Title :
A quantitative framework of transcriptional dynamics by integrating multiple sources of knowledge
Author :
Wang, Shu-Qiang ; Li, Han-Xiong
Author_Institution :
Dept. of Manuf. Eng. & Eng. Manage., City Univ. of Hong Kong, Hong Kong, China
Abstract :
A key challenge in the post genome era is to identify genome-wide transcriptional regulatory networks, which specify the interactions between transcription factors and their target genes. In this work, a regulatory model based binding energy is proposed to quantify the transcriptional regulatory network. Multiple quantities, including binding affinity and the activity level of transcription factor (TF) are incorporated into a general learning model. The sequence features of the promoter and the possible occupancy of nucleosomes are exploited to estimate the binding probability of regulators. 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.
Keywords :
binding energy; genetics; genomics; molecular biophysics; binding affinity; binding energy; genome-wide transcriptional regulatory network; multiple knowledge sources integration; nucleosomes; sequence features; transcription factor activity level; transcriptional dynamics; Approximation methods; Biological system modeling; Markov processes; Mathematical model; Regulators; Systems biology; Bayesian inference; Sequence feature; Transcription rate; Transcriptional dynamics;
Conference_Titel :
Systems Biology (ISB), 2011 IEEE International Conference on
Conference_Location :
Zhuhai
Print_ISBN :
978-1-4577-1661-4
Electronic_ISBN :
978-1-4577-1665-2
DOI :
10.1109/ISB.2011.6033162