DeleteomeTools: Utilizing a compendium of yeast deletion strain transcriptomes to identify co-functional genes.

ABSTRACT: We introduce DeleteomeTools, an R package that leverages the Deleteome compendium of yeast single-gene deletion transcriptomes to predict gene function. Primarily, the package provides functions for identifying similarities between the transcriptomic signatures of deletion strains, thereby associating genes of interest with others that may be functionally related. We describe how our software predicted a novel relationship between the yeast nucleoporin Nup170 and the Ctf18-RFC complex, which was confirmed experimentally, revealing a previously unknown link between nuclear pore complexes and the DNA replication machinery. To assess the package's broader predictive capabilities, we performed a systematic evaluation that tested how well it predicted Gene Ontology (GO) annotations already appl

SUBMITTER: Neal ML 

PROVIDER: S-EPMC10871253 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature