CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Background: The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments.

Results: We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes.

Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data.

The major public microarray repositories Gene Expression Omnibus and ArrayExpress are growing rapidly. This enables meta-analysis studies, in which expression data from multiple individual studies are combined. To facilitate these types of studies, we developed Microarray Retriever for searching and retrieval of data from GEO and ArrayExpress.