Bioinformatics
International Journal of Computational Intelligence in Bioinformatics and Systems Biology
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A bidirectional promoter is a region along a strand of DNA that regulates the expression of two genes flanking the region. Each of these genes is transcibed in a direction that points away from the other gene; two such genes are said to be in a head-to-head configuration. We search the UCSC List of Known Genes and GenBank Expressed Sequence Tag (EST) data for pairs of genes in such a configuration in order to identify new bidirectional promoters. The EST data constitutes a larger and more intricate dataset than the UCSC List of Known Genes. However, working with EST data presents a challenge, as the EST database may be highly redundant and may also contain overlapping ESTs. To deal with these problems, we have developed an algorithm to identify bidirectional promoters based on the above data sources; the algorithm is capable of handling redundant ESTs, and also ESTs that overlap or disagree in orientation. This analysis resulted in the identification of thousands of new candidate head-to-head gene pairs, corroborated the 5' ends of many known human genes, revealed new 5' exons of previously characterized genes, and in some cases identified novel genes. Further analyses yielded evidence for coordinate expression of genes in a head-to-head configuration, and examined the prevalence of bidirectional promoters in different biological pathways.