A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription.

Bioinformatics
Guido SanguinettiNeil D Lawrence

Abstract

Quantitative estimation of the regulatory relationship between transcription factors and genes is a fundamental stepping stone when trying to develop models of cellular processes. This task, however, is difficult for a number of reasons: transcription factors' expression levels are often low and noisy, and many transcription factors are post-transcriptionally regulated. It is therefore useful to infer the activity of the transcription factors from the expression levels of their target genes. We introduce a novel probabilistic model to infer transcription factor activities from microarray data when the structure of the regulatory network is known. The model is based on regression, retaining the computational efficiency to allow genome-wide investigation, but is rendered more flexible by sampling regression coefficients independently for each gene. This allows us to determine the strength with which a transcription factor regulates each of its target genes, therefore providing a quantitative description of the transcriptional regulatory network. The probabilistic nature of the model also means that we can associate credibility intervals to our estimates of the activities. We demonstrate our model on two yeast datasets. In both ca...Continue Reading

References

Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Oct 7, 2003·Proceedings of the National Academy of Sciences of the United States of America·Rebecca MartoneMichael Snyder
Dec 16, 2003·Proceedings of the National Academy of Sciences of the United States of America·James C LiaoVwani P Roychowdhury
Jul 21, 2004·Bioinformatics·I NachmanN Friedman
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Sep 17, 2004·Nature·Nicholas M LuscombeMark Gerstein
Nov 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Orly Alter, Gene H Golub
Jan 14, 2005·Theoretical Biology & Medical Modelling·Ekaterina Shelest, Edgar Wingender
Aug 11, 2005·Bioinformatics·Guido SanguinettiNeil D Lawrence

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Citations

Nov 16, 2011·Bioinformatics·Mark Maienschein-ClineAaron R Dinner
May 12, 2007·BMC Bioinformatics·Simon RogersMark Girolami
Feb 2, 2008·BMC Bioinformatics·Guanrao ChenYang Dai
Feb 5, 2008·Yi chuan = Hereditas·Zheng-Hua WangYun-Ping Zhu
Dec 22, 2015·Molecular BioSystems·Jun WuZhifeng Shao
Mar 8, 2016·Current Opinion in Genetics & Development·Bing He, Kai Tan
Oct 16, 2015·Bioprocess and Biosystems Engineering·Shuqiang WangJinxing Hu
Apr 7, 2010·Genomics·Naoki KiyosawaTakashi Yamoto

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