Difference between revisions of "CNKB Data"

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Revision as of 16:53, 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 date 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 date 118,114 Califano lab
HGi_Sun 1.0 "protein-dna" pending publication date 54,595 Califano lab
HGi_TCGA 1.0 "protein-dna" open date number Califano lab
HGi_TCGA 2.0 protein-protein (post-translational) pending publication date number Califano lab
HPRD 8.0 "protein-protein" open date 44,428 Data source


IntAct 2.0.0 Interaction Types not ready date number Data source
Reactome 31 "neighboring_reaction","reaction","direct_complex","indirect_complex" open date 172,295 Data source
MINT 2.6 protein-protein 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).