Supplementary Tables
Download:
ZIP archive with all tables.
Raw microarray data from ArrayExpress
(accessions
E-TABM-92 [promoter binding]
and
E-TABM-93 [gene expression])
Perl scripts that may be useful.
See comments in each script for example usage.
| 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. |
|
