RT Journal Article
SR Electronic
T1 Phylogenetic expression profiling reveals widespread coordinated evolution of gene expression
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 045211
DO 10.1101/045211
A1 Trevor Martin
A1 Hunter B. Fraser
YR 2016
UL http://biorxiv.org/content/early/2016/03/22/045211.abstract
AB Phylogenetic profiling, which infers functional relationships between genes based on patterns of gene presence/absence across species, has proven to be highly effective. Here we introduce a complementary approach, phylogenetic expression profiling (PEP), which detects gene sets with correlated expression levels across a phylogeny. Applying PEP to RNA-seq data consisting of 657 samples from 309 diverse unicellular eukaryotes, we found several hundred gene sets evolving in a coordinated fashion. These allowed us to predict a role of the Golgi apparatus in Alzheimer’s disease, as well as novel genes related to diabetes pathways. We also detected adaptive evolution of tRNA ligase levels to match genome-wide codon usage. In sum, we found that PEP is an effective method for inferring functional relationships—especially among core cellular components that are never lost, to which phylogenetic profiling cannot be applied—and that many subunits of the most conserved molecular machines are coexpressed across eukaryotes.