Quantitative construction of regulatory networks using multiple sources of knowlege

In this work, a regulatory model based binding energy is proposed to quantify the transcriptional regulatory network. Multiple quantities, including binding affinity, regulatory efficiency and the activity level of transcription factor (TF) are incorporated into a general learning model. The sequence features of the promoter are exploited to derive the binding energy. Comparing with the previous models that only employ microarray data, the proposed model can bridge the gap between the relative background frequency of the observed nucleotide and the gene's transcription rate. Experimental results show that the proposed model can effectively identify the parameters and the activity level of TF. Moreover, the kinetic parameters introduced in the proposed model can reveal more biological sense than some previous models can do. © 2011 IEEE.