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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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).

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• 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.

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© 2010 American Association for the Advancement of Science