Hierarchy

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by Nitin Bhardwaj, Philip M. Kim and Mark B. Gerstein

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Data:

The regulatory network for Yeast and E. coli. The file is in a tab-delimited format with the regulator followed by the target in the same line. For E. coli, the last column also list the type of regulation: "+" for positive, "-" for negative and "+-" for dual regulation.

Properties of the regulatory networks used

	Yeast	E. coli
Number of regulatory interactions	12873	3123
Number of Regulators	288	143
Number of Targets	4410	1420
Number of Inter-Regulator interactions	632	220

Assignment into hierarchies for Yeast and E. coli.

Changes in hierarchies:

Indirect Targets and Number of targets vs position in the hierarchy (in one of the four levels) for E. coli and Yeast.

Indirect targets

Effects of Overexpression

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Fraction of toxic genes in Yeast