PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

Modelling transcriptional regulation using Gaussian processes
Neil Lawrence, Guido Sanguinetti and Magnus Rattray
In: NIPS 2006, 5-7 Dec 2007, Vancouver, Canada.


Modelling the dynamics of transcriptional processes in the cell requires the knowledge of a number of key biological quantities. While some of them are relatively easy to measure, such as mRNA decay rates and mRNA abundance levels, it is still very hard to measure the active concentration levels of the transcription factor proteins that drive the process and the sensitivity of target genes to these concentrations. In this paper we show how these quantities for a given transcription factor can be inferred from gene expression levels of a set of known target genes. We treat the protein concentration as a latent function with a Gaussian Process prior, and include the sensitivities, mRNA decay rates and baseline expression levels as hyperparameters. We apply this procedure to a human leukemia dataset, focusing on the tumour repressor p53 and obtaining results in good accordance with recent biological studies.

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EPrint Type:Conference or Workshop Item (Paper)
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Theory & Algorithms
ID Code:3812
Deposited By:Neil Lawrence
Deposited On:25 February 2008