Supplemental Tables

Table Transcription factor binding data (ChIP-chip) Log ratios [1] P-values
S1 MMS treated cells. Annotated by intergenic ID [2, 3] table table
S2 MMS treated cells. Annotated by gene ID [2] table table
S3 Untreated cells. Annotated by intergenic ID [2, 3] table table
S4 Untreated cells. Annotated by gene ID [2] table table
 
  Expression and deletion-buffering data Log ratios [1] P-values
S5 mRNA expression data in TF knockouts and wild-type table table
S6 Deletion-buffering analysis   table
S7 Deletion-enhancement analysis   table
 
  Pathway models  
S8 Direct and indirect regulatory pathways [4] listed by gene name
listed by ORF ID
S9 Pathways combined into a single model of the DNA damage response (Figure 5b).

[Suitable for visualization with Cytoscape]

Notes

[1] Log base 10
[2] In ChIP-chip experiments, log ratios less than zero indicated instances where the immunoprecipitated (IP) sample had less fluorescence signal than the non-IP channel, suggesting that promoter-binding did not occur. Thus, these negative log ratios were set to be zero.
[3] The promoter sequences spotted on ChIP-chip microarrays were identified by "intergenic IDs." In some cases, one promoter sequence may be located between two closely spaced genes on opposite strands of a chromosome. In these cases, both genes were listed in the "ORF_ID" column of the data files (e.g. the promoter sequence identified by "iYOL114C" is between ORFs YOL113W and YOL114C).
[4] Each line in these files lists one hypothetical regulatory path consisting of two or three genes. Each path starts (left-most gene on a line) with one of the 27 transcription factors for which deletion-buffering experiments were performed. Each path terminates (right-most gene) with a gene that was found to be deletion-buffered by the TF at the start of the path.

For paths consisting of two genes, the deletion-buffering effect validates a single interaction, in which the TF binds the promoter of the deletion-buffered gene.

For paths consisting of three genes, the deletion-buffering effect validates two interactions. The deleted TF is connected via a promoter-binding or protein-protein interaction to a second, intermediate TF which, in turn, binds the promoter of the deletion-buffered gene.

Genes are identified by gene or ORF name from the Saccharomyces Genome Database
[5] Log ratios (base 10) of differentially expressed genes (P < 0.005) in the model.