Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters.

ABSTRACT:

Background

Proximity-based methods and co-evolution-based phylogenetic profiles methods have been successfully used for the identification of functionally related genes. Proximity-based methods are effective for physically clustered genes while the phylogenetic profiles method is effective for co-occurring gene sets. However, both methods predict many false positives and false negatives. In this paper, we propose the Gene Cluster Profile Vector (GCPV) method, which combines these two methods by using phylogenetic profiles of whole gene clusters. The GCPV method is, currently, the only genome comparison based method that allows for the characterization of relationships between gene clusters based profiles of individual genes in clusters.

Results

The GCPV method groups togethe

SUBMITTER: Pejaver VR 

PROVIDER: S-EPMC3194233 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature