## 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. 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 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.

## Display Conventions

The scoring ranges from 200 to 1000 and is based on the number of lines of evidence that support the motif being active. Each of the two sensu stricto species in which the motif was conserved counts as a line of evidence. If the ChIP-chip data showed good (P ≤ 0.001) evidence of binding to the transcription factor associated with the motif, that counts as two lines of evidence. If the ChIP-chip data showed weaker (P ≤ 0.005) evidence of binding, that counts as just one line of evidence. The following table shows the relationship between lines of evidence and score:

> > Evidence | Score
> > --- | ---
> > 4 | 1000
> > 3 | 500
> > 2 | 333
> > 1 | 250
> > 0 | 200

## 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 CT, Gordon DB, Lee TI, Rinaldi NJ, MacIsaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004 Sep 2;431(7004):99-104.
Supplementary data at http://web.wi.mit.edu/young/regulatory_code and http://fraenkel.mit.edu/Harbison/.