Finding Transcription Factor Binding Sites in Coregulated Genes by Exhaustive Sequence Search

Growing amounts of gene expression data provide the possibility of finding coregulated genes by clustering methods. By analysis of the promoter regions of these genes, rather weak signals of transcription factor binding sites may be detected [Zhang, 1999]. We compare existing programs and own software on yeast clusters. Therefore, we introduce the new algorithm ITB, an integrated tool for box finding, which exhaustively analyses regular expression-like patterns in promoter sequences, allowing gaps and the matching of more than one base at any position within the candidates. The applicability of ITB to predict transcription factor binding sites in human promoter sequences is evaluated.