G=MAT: Linking Transcription Factor Expression with DNA Binding
1 Institute of Computer Science, University of Tartu, Estonia
2 Quretec Ltd, Tartu, Estonia
* Corresponding author
Transcription factors are proteins that bind to motifs on the DNA and thus affect gene expression regulation. The qualitative description of the corresponding processes is therefore important for a better understanding of essential biological mechanisms. However, wet lab experiments targeted at the discovery of the regulatory interplay between transcription factors and binding sites are expensive. We propose a new purely computational method for finding putative associations between transcription factors and motifs. This method is based on a linear model that combines sequence information with expression data. We present various methods for model parameter estimation and show, via experiments on simulated data, that these methods are reliable. Finally, we examine the performance of this model on biological data and conclude that it can indeed be used to discover meaningful associations. The developed software is available as a web tool and Scilab source code at http://biit.cs.ut.ee/gmat/.
GMAT-Web is an online tool that allows to conveniently explore the results of the paper as well as perform new analyses.
Text and Supplementary Files
- Research paper at PLoS ONE
- ISMB 2007 poster (pdf)
- Master's thesis (pdf)
- Master's thesis supplementary CD (iso.zip, 55MB)
- Scilab implementations of G=MAT (zip)
Page last updated: 31.01.2011