PathNet: a tool for pathway analysis using topological information.

ABSTRACT:

Unlabelled

Background

Identification of canonical pathways through enrichment of differentially expressed genes in a given pathway is a widely used method for interpreting gene lists generated from high-throughput experimental studies. However, most algorithms treat pathways as sets of genes, disregarding any inter- and intra-pathway connectivity information, and do not provide insights beyond identifying lists of pathways.

Results

We developed an algorithm (PathNet) that utilizes the connectivity information in canonical pathway descriptions to help identify study-relevant pathways and characterize non-obvious dependencies and connections among pathways using gene expression data. PathNet considers both the differential expression of genes and their pathway neighbor

SUBMITTER: Dutta B 

PROVIDER: S-EPMC3563509 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature