title: Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge.
abstract: BACKGROUND
  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. Numerous methods have been developed for reconstructing gene regulatory networks from expression data. However, most of them are based on coarse grained qualitative models, and cannot provide a quantitative view of regulatory systems.
  
  
  RESULTS
  A binding affinity based regulatory model 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.
  
  
  CONCLUSIONS
  We testify the proposed approach on two real-world microarray datasets. 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 previous models can do.
authors.affiliation: Department of Systems Engineering and Engineering Management, City University of Hong Kong, Hong Kong.
authors.forename: Shu-Qiang
authors.initials: SQ
authors.lastname: Wang
authors.forename: Han-Xiong
authors.initials: HX
authors.lastname: Li
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002940:Circadian Rhythm / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics*; D053263:Gene Regulatory Networks; D007700:Kinetics; D008099:Liver / Q000378:metabolism / Q000502:physiology; D008297:Male; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000235:genetics; D049490:Systems Biology / Q000379:methods*; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D009707:Nucleosomes; D014157:Transcription Factors