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CERMT

CERMT (Covariance-based Extraction of Regulatory targets using Multiple Time series) is a method for predicting transcription factor targets given a particular transcription factor of interest. Targets are defined as the genes that responds similarly, but possibly time shifted, to the transcription factor under two or more treatments.

 

general

CERMT (Covariance-based Extraction of Regulatory targets using Multiple Time series) is a method for predicting transcription factor targets given a particular transcription factor of interest. Targets are defined as the genes that responds similarly, but possibly time shifted, to the transcription factor under two or more treatments.

 

Since CERMT only uses gene expression patterns to search for putative targets it is applicable even if no information on the cis-regulatory elements available.

 

availability
CERMT is implemented as an R package and can be downloaded on this page for use with a local collection of microarray time series. Alternatively, the CERMT web interface can be used to mine the abiotic stress time series for Arabidopsis thaliana provided by the AtGenExpress project.

 

dependencies
R [tested with v2.4.1 on FC4 GNU/Linux]
Following packages are also needed: Biobase, tools.

 

contact
For questions, comments, bugs etc, please contact Henning Redestig.
downloads
program file: cermt_0.0.12.tar.gz
R documentation: cermt.pdf


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