Hierarchy

From GersteinInfo

Latest revision as of 15:14, 5 November 2013

Reorganization of regulatory networks into hierarchies: Resource page from Gerstein Lab

This page provides the data used in articles related with organization of regulatory networks into hierarchies and their downstream analysis from Gerstein Lab.

Genomic analysis of the hierarchical structure of regulatory networks.

by Haiyuan Yu, and Mark B. Gerstein. Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14724-31. Epub 2006 Sep 26..

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

Data:

Networks: First column lists the regulator (transcription factor) and the other column are the targets of that regulator. The file is tab delimited.

Transcriptional regulatory network for Yeast

Transcriptional regulatory network for E. coli

For layer assignment for transcriptional regulatory network for Yeast and E. coli, please see the PDF of the paper.

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels

by Nitin Bhardwaj, Koon-Kiu Yan, and Mark B. Gerstein. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6841-6. Epub 2010 Mar 29.

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

Data:

Networks: First column lists the regulator (transcription factor or kinase) and the second column the targets.

Transcriptional regulatory network for Yeast

Transcriptional regulatory network for E. coli

Transcriptional regulatory network for Mouse

Transcriptional regulatory network for Rat

Transcriptional regulatory network for Human

Transcriptional regulatory network for M. tuberculosis

Modification network for Human

Phosphorylation network for Yeast

Layer assignment: First column lists the regulator (transcription factor or kinase) and the second column the layer it belongs to.

Layer assignment for transcriptional regulatory network for Yeast

Layer assignment for transcriptional regulatory network for E. coli

Layer assignment for transcriptional regulatory network for Mouse

Layer assignment for transcriptional regulatory network for Rat

Layer assignment for transcriptional regulatory network for Human

Layer assignment for transcriptional regulatory network for M. tuberculosis

Layer assignment for modification network for Human

Layer assignment for phosphorylation network for Yeast

Phenotypic Effects of Network Rewiring in Transcriptional Regulatory Hierarchies

by Nitin Bhardwaj, Philip M. Kim and Mark B. Gerstein. Sci Signal. 2010 Nov 2;3(146):ra79.

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

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. For E. coli, the transcriptional regulatory network was obtained from RegulonDB (as of July 2009) (S. Gama-Castro et al., Nucleic Acids Res 36, D120, 2008). For S. cerevisiae, the data was obtained from various biochemical and genetic experiments (T. I. Lee et al., Science 298, 799, 2002, C. T. Harbison et al., Nature 431, 99, 2004, C. E. Horak et al., Genes Dev 16, 3017, 2002, V. V. Svetlov, T. G. Cooper, Yeast 11, 1439, 1995).

Assignment into hierarchies for Yeast and E. coli.

Changes in hierarchies:

Yeast Gene Deletion from Deutschbauer et al. Columns are as follows:

Column 1: Delete: the gene deleted

Column 2: Current_level: the position in the wild-type hierarchy. Bottom=Level 1. First = Level 2. Two = Level 3. Three = Level 4.

Column 3: Out_TF: the number of TFs it regulates. Equals 0 for all bottom level rgulators.

Column 4: Out_overall: the total number of targets

Column 5: In: In-degree, the number of its regulators

Column 6: Het: tag fitness of the heterozygous deletion in ypd

Column 7: Hom: tag fitness of the homozygous deletion in ypd

Column 8: Ave_hom_het: average fitness of the homozygous and heterozygous deletion in ypd

Column 9: Changes: the number of changes in the hierarchy upon deletion of that gene.

The next set of 3 columns are as follows:

Column 10, 13, 16 etc: Gene_moved: gene that moved its position in the hierarchy

Column 11, 14, 17 etc: Initial_level: its initial level in the WT hierarchy

Column 12, 15, 18 etc:Final_level: its final position in the rearranged hierarchy.

Yeast gene deletion from Synthetic array by Costanzo et al. Columns are as follows:

Column 1: Deleted1: first gene deleted.

Column 2: Deleted2: second gene deleted.

Column 3: level1: first gene's position in the wild-type hierarchy. Bottom=Level 1. First = Level 2. Two = Level 3. Three = Level 4.

Column 3: level2: second gene's position in the wild-type hierarchy. Bottom=Level 1. First = Level 2. Two = Level 3. Three = Level 4.

Column 5: P-value: P-value of the genetic interaction between them.

Column 6: Pheno: cell growth upon deletion of that pair.

Column 7: Changes: the number of changes in the hierarchy upon deletion of that pair.

The next set of 3 columns are as follows (empty if the number of changes =0):

Column 8, 11, 14 etc: Gene_moved: gene that moved its position in the hierarchy.

Column 9, 12, 15 etc: Initial_level: its initial level in the WT hierarchy.

Column 10, 13, 16 etc:Final_level: its final position in the rearranged hierarchy.

E. coli gene deletion from Baba et al. Columns are as follows:

Column 1: Delete: the gene deleted

Column 2: Current_level: the position in the wild-type hierarchy. Bottom=Level 1. First = Level 2. Two = Level 3. Three = Level 4.

Column 3: Out_TF: the number of TFs it regulates. Equals 0 for all bottom level rgulators.

Column 4: Out_overall: the total number of targets

Column 5: Colonies: the fraction of colonies that survived.

Column 6: Changes: the number of changes in the hierarchy upon deletion of that gene.

The next set of 3 columns are as follows:

Column 7, 10, 13 etc: Gene_moved: gene that moved its position in the hierarchy

Column 8, 11, 14 etc: Initial_level: its initial level in the WT hierarchy

Column 9, 12, 15 etc:Final_level: its final position in the rearranged hierarchy.

E. coli edge addition from Isalan et al. Columns are as follows:

Column 1: promoter_ORF_pair: the promoter and ORF fused together. This creates a new edge between the regulators of promotor and the ORF.

Column 2: Number of changes: the number of changes in the hierarchy upon addition of that new edge.

Column 3: l.s.d.: It measures the ‘least square difference’ between the mutant growth and the wild-type growth so a higher value indicates a slower cell growth.

Caution: the types of changes in this file are listed above that line. For example

appY_rpoD 0 1.58E-09

rpoE first two

appY_rpoE 1 7.23E-09

means that appY_rpoE fusion leads to 1 change which "rpoE changing from level two to level first".

Programs used to generate the data

BFS.pl : Program used to generate the hierarchy from a tab-delimited network

count_changes_modified_hierarchy.pl  : program to count the number of changes in a modified hierarchy upon deletion of TFs/nodes.

Supplementary Figures and Results

Regulators involved in sensing different kinds of signals. The data was obtained from (A. Martinez-Antonio et al, Trends Microbiol 14, 22, 2006). For each category, the file lists the total number TFs involved in that category and the number of regulators that were mapped to the category followed by the TFs listed in each category. Bottom=Level 1. First = Level 2. Two = Level 3. Three = Level 4.

For questions/comments, contact: nbhardwaj@gmail.com