EURASIP Journal on Bioinformatics and Systems Biology
Integrative network component analysis for regulatory network reconstruction
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
A combined expression-interaction model for inferring the temporal activity of transcription factors
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Uncovering transcriptional regulatory networks by sparse Bayesian factor model
EURASIP Journal on Advances in Signal Processing - Special issue on genomic signal processing
Noniterative Convex Optimization Methods for Network Component Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reverse engineering of gene regulatory networks from biological data
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
| Hi-index | 3.84 |
Motivation: In systems like Escherichia Coli, the abundance of sequence information, gene expression array studies and small scale experiments allows one to reconstruct the regulatory network and to quantify the effects of transcription factors on gene expression. However, this goal can only be achieved if all information sources are used in concert. Results: Our method integrates literature information, DNA sequences and expression arrays. A set of relevant transcription factors is defined on the basis of literature. Sequence data are used to identify potential target genes and the results are used to define a prior distribution on the topology of the regulatory network. A Bayesian hidden component model for the expression array data allows us to identify which of the potential binding sites are actually used by the regulatory proteins in the studied cell conditions, the strength of their control, and their activation profile in a series of experiments. We apply our methodology to 35 expression studies in E.Coli with convincing results. Availability: www.genetics.ucla.edu/labs/sabatti/software.html Supplementary information: The supplementary material are available at Bioinformatics online. Contact: csabatti@mednet.ucla.edu