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.
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:
The data for this track was provided by the Young and Fraenkel labs at
MIT/Whitehead/Broad. The track was created by Jim Kent.
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.
PMID: 15343339; PMC: PMC3006441
Supplementary data at http://younglab.wi.mit.edu/regulatory_code/ and