Description

This track shows putative regulatory elements in Saccharomyces cerevisiae that are supported by cross-species evidence (Harbison, Gordon, et al., 2004). Harbison, Gordon, et al. performed a genome-wide location analysis with 203 known DNA-binding transcriptional regulators (some under multiple environmental conditions), and identified 11,000 high-confidence interactions between regulators and promoter regions. They then compiled a compendium of motifs for 102 transcriptional regulators based on a combination of their experimental results, cross-species conservation data for four species of yeast, and motifs from the literature, and finally, they mapped these motifs to the S. cerevisiae genome. This track shows positions at which these motifs matched the genome with high confidence and at which the matching sequence was well conserved across yeast species.

The details page for each putative binding site shows the sequence at that site compared to the position-specific probability matrix for the associated transcriptional regulator (shown as both a table and a graphical logo). It also indicates whether the the binding site is supported by experimental (CHIP/CHIP) results and the number of other yeast species in which it is conserved.

See also the "Reg. CHIP/CHIP" track for additional related information.

Credits

The data for this track was provided by the Young and Fraenkel labs at MIT/Whitehead/Broad. The track was created by Jim Kent.

References

Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., MacIsaac, K.D., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431:99-104 (2004).

Supplementary data at http://web.wi.mit.edu/young/regulatory_code and http://jura.wi.mit.edu/fraenkel/regulatory_map.