geWorkbench

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	Interactome 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"

Data Sources and Descriptions

• 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 - derived from data published by Phillips et al., 2006.
  • Sun - derived from data published by Sun et al., 2006.
  • TCGA - derived from data obtained from The Cancer Genome Atlas project (NCI) (2008).
• ceRNET - ceRNA (competitive endogenous RNA) networks
• BRCA - Breast cancer
• GBM - Glioblastoma Multiforme
• OV - Ovarian cancer
• PRAD - Protate cancer
• MCF7 - breast cancer cell line (Chiu et al., 2013)
• PrePPI - Predicting Protein-Protein Interactions by Combining Structural and non-Structural Information. See Zhang et al., 2012, 2013.

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).

References

• Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW. (2001) BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res. 29(1):242-5. PubMed 11125103

• Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8 PubMed 18772890

• Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. (Database issue):D691-7. PubMed PubMed 21067998

• Hua-Sheng Chiu, Xuerui Yang, María Rodríguez Martínez, Archana Iyer, Pavel Sumazin, Andrea Califano (2013) Highly conserved ceRNA regulatory interactions cooperate with genomic variability to modulate drivers of tumorigenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5231. doi:10.1158/1538-7445.AM2013-5231 link to abstract

• Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37:D619-22. PubMed:18981052

• Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, et al. (2006) Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis". Cancer Cell 9(3):157-73 PubMed 16530701

• Sun L, Hui AM, Su Q, Vortmeyer A, Kotliarov Y, Pastorino S, et al. (2006) Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. Cancer Cell. 9(4):287-300 PubMed 16616334

• Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. (2002) MINT: a Molecular INTeraction database. FEBS Lett. 513(1):135-40. PubMed:11911893

• Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale Nature 490(7421):556-60. doi: 10.1038/nature11503. Epub 2012 Sep 30. PubMed 23023127

• Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. (2013) PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. 41(Database issue):D828-33. doi: 10.1093/nar/gks1231. Epub 2012 Nov 27. PubMed 23193263