Optimal structural inference of signaling pathways from unordered and overlapping gene sets.

ABSTRACT:

Motivation

A plethora of bioinformatics analysis has led to the discovery of numerous gene sets, which can be interpreted as discrete measurements emitted from latent signaling pathways. Their potential to infer signaling pathway structures, however, has not been sufficiently exploited. Existing methods accommodating discrete data do not explicitly consider signal cascading mechanisms that characterize a signaling pathway. Novel computational methods are thus needed to fully utilize gene sets and broaden the scope from focusing only on pairwise interactions to the more general cascading events in the inference of signaling pathway structures.

Results

We propose a gene set based simulated annealing (SA) algorithm for the reconstruction of signaling pathway structures. A signa

SUBMITTER: Acharya LR 

PROVIDER: S-EPMC3278757 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature