Hierarchy

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'''
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'''The regulatory network for [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls  Yeast] and [http://homes.gersteinlab.org/people/nbhardwaj/Human_TFs_with_Intensity.xls ''E. coli''].'''
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'''The regulatory network for [/nfs/archive/html/proj/Hierarchy_Rewiring/Yeast_reg.txt Yeast] and [/nfs/archive/html/proj/Hierarchy_Rewiring/Ecoli_reg.txt ''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.
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|-
|-
! Number of regulatory interactions
! Number of regulatory interactions
-
| Cell 2 || Cell 3
+
| 12873 || 3123
|-
|-
! Number of Regulators
! Number of Regulators
-
| Cell B
+
| 288
-
| Cell C
+
| 143
|-
|-
! Number of Targets
! Number of Targets
-
| Cell B
+
| 4410
-
| Cell C
+
| 1420
|-
|-
! Number of Inter-Regulator interactions
! Number of Inter-Regulator interactions
-
| Cell B
+
| 632
-
| Cell C
+
| 220
|}
|}

Revision as of 13:10, 5 July 2010

Information page for the article:

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

Please cite the above article if usage of the following date results in a publication.


Data:

The regulatory network for [/nfs/archive/html/proj/Hierarchy_Rewiring/Yeast_reg.txt Yeast] and [/nfs/archive/html/proj/Hierarchy_Rewiring/Ecoli_reg.txt 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

Fraction of toxic genes in Yeast
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