{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:19:26Z","timestamp":1773289166327,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Diagnosis and prognosis of cancer and understanding oncogenesis within the context of biological pathways is one of the most important research areas in bioinformatics. Recently, there have been several attempts to integrate interactome and transcriptome data to identify subnetworks that provide limited interpretations of known and candidate cancer genes, as well as increase classification accuracy. However, these studies provide little information about the detailed roles of identified cancer genes.<\/jats:p>\n               <jats:p>Results: To provide more information to the network, we constructed the network by incorporating genetic interactions and manually curated gene regulations to the protein interaction network. To make our newly constructed network cancer specific, we identified edges where two genes show different expression patterns between cancer and normal phenotypes. We showed that the integration of various datasets increased classification accuracy, which suggests that our network is more complete than a network based solely on protein interactions. We also showed that our network contains significantly more known cancer-related genes than other feature selection algorithms. Through observations of some examples of cancer-specific subnetworks, we were able to predict more detailed and interpretable roles of oncogenes and other cancer candidate genes in the prostate cancer cells.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/embio.yonsei.ac.kr\/~Ahn\/tc.php.<\/jats:p>\n               <jats:p>Contact: \u00a0sanghyun@cs.yonsei.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr283","type":"journal-article","created":{"date-parts":[[2011,5,7]],"date-time":"2011-05-07T00:34:56Z","timestamp":1304728496000},"page":"1846-1853","source":"Crossref","is-referenced-by-count":32,"title":["Integrative gene network construction for predicting a set of complementary prostate cancer genes"],"prefix":"10.1093","volume":"27","author":[{"given":"Jaegyoon","family":"Ahn","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Yonsei University, Seoul and 2Division of Information Engineering, Gachon University of Medicine and Science, Inchon, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Youngmi","family":"Yoon","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Yonsei University, Seoul and 2Division of Information Engineering, Gachon University of Medicine and Science, Inchon, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chihyun","family":"Park","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Yonsei University, Seoul and 2Division of Information Engineering, Gachon University of Medicine and Science, Inchon, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eunji","family":"Shin","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Yonsei University, Seoul and 2Division of Information Engineering, Gachon University of Medicine and Science, Inchon, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanghyun","family":"Park","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Yonsei University, Seoul and 2Division of Information Engineering, Gachon University of Medicine and Science, Inchon, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,5,6]]},"reference":[{"key":"2023012512011724300_B1","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/BF00153759","article-title":"Instance-based learning algorithms","volume":"6","author":"Aha","year":"1991","journal-title":"Mach. 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