Schema for Regulatory Code - Transcriptional Regulatory Code from Harbison Gordon et al.
  Database: sacCer3    Primary Table: transRegCode    Row Count: 206,558   Data last updated: 2011-08-31
Format description: Transcription factor binding sites from ChIP-chip experiments and conservation
fieldexampleSQL type info description
bin 585smallint(6) range Indexing field to speed chromosome range queries.
chrom chrIvarchar(255) values Reference sequence chromosome or scaffold
chromStart 2179int(10) unsigned range Start position in chromosome
chromEnd 2187int(10) unsigned range End position in chromosome
name FKH1varchar(255) values Name of transcription factor
score 200int(10) unsigned range Score from 0 to 1000
chipEvidence nonevarchar(255) values Evidence strength from ChIP-chip assay
consSpecies 0int(10) unsigned range Number of species conserved in

Connected Tables and Joining Fields
        sacCer3.transRegCodeCondition.name (via transRegCode.name)
      sacCer3.transRegCodeMotif.name (via transRegCode.name)
      sacCer3.transRegCodeProbe.tfList (via transRegCode.name)

Sample Rows
 
binchromchromStartchromEndnamescorechipEvidenceconsSpecies
585chrI21792187FKH1200none0
585chrI21902196SWI5200none0
585chrI22082215TEC1200none0
585chrI22182230YOX1200none0
585chrI22212232SPT2200none0
585chrI22382244MOT3200none0
585chrI22502257STE12200none0
585chrI22502257DIG1200none0
585chrI22712278TEC1200none0
585chrI23062312ASH1200none0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Regulatory Code (transRegCode) Track Description
 

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:

EvidenceScore
41000
3500
2333
1250
0200

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. PMID: 15343339; PMC: PMC3006441

Supplementary data at http://younglab.wi.mit.edu/regulatory_code/ and http://fraenkel.mit.edu/Harbison/.