Difference between revisions of "CNKB Data"
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Revision as of 12:40, 7 November 2013
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 |
| BioGRID | 2.0.61 | "protein-protein" | open | — | 178,546 | — |
| DIP | 2.4 | "physical interaction","direct interaction","physical association","covalent binding","association","deacetylation reaction","acetylation reaction","phosphorylation reaction","dephosphorylation reaction" | not ready | — | 39,412 | — |
| 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 |
| HPRD | 8.0 | "protein-protein" | open | — | 44,428 | —
|
| IntAct | 2.0.0 | "protein-protein" | not ready | — | 202,052 | — |
| Reactome | 31 | "neighboring_reaction","reaction","direct_complex","indirect_complex" | open | — | 172,295 | — |
| 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 | — | 18,634 | — |
| — | — | — | — | — | — | — |
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).
