Gene set-based module discovery in the breast cancer transcriptome.

ABSTRACT:

Background

Although microarray-based studies have revealed global view of gene expression in cancer cells, we still have little knowledge about regulatory mechanisms underlying the transcriptome. Several computational methods applied to yeast data have recently succeeded in identifying expression modules, which is defined as co-expressed gene sets under common regulatory mechanisms. However, such module discovery methods are not applied cancer transcriptome data.

Results

In order to decode oncogenic regulatory programs in cancer cells, we developed a novel module discovery method termed EEM by extending a previously reported module discovery method, and applied it to breast cancer expression data. Starting from seed gene sets prepared based on cis-regulatory elements, ChIP-c

SUBMITTER: Niida A 

PROVIDER: S-EPMC2674431 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature