Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.

ABSTRACT:

Motivation

Genome-wide mRNA profiling provides a snapshot of the global state of cells under different conditions. However, mRNA levels do not provide direct understanding of upstream regulatory mechanisms. Here, we present a new approach called Expression2Kinases (X2K) to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. By integrating chromatin immuno-precipitation (ChIP)-seq/chip and position weight matrices (PWMs) data, protein-protein interactions and kinase-substrate phosphorylation reactions, we can better identify regulatory mechanisms upstream of genome-wide differences in gene expression. We validated X2K by applying it to recover drug targets of food and drug administration (FDA)-approved drugs from drug perturbations f

SUBMITTER: Chen EY 

PROVIDER: S-EPMC3244772 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature