CNKB Data

Revision as of 13:31, 7 November 2013 by Smith (talk | contribs) (CNKB Data Summary)

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", "protein-protein", "TF-modulator" open 01/2008 41,727; 22,554; 1,912 Califano lab
Geneways 6.0 "protein-protein" open 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", "mRNA-miRNA" open 12/15/2009 46,227; 5,156 Califano lab
HGi_TCGA 2.0 "TF-modulator" pending publication 03/15/2010 15,071 Califano lab


BRCA_ceRNET 1.0 "rna-rna-miRNA" pending publication 2702102 Califano lab
GBM_ceRNET 1.0 "rna-rna-miRNA" pending publication 4079082 Califano lab
OV_ceRNET 1.0 "rna-rna-miRNA" pending publication 4218414 Califano lab
PRAD_ceRNET 1.0 "rna-rna-miRNA" pending publication 2884011 Califano lab


Reactome 33 protein-protein (see note 1) open 84442
MINT 2.6 protein-protein (see note 2) open 2010-09-09 18,516
  • Note 1 - includes "neighboring_reaction","reaction","direct_complex","indirect_complex"
  • Note 2 - includes "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"

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).