NDLI: A quantitative framework of transcriptional dynamics by integrating multiple sources of knowledge

Content Provider	IEEE Xplore Digital Library
Author	Shu-Qiang Wang Han-Xiong Li
Copyright Year	2011
Description	Author affiliation: Department of Manufacturing Engineering and Engineering Management, City University of Hong Kong, Hong Kong (Shu-Qiang Wang; Han-Xiong Li)
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.
Starting Page	255
Ending Page	260
File Size	679486
Page Count	6
File Format	PDF
ISBN	9781457716614
e-ISBN	9781457716669
e-ISBN	9781457716652
DOI	10.1109/ISB.2011.6033162
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-09-02
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Regulators Biological system modeling Systems biology Markov processes Transcription rate Sequence feature Mathematical model Approximation methods Bayesian inference Transcriptional dynamics
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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