Supplementary information

FROM:

Backup in gene regulatory networks explains differences between binding and knockout results

Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon & Ziv Bar-Joseph

doi:10.1038/msb.2009.33

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General supplementary information

Supplementary Results and Methods

This file includes Supplementary Results as referenced in the main text. The Supplementary Methods describe the techniques used to obtain the findings reported in the Supplementary Results and also provide additional details that were omitted from the Materials and Methods section of the main text.

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BLASTP-defined paralog sets

This table contains the assignment of TFs to paralog sets defined using the BLASTP E-value and percentage of shared PPI along. In addition, it provides the binding and knockout overlaps for each TF. Only TFs for which we have conservation-supported binding data and knockout data are included. For TFs without a putative paralog, we calculated shared PPI using approximate paralogs.

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YPD and non-YPD GO terms

This table contains the list of GO terms that were used to assess whether a TF is active only in YPD or if it may be active in non-YPD conditions as well.

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