Employing conservation of co-expression to improve functional inference

by Erik Sonnhammer (SBC)

Wednesday 10 Dec 2008, 16:00 → 17:00 Europe/Stockholm

RB35 (RB35)

Observing co-expression between genes suggests that they are functionally coupled. Co-expression of orthologous gene pairs across species may improve function prediction beyond the level achieved in a single species. We used orthology between genes of the three different species S. cerevisiae, D. melanogaster, and C. elegans to combine co-expression across two species at a time. This led to increased function prediction accuracy when we incorporated expression data from either of the other two species and even further increased when conservation across both of the two other species was considered at the same time. To be able to employ the most suitable co-expression distance measure for our analysis, we evaluated the ability of four popular gene co-expression distance measures to detect biologically relevant interactions between pairs of genes. While the differences between distance measures were small, Spearman correlation gave most robust results. See PMID: 18808668.