Difference between revisions of "CNKB Data"

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Revision as of 17:09, 18 June 2010

The Cellular Networks Knowledge Base (CNKB) component in geWorkbench 2.0.0 lists the following interactomes for query. However, some data has not yet be released and is password protected, and other data sets are not yet ready for query.

Data that is currently available for query is shown in light green.

CNKB Data Summary

Name Version Interaction Types Availability Date of release Number of interactions Data source
BCi 1.0 "protein-dna" open 01/2008 41,727 Califano lab
BioGRID 2.0.61 "protein-protein" open date 178,546 Data source
DIP 2.4 "physical interaction","direct interaction","physical association","covalent binding","association","deacetylation reaction","acetylation reaction","phosphorylation reaction","dephosphorylation reaction" not ready date 39,412 Data source
Geneways 6.0 "protein-protein" open date 26,931 Rzhetsky lab
HGi_Phillips 1.0 "protein-dna" open 12/15/2009 118,114 Califano lab
HGi_Sun 1.0 "protein-dna" pending publication 12/15/2009 54,595 Califano lab
HGi_TCGA 1.0 "protein-dna" open 12/15/2009 46,227 Califano lab
HGi_TCGA 2.0 "TF-modulator" pending publication 03/15/2010 15,071 Califano lab
HPRD 8.0 "protein-protein" open date 44,428 Data source


IntAct 2.0.0 "protein-protein" not ready date 202,052 Data source
Reactome 31 "neighboring_reaction","reaction","direct_complex","indirect_complex" open date 172,295 Data source
MINT 2.6 "physical association","colocalization","phosphorylation reaction","direct interaction","sumoylation reaction","dephosphorylation reaction","association","methylation reaction","ubiquitination reaction","covalent binding","deacetylation reaction","physical interaction","cleavage reaction","enzymatic reaction","disulfide bond","glycosylation reaction","acetylation reaction","neddylation reaction","hydroxylation reaction","deneddylation reaction" not ready date 18,634 Data source

Local abbreviations used

  • BCi - B-Cell interactome, produced by an ARACNe run on B-Cell microarray data from the lab of Dr. Ricardo Dalla-Favera.
  • HGi - Human High-Grade Glioma interactome, produced by analysis of microarray data from several sources:
    • Phillips - data published by Phillips et al. ...
    • Sun - data published by Sun et al. ...
    • TCGA - data obtained from The Cancer Genome Atlas project (NCI).


Notes

  • HGi version 1.0 - interactome derived from ARACNe runs (transcriptional).
  • HGi version 2.0 - interactome derived from a MINDy run (TCGA data only) (post-translational).