CNKB Data
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 | 2007 | 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" | open | 03/15/2010 | 15,071 | Califano lab |
| HGi (integrates Sun, Phillips and TCGA) | 3.0 | "miRNA-mRNA" | open | 9/15/2011 | 314,974 | Califano lab |
| HGi (integrates Sun, Phillips and TCGA) | 4.0 | "miRNA-mRNA", "protein-dna", "protein-protein" | pending publication | 3/15/2012 | 862,643 | Califano lab |
| BRCA_ceRNET | 1.0 | "rna-rna-miRNA" | pending publication | 8/1/2013 | 2,702,102 | Califano lab |
| GBM_ceRNET | 1.0 | "rna-rna-miRNA" | pending publication | 8/1/2013 | 4,079,082 | Califano lab |
| OV_ceRNET | 1.0 | "rna-rna-miRNA" | pending publication | 8/1/2013 | 4,218,414 | Califano lab |
| PRAD_ceRNET | 1.0 | "rna-rna-miRNA" | pending publication | 8/1/2013 | 2,884,011 | Califano lab |
| TCGA_MCF7 | 1.0 | "protein-dna" | pending publication | 01/2013 | 448,457 | Califano lab |
| PrePPI | 1.0 | "protein-protein" | open | 10/2011 | 8,301,885 | Honig lab |
| BIND | — | protein-protein, protein-dna | open | 08/20/2010 | 45,454 | — |
| Reactome | 33 | protein-protein (see note 1) | open | 06/2010 | 84,442 | — |
| MINT | 2.6 | protein-protein (see note 2) | open | 09/09/2010 | 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"
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).
- ceRNET - ceRNA (competitive endogenous RNA) networks
- BRCA - Breast cancer
- GBM - Glioblastoma Multiforme
- OV - Ovarian cancer
- PRAD - Protate cancer
- MCF7 - breast cancer cell line
- PrePPI - Predicting Protein-Protein Interactions by Combining Structural and non-Structural Information
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).
