to well-known altered genes in cancer such as <jats:italic>AR, RB1, MYC,<\/jats:italic> and <jats:italic>BRCA1<\/jats:italic>. Finally, using clinical outcome data of prostate cancer patients, potential rearranged genes demonstrated significant association with prostate cancer specific death.<\/jats:p>","DOI":"10.1155\/2012\/373506","type":"journal-article","created":{"date-parts":[[2012,6,28]],"date-time":"2012-06-28T21:00:31Z","timestamp":1340917231000},"page":"1-13","source":"Crossref","is-referenced-by-count":8,"title":["Detecting Cancer Outlier Genes with Potential Rearrangement Using Gene Expression Data and Biological Networks"],"prefix":"10.1155","volume":"2012","author":[{"given":"Mohammed","family":"Alshalalfa","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Calgary, Calgary, AB, Canada T2N 1N4"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tarek A.","family":"Bismar","sequence":"additional","affiliation":[{"name":"Departments of Pathology, Oncology and Molecular Biology and Biochemistry, Faculty of Medicine, University of Calgary, Calgary, AB, Canada T2N 1N4"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reda","family":"Alhajj","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Calgary, Calgary, AB, Canada T2N 1N4"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","reference":[{"issue":"5894","key":"1","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1038\/300765a0","volume":"300","year":"1982","journal-title":"Nature"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1038\/nature05945"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1038\/nrc2402"},{"key":"4","doi-asserted-by":"publisher","DOI":"10.1038\/ng0509-509"},{"key":"5","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/nature09744","volume":"470","year":"2011","journal-title":"Nature"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1186\/1476-4598-8-5"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-1-r6"},{"key":"8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq336"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq622"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1001138"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1038\/labinvest.3700477"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1093\/biostatistics\/kxl029"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1152\/physiolgenomics.00259.2006"},{"key":"14","doi-asserted-by":"publisher","DOI":"10.1126\/science.1117679"},{"key":"15","doi-asserted-by":"publisher","DOI":"10.1093\/biostatistics\/kxl005"},{"key":"16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0017259"},{"key":"17","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-5-r53"},{"key":"18","doi-asserted-by":"publisher","DOI":"10.1016\/S1535-6108(02)00030-2"},{"key":"19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ccr.2010.06.011","volume":"18","year":"2010","journal-title":"Cancer Cell"},{"issue":"2","key":"20","doi-asserted-by":"crossref","first-page":"125","DOI":"10.4161\/cbt.8.2.7134","volume":"8","year":"2009","journal-title":"Cancer Biology and Therapy"},{"key":"21","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2008.04.016"},{"key":"22","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/djn150"},{"key":"23","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(99)00487-4"},{"key":"24","doi-asserted-by":"publisher","DOI":"10.1038\/nrc2223"},{"key":"25","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M402492200"},{"issue":"4","key":"26","first-page":"767","volume":"32","year":"2008","journal-title":"International Journal of Oncology"}],"container-title":["Advances in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/archive\/2012\/373506.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2012\/373506.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2012\/373506.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T03:58:05Z","timestamp":1607572685000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/abi\/2012\/373506\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,28]]},"references-count":26,"alternative-id":["373506","373506"],"URL":"https:\/\/doi.org\/10.1155\/2012\/373506","relation":{},"ISSN":["1687-8027","1687-8035"],"issn-type":[{"type":"print","value":"1687-8027"},{"type":"electronic","value":"1687-8035"}],"subject":[],"published":{"date-parts":[[2012,6,28]]}}}