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

  • Authors:

  • Tao Huang;Lei Chen;Xiao-Jun Liu;Yu-Dong Cai

  • Affiliations:

  • Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China and Shanghai Center for Bioinformation Technology, Shanghai 2 ...;College of Information Engineering, Shanghai Maritime University, Shanghai 200135, PR China and Centre for Computational Systems Biology, Fudan University, Shanghai 200433, PR China;College of Animal Science and Technology, Shihezi University, Shihezi City 832003, PR China;Institute of Systems Biology, Shanghai University, Shanghai 200444, PR China and Centre for Computational Systems Biology, Fudan University, Shanghai 200433, PR China

  • Venue:
  • Neurocomputing
  • Year:
  • 2011

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Abstract

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.