A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.

ABSTRACT:

Motivation

Deregulated signaling cascades are known to play a crucial role in many pathogenic processes, among them are tumor initiation and progression. In the recent past, modern experimental techniques that allow for measuring the amount of mRNA transcripts of almost all known human genes in a tissue or even in a single cell have opened new avenues for studying the activity of the signaling cascades and for understanding the information flow in the networks.

Results

We present a novel dynamic programming algorithm for detecting deregulated signaling cascades. The so-called FiDePa (Finding Deregulated Paths) algorithm interprets differences in the expression profiles of tumor and normal tissues. It relies on the well-known gene set enrichment analysis (GSEA) and efficientl

SUBMITTER: Keller A 

PROVIDER: S-EPMC2781748 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature