Integrative gene network construction for predicting a set of complementary prostate cancer genes

Jaegyoon Ahn, Youngmi Yoon, Chihyun Park, Eunji Shin, Sanghyun Park

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

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. 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.

Original languageEnglish
Article numberbtr283
Pages (from-to)1846-1853
Number of pages8
JournalBioinformatics
Volume27
Issue number13
DOIs
Publication statusPublished - 2011 Jul 1

Fingerprint

Prostate Cancer
Gene Networks
Gene Regulatory Networks
Neoplasm Genes
Prostatic Neoplasms
Cancer
Genes
Gene
Neoplasms
Protein Interaction Maps
Information Services
Proteins
Computational Biology
Oncogenes
Transcriptome
Bioinformatics
Carcinogenesis
Gene expression
Feature extraction
Phenotype

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Ahn, Jaegyoon ; Yoon, Youngmi ; Park, Chihyun ; Shin, Eunji ; Park, Sanghyun. / Integrative gene network construction for predicting a set of complementary prostate cancer genes. In: Bioinformatics. 2011 ; Vol. 27, No. 13. pp. 1846-1853.
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Integrative gene network construction for predicting a set of complementary prostate cancer genes. / Ahn, Jaegyoon; Yoon, Youngmi; Park, Chihyun; Shin, Eunji; Park, Sanghyun.

In: Bioinformatics, Vol. 27, No. 13, btr283, 01.07.2011, p. 1846-1853.

Research output: Contribution to journalArticle

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