Link-based quantitative methods to identify differentially coexpressed genes and gene pairs.

ABSTRACT:

Background

Differential coexpression analysis (DCEA) is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance.

Results

We developed two link-based quantitative methods, DCp and DCe,

SUBMITTER: Yu H 

PROVIDER: S-EPMC3199761 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature