Automatic context-specific subnetwork discovery from large interaction networks

Ashis Saha, Aik-Choon Tan, Jaewoo Kang

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Genes act in concert via specific networks to drive various biological processes, including progression of diseases such as cancer. Under different phenotypes, different subsets of the gene members of a network participate in a biological process. Single gene analyses are less effective in identifying such core gene members (subnetworks) within a gene set/network, as compared to gene set/network-based analyses. Hence, it is useful to identify a discriminative classifier by focusing on the subnetworks that correspond to different phenotypes. Here we present a novel algorithm to automatically discover the important subnetworks of closely interacting molecules to differentiate between two phenotypes (context) using gene expression profiles. We name it COSSY (COntext-Specific Subnetwork discoverY). It is a non-greedy algorithm and thus unlikely to have local optima problems. COSSY works for any interaction network regardless of the network topology. One added benefit of COSSY is that it can also be used as a highly accurate classification platform which can produce a set of interpretable features.

Original languageEnglish
Article numbere84227
JournalPLoS One
Volume9
Issue number1
DOIs
Publication statusPublished - 2014 Jan 1

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Genes
Biological Phenomena
Gene Regulatory Networks
Phenotype
genes
phenotype
Transcriptome
Names
Disease Progression
disease course
Gene expression
topology
Classifiers
Topology
Neoplasms
gene expression
Molecules
neoplasms

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Automatic context-specific subnetwork discovery from large interaction networks. / Saha, Ashis; Tan, Aik-Choon; Kang, Jaewoo.

In: PLoS One, Vol. 9, No. 1, e84227, 01.01.2014.

Research output: Contribution to journalArticle

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