Motivation: The end result of analyzing microarray datasets is a list of differentially expressed genes. Such gene lists are grouped by the functions of the gene products and common transcription factor binding sites contained in their promoters. Functional categorization is most commonly accomplished using Gene Ontology (GO) categories and promoters are analyzed for the presence and enrichment of binding sites for transcription factors known to be involved in the process under study. Although there are several programs that identify and analyze functional categories, few of them analyze both promoter sequences and functional categories. Moreover, the integrated visualization of the three data types, expression, annotation and transcription factor binding sites in the promoters, is important for drawing meaningful inferences.
Results: In order to address this need for A. thaliana community, we have radically modified and extended our CLENCH tool, which performed functional category analysis. Clench2.0 performs functional analysis, searches promoter sequence for known TF binding sites, and visualizes the expression, annotation and transcription factor binding site data for lists of genes provided by the user. Although developed for A. thaliana, Clench2.0 can be easily adapted to work for other model organisms.
Availability: www.stanford.edu/~nigam/Clench
