Multi-edge gene set networks reveal novel insights into global relationships between biological themes.

ABSTRACT: Curated gene sets from databases such as KEGG Pathway and Gene Ontology are often used to systematically organize lists of genes or proteins derived from high-throughput data. However, the information content inherent to some relationships between the interrogated gene sets, such as pathway crosstalk, is often underutilized. A gene set network, where nodes representing individual gene sets such as KEGG pathways are connected to indicate a functional dependency, is well suited to visualize and analyze global gene set relationships. Here we introduce a novel gene set network construction algorithm that integrates gene lists derived from high-throughput experiments with curated gene sets to construct co-enrichment gene set networks. Along with previously described co-membership and linkage al

SUBMITTER: Parikh JR 

PROVIDER: S-EPMC3441533 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature