G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.

ABSTRACT:

Background

In previous studies, gene neighborhoods-spatial clusters of co-expressed genes in the genome-have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST) which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously.

Results

Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest s

SUBMITTER: Lemay DG 

PROVIDER: S-EPMC3575404 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature