Predicting triplet of transcription factor - mediating enzyme - target gene by functional profiles

Usually the functioning of a transcription factor to regulate a target gene requires a modifying enzyme. The triplet of transcription factor, mediating enzyme and target gene, MFG triplet for short, is like a switchboard that transmits signals from signaling network to gene regulatory network. Using PTM-Switchboard database, we systematically studied the MFG triplets in yeast and constructed a predictor to identify MFG triplets based on functional profiles of each element in the triplet. The sensitivity (Sn) and specificity (Sp) of Nearest Neighbor Algorithm (NNA) were 75.106% and 99.585%, respectively. Our method had higher sensitivity than Bayesian network (NaiveBayes), decision tree (J48), Random Forest (RandomForest) and k-nearest neighbor (KNN, K=3). The established predictor may be used to identify MFG triplet, which can link up cellular signaling transduction with transcriptional regulation, two major subjects in biological research. (C) 2011 Elsevier B.V. All rights reserved.