reducing false-positive prediction of minimotifs with a genetic interaction filter减少假阳性预测minimotifs基因交互过滤器.pdfVIP

Reducing False-Positive Prediction of Minimotifs with a Genetic Interaction Filter 1. 1 . 1. 2 Jerlin C. Merlin , Sanguthevar Rajasekaran * , Tian Mi , Martin R. Schiller * 1 Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America, 2 School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States of America Abstract Background: Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists. Methods and Findings: We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target protein pairs have a known genetic interaction. The HomoloGene genetic interaction filter extends these predictions to predicted genetic interactions of orthologous proteins and the node-based filter identifies those minimotifs where proteins that have a genetic interaction with the source or target have a genetic interaction. Each filter was evaluated with a test data set containing thousands of true and false-positives. Based on sensitivity and selectivity performance metrics, the basic filter had the best discrimination for true positives, whereas the n