DeleteomeTools: utilizing a compendium of yeast deletion strain transcriptomes to identify co-functional genes
NAR Nucleic Acids Research
Published by Oxford University Press - Impact Factor 16.7
by Maxwell L Neal, Sanjeev K Choudhry and John D Aitchison
DeleteomeTools is an R package designed to predict gene functions by analyzing yeast single-gene deletion data. It identifies similarities between the gene expression patterns of different deletion strains, helping to associate genes with similar functions. The tool successfully predicted a new relationship between the yeast nucleoporin Nup170 and the Ctf18-RFC complex, which was experimentally confirmed, revealing a link between nuclear pore complexes and DNA replication. The package was also tested for its ability to predict known gene functions, showing high accuracy. This approach, which focuses on differential expression signatures, can uncover functional relationships that other methods might miss.