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Sci. Signal., 2 November 2010
[DOI: 10.1126/scisignal.2001014]

Supplementary Materials for:

Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators

Nitin Bhardwaj, Philip M. Kim,* Mark B. Gerstein*

*To whom correspondence should be addressed. E-mail: pi{at}kimlab.org (P.M.K.); mark.gerstein{at}yale.edu (M.B.G.)

This PDF file includes:

  • Text
  • Fig. S1. Operon-based hierarchy in E. coli.
  • Fig. S2. Condition-specific hierarchies in yeast.
  • Fig. S3. Effects of overexpression, a means of increasing the strength of regulatory interactions.
  • Fig. S4. Phenotypic effect of deletion of nodes from various levels in the yeast regulatory subnetworks coming from individual studies.
  • Fig. S5. Phenotypic effect of deletion of nodes from various levels in yeast regulatory subnetworks coming from individual studies.
  • Fig. S6. Indirect targets and number of targets versus position in the hierarchy for E. coli and S. cerevisiae.
  • Fig. S7. Phenotypic effect versus out-degree.
  • Table S1. Properties of the regulatory networks used.
  • Table S2. Description of data S1.
  • Table S3. Description of data S2.
  • Table S4. Description of data S3.
  • Table S5. Description of data S4.
  • References

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Technical Details

Format: Adobe Acrobat PDF

Size: 311 KB


Other Supplementary Material for this manuscript includes the following:

  • List S1. E. coli transcriptional regulatory network hierarchy (PDF format).
  • List S2. Yeast transcriptional regulatory network hierarchy (PDF format).
  • List S3. E. coli transcriptional regulatory network (PDF format).
  • List S4. S. cerevisiae transcriptional regulatory network (PDF format).
  • List S5. Regulatory network based on grouping a subset of the genes in E. coli by operon (PDF format).
  • List S6. Regulatory network based on specific conditions in S. cerevisiae (PDF format).

[Download PDF of Lists S1-S6]

Technical Details

Format: Adobe Acrobat PDF

Size: 286 KB

  • Data S1 to S4. The rewiring events and effects of gene deletion or edge addition to E. coli and S. cerevisiae transcriptional networks (Microsoft Excel format). Files are packaged as a compressed archive, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the instructions below.

[Download Data S1 to S4.zip]

Technical Details

Format: Microsoft Excel files in a zipped archive

Size: 478 KB


Instructions for downloading and decompressing files:

  1. Create a temporary folder on your machine's hard drive.
  2. Save the compressed archive to the temporary folder you created, using the links above.
  3. Decompress the compressed file in the temporary folder using decompression software such as WinZip (Windows; www.winzip.com) or StuffIt Expander (Windows and Mac; www.stuffit.com).

Citation: N. Bhardwaj, P. M. Kim, M. B. Gerstein, Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators. Sci. Signal. 3, ra79 (2010).

© 2010 American Association for the Advancement of Science


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