Integration of gene expression data with prior knowledge for network analysis and validation.

ABSTRACT:

Background

Reconstruction of protein-protein interaction or metabolic networks based on expression data often involves in silico predictions, while on the other hand, there are unspecific networks of in vivo interactions derived from knowledge bases.We analyze networks designed to come as close as possible to data measured in vivo, both with respect to the set of nodes which were taken to be expressed in experiment as well as with respect to the interactions between them which were taken from manually curated databases

Results

A signaling network derived from the TRANSPATH database and a metabolic network derived from KEGG LIGAND are each filtered onto expression data from breast cancer (SAGE) considering different levels of restrictiveness in edge and vertex selection.We pe

SUBMITTER: Ante M 

PROVIDER: S-EPMC3298547 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature