Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis

Jie Zhang, Shiwei Ni, Yang Xiang, Jeffrey D. Parvin, Yufeng Yang, Yongjian Zhou, Kun Huang

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Gene Co-expression Network (GCN) analysis has been widely used for gene function and disease biomarker discovery. In this study, we present a workflow for identifying GCN associated with colon cancer metastasis. The workflow includes dense network discovery from weighted GCN followed by network activity analysis using a mutual information-based approach to identify gene networks related to metastasis. Our findings suggest several genomic regions as genetic aberrations related to colon cancer malignancy including chr11q13, 20q13, 8q24 and 14q22-23. Our work also demonstrates a novel way of interpreting gene co-expression analysis results besides functional relationships and the effectiveness of the mutual information based network analysis in detecting subtle changes between different disease states.

Original languageEnglish (US)
Pages (from-to)60-71
Number of pages12
JournalInternational Journal of Computational Biology and Drug Design
Volume6
Issue number1-2
DOIs
StatePublished - Mar 5 2013
Externally publishedYes

Fingerprint

Genetic Loci
Aberrations
Colonic Neoplasms
Genes
Neoplasm Metastasis
Gene Expression
Workflow
Electric network analysis
Information Services
Gene Regulatory Networks
Biomarkers
Neoplasms

Keywords

  • Cancer genome hotspot
  • Colon cancer
  • Copy number variation
  • GCN
  • Gene co-expression network
  • Metastasis
  • Network mining
  • Quasi-clique

ASJC Scopus subject areas

  • Drug Discovery
  • Computer Science Applications

Cite this

Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis. / Zhang, Jie; Ni, Shiwei; Xiang, Yang; Parvin, Jeffrey D.; Yang, Yufeng; Zhou, Yongjian; Huang, Kun.

In: International Journal of Computational Biology and Drug Design, Vol. 6, No. 1-2, 05.03.2013, p. 60-71.

Research output: Contribution to journalArticle

Zhang, Jie ; Ni, Shiwei ; Xiang, Yang ; Parvin, Jeffrey D. ; Yang, Yufeng ; Zhou, Yongjian ; Huang, Kun. / Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis. In: International Journal of Computational Biology and Drug Design. 2013 ; Vol. 6, No. 1-2. pp. 60-71.
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