Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model.
RESULTS
We have developed LeTICE (Learning Transcriptional networks from the Integration of ChIP-chip and Expression data), an algorithm for learning a transcriptional network from ChIP-chip and expression data. The network is specified by a binary matrix of transcription factor (TF)-gene interactions partitioning genes into modules and a background of genes that are not involved in the transcriptional regulation. We define a likelihood of a network, and then search for the network optimizing the likelihood. We applied LeTICE to the location and expression data from yeast cells grown in rich media to learn the transcriptional network specific to the yeast cell cycle. It found 12 condition-specific TFs and 15 modules each of which is highly represented with functions related to particular phases of cell-cycle regulation.


BACKGROUND
Our algorithm is available at http://linus.nci.nih.gov/Data/YounA/LeTICE.zip
Youn
Ahrim
A
National Cancer Institute, Bethesda, MD 20892, USA. youna2@mail.nih.gov
Reiss
David J
DJ
Stuetzle
Werner
W
D000465:Algorithms; D002453:Cell Cycle / Q000235:genetics / Q000502:physiology; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D018797:Cell Cycle Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors