title: Integrative gene network construction for predicting a set of complementary prostate cancer genes.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  BACKGROUND
  http://embio.yonsei.ac.kr/~Ahn/tc.php.
  
  
  BACKGROUND
  sanghyun@cs.yonsei.ac.kr
authors.affiliation: Department of Computer Science, Yonsei University, Seoul, South Korea.
authors.forename: Jaegyoon
authors.initials: J
authors.lastname: Ahn
authors.forename: Youngmi
authors.initials: Y
authors.lastname: Yoon
authors.forename: Chihyun
authors.initials: C
authors.lastname: Park
authors.forename: Eunji
authors.initials: E
authors.lastname: Shin
authors.forename: Sanghyun
authors.initials: S
authors.lastname: Park
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008297:Male; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000235:genetics*; D011506:Proteins / Q000378:metabolism
chemical_list: D011506:Proteins