COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.

ABSTRACT:

Motivation

The identification of condition specific sub-networks from gene expression profiles has important biological applications, ranging from the selection of disease-related biomarkers to the discovery of pathway alterations across different phenotypes. Although many methods exist for extracting these sub-networks, very few existing approaches simultaneously consider both the differential expression of individual genes and the differential correlation of gene pairs, losing potentially valuable information in the data.

Results

In this article, we propose a new method, COSINE (COndition SpecIfic sub-NEtwork), which employs a scoring function that jointly measures the condition-specific changes of both 'nodes' (individual genes) and 'edges' (gene-gene co-expression). It u

SUBMITTER: Ma H 

PROVIDER: S-EPMC3138081 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature