Schema for Reg. Module - Eran Segal Regulatory Module
  Database: sacCer3    Primary Table: esRegGeneToMotif    Row Count: 3,993   Data last updated: 2011-09-06
Format description: arCOG Information
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chrIvarchar(255) values chromosome
chromStart 9321int(11) range Start position in chromosome
chromEnd 9336int(11) range End position in chromosome
name Motif_499varchar(255) values hit name
score 1000int(11) range Score from 900-1000. 1000 is best
strand +char(1) values Value should be + or -
gene YAL067Cvarchar(255) values standard name

Connected Tables and Joining Fields
        sacCer3.ceBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.choExpDistance.query (via esRegGeneToMotif.gene)
      sacCer3.choExpDistance.target (via esRegGeneToMotif.gene)
      sacCer3.dmBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.drBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.esRegGeneToModule.gene (via esRegGeneToMotif.gene)
      sacCer3.esRegUpstreamRegion.name (via esRegGeneToMotif.gene)
      sacCer3.hgBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.mmBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.rnBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.sgdBlastTab.query (via esRegGeneToMotif.gene)
      sacCer3.sgdBlastTab.target (via esRegGeneToMotif.gene)
      sacCer3.sgdCanonical.transcript (via esRegGeneToMotif.gene)
      sacCer3.sgdDescription.name (via esRegGeneToMotif.gene)
      sacCer3.sgdGene.name (via esRegGeneToMotif.gene)
      sacCer3.sgdIsoforms.transcript (via esRegGeneToMotif.gene)
      sacCer3.sgdPep.name (via esRegGeneToMotif.gene)
      sacCer3.sgdToName.name (via esRegGeneToMotif.gene)
      sacCer3.sgdToSwissProt.name (via esRegGeneToMotif.gene)
      sacCer3.esRegMotif.name (via esRegGeneToMotif.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandgene
585chrI93219336Motif_4991000+YAL067C
585chrI94619467ADR1_011000+YAL067C
585chrI3486934884Motif_5051000-YAL060W
585chrI3486934884Motif_5651000-YAL060W
585chrI3486934884Motif_5711000-YAL060W
585chrI3486934884Motif_5831000-YAL060W
585chrI3487034885Motif_5651000-YAL060W
585chrI3487034885Motif_5831000-YAL060W
585chrI3487034885Motif_6071000+YAL060W
585chrI3487134886Motif_4151000+YAL060W

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

Reg. Module (esRegGeneToMotif) Track Description
 

Description

This track shows predicted transcription factor binding sites based on sequence similarities upstream of coordinately expressed genes.

In dense display mode the gold areas indicate the extent of the area searched for binding sites; black boxes indicate the actual binding sites. In other modes the gold areas disappear and only the binding sites are displayed. Clicking on a particular predicted binding site displays a page that shows the sequence motif associated with the predicted transcription factor and the sequence at the predicted binding site. Where known motifs have been identified by this method, they are named; otherwise, they are assigned a motif number.

Methods

This analysis was performed according to Genome-wide discovery of transcriptional modules from DNA sequence and gene expression on various pre-existing microarray datasets. A regulatory module is comprised of a set of genes predicted to be regulated by the same combination of DNA sequence motifs. The predictions are based on the co-expression of the set of genes in the module and on the appearance of common combinations of motifs in the upstream regions of genes assigned to the same module.

Credits

Thanks to Eran Segal for providing the data analysis that forms the basis for this track. The display was programmed by Jim Kent.

References

Segal E, Yelensky R, Koller D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics. 2003;19 Suppl 1:i273-82. PMID: 12855470