Schema for Reg. ChIP-chip - ChIP-chip Results from Harbison Gordon et al.
  Database: sacCer3    Primary Table: transRegCodeProbe    Row Count: 6,178   Data last updated: 2011-08-31
Format description: ChIP-chip Probe and Transcription Factor Binding Info
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 20226int(10) unsigned range Start position in chromosome
chromEnd 21535int(10) unsigned range End position in chromosome
name iYAL064C-A-5varchar(255) values Name of probe
tfCount 10int(10) unsigned range Count of bound transcription factors_conditions
tfList DAL82_RAPA,DAL82_SM,IXR1_YP...longblob   List of bound transcription factors_conditions
bindVals 0.001,0.001,0.001,0.001,0.0...longblob   E values for factor binding (lower is better)

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

Sample Rows
 
binchromchromStartchromEndnametfCounttfListbindVals
585chrI2022621535iYAL064C-A-510DAL82_RAPA,DAL82_SM,IXR1_YPD,NRG1_YPD,PHD1_YPD,SUT1_YPD,ARG81_SM,PHD1_BUT90,ROX1_H2O2Hi,YAP6_YPD,0.001,0.001,0.001,0.001,0.001,0.001,0.005,0.005,0.005,0.005,
585chrI2185022221iYAL064W21ACE2_YPD,ADR1_YPD,MIG2_YPD,SFP1_H2O2Lo,STB2_YPD,UGA3_SM,UPC2_YPD,YRR1_YPD,ADR1_HEAT,AFT2_YPD,BAS1_SM,CST6_YPD,EDS1_YPD,GAL80_YPD ...0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,
585chrI2253623994iYALWdelta10
585chrI2797029178iYAL063C-015CIN5_H2O2Lo,DAL82_SM,NRG1_H2O2Lo,PHD1_BUT90,PHD1_YPD,ROX1_H2O2Lo,SKN7_H2O2Lo,SOK2_BUT14,SUT1_YPD,YAP6_H2O2Hi,YAP6_H2O2Lo,HMS2_YP ...0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.001,0.005,0.005,0.005,0.005,
585chrI2917130368iYAL063C-12FHL1_YPD,WAR1_YPD,0.001,0.005,
585chrI3034931581iYAL063C-219ACE2_YPD,ARR1_H2O2Hi,MAL33_H2O2Hi,MBP1_YPD,RCO1_YPD,RTG3_H2O2Hi,AFT2_H2O2Lo,ARG81_SM,CST6_YPD,GAL4_YPD,HMS2_YPD,MOT3_H2O2Hi,MOT3 ...0.001,0.001,0.001,0.001,0.001,0.001,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,0.005,
585chrI3292333461iYAL062W1SOK2_BUT14,0.001,
585chrI3468435168iYAL061W9BAS1_SM,MSN2_H2O2Hi,NRG1_H2O2Hi,DAL82_YPD,MOT3_H2O2Hi,MSN4_H2O2Hi,PHO2_H2O2Hi,PHO2_Pi-,RPH1_H2O2Hi,0.001,0.001,0.001,0.005,0.005,0.005,0.005,0.005,0.005,
585chrI3628636511iYAL060W1IME1_H2O2Hi,0.005,
585chrI3716037451iYAL059W2RFX1_YPD,USV1_YPD,0.005,0.005,

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

Reg. ChIP-chip (transRegCodeProbe) Track Description
 

Description

This track shows the location of the probes spotted on a slide in the chromatin immunoprecipitation/microarray hybridization (ChIP-chip) experiments described in Harbison, Gordon et al. below. Click on an item in this track to display a page showing which transcription factors pulled down DNA that is enriched for this probe sequence, which transcription factor binding site motifs are present in the probe and whether these motifs are conserved in related yeast species. See also the "Regulatory Code" track for the position of the individual motifs.

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/.