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《Journal of Fudan University(Natural Science)》 2012-06
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TF-coEx: Transcription Factor Function Prediction based on Gene Co-expression Network

CHEN Jing-qi1,LIU Jing-jing1,2,TIAN Wei-dong1(1.Institute of Biostatistics,Fudan University,Shanghai 200433,China; 2.Institute of Plant Biology,Fudan University,Shanghai 200433,China)  
Transcription factors are important for regulating various biological processes.In human genome,more than one thousand genes were annotated to encode transcription factors.Few of them were specified with biological mechanism and DNA-binding motif,the majority not.Here,we are proposing a new computational method-co-expression-based transcription factor function prediction(TF-coEx)-to predict function of transcription factors.In order to cover as much function as possible,we recruited a great deal of microarray data from experiments with multiple conditions.By constructing co-expression networks derived from each microarray data and dividing them into functional modules,we inferred the function of transcription factors based on module function enrichment.After integration the results from all modules,TF-coEx predicted function for all candidate transcription factors,and had a much better performance than random.Moreover,paper validation showed that 54% of the 50 top scored predictions were supported by experimental evidences.Hence,TF-coEx provided guidance for further experiments to unravel function of transcription factors.
【CateGory Index】: Q75
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