Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation.

ABSTRACT: Computational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes--positional and inter-motif distance specificity--that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distance-specific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and po

SUBMITTER: Vardhanabhuti S 

PROVIDER: S-EPMC1904283 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature