VaLPAS: Leveraging variation in experimental multi-omics data to elucidate protein function

MotivationDespite continuing advances in sequencing and computational function determination, large parts of the studied gene, protein, and metabolite space remain functionally undetermined. Most function assignment is driven by homology searches and annotation transfer from known and extensively studied proteins but often fails to leverage available experimental omics data generated via technologies like mass-spectrometry. ResultsThe VaLPAS (Variation-Leveraged Phenomic Association Screen) framework is available as a Python package and provides a user-friendly platform for calculation of associations between expression patterns of genes or proteins in multi-omic datasets based on various statistical and learning methods. The goal of this approach is to shed light on the functional dark matter of protein space by elucidating previously unknown functions of molecules using guilt by association with molecules of known function. We present results demonstrating the utility of VaLPAS to identify high-confidence predictions for a subset of genes/proteins of unknown function in a previously published multi-omics dataset from the oleaginous yeast, Rhodotorula toruloides. AvailabilityVaLPAS is written in Python. The code is hosted on github (https://github.com/PNNL-Predictive-Phenomics/valpas/).