Deleteome-Tools: Utilizing a compendium of yeast deletion strain transcriptomes to identify co-functional genes

We developed an R codebase that uses a publicly-available compendium of transcriptomes from yeast single-gene deletion strains - the Deleteome - to predict gene function. Primarily, the codebase 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 tool 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. We also discuss how our strategy for quantifying similarity between deletion strains differs from other approaches and why it has the potential to identify functional relationships that similar approaches may not. Deleteome-Tools is implemented in R and is freely available at https://github.com/AitchisonLab/Deleteome-Tools .