Latest revision as of 18:06, 11 February 2015

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

• 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

Columbia Interactomes

• BCi - B-Cell interactome, produced by an ARACNe run on B-Cell microarray data from the lab of Dr. Ricardo Dalla-Favera. See Wang et al. 2006 and Lefebvre et al. 2007.
• ceRNET - ceRNA (competitive endogenous RNA) networks (Sumazin et al., 2011). Publication of the networks below expected 2014.
  • BRCA - Breast cancer
  • GBM - Glioblastoma Multiforme
  • OV - Ovarian cancer
  • PRAD - Protate cancer
• GeneWays - Rzhetsky et al., (2004).
• 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 Cancer Genome Atlas Research Network, 2008.
• 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.

External Interaction Databases

• BIND - The Biomolecular Interaction Network Database. Bader et al., 2001.
• MINT - MINT: a Molecular INTeraction database. Zanzoni et al., 2002.
• Reactome - Croft et al., 2011, Matthews et al., 2009.

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

• Lefebvre C, Lim WK, Basso K, Dalla Favera R, and Califano A. A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells (2007) Lecture Notes in Bioinformatics (LNCS) 4532:42-56. link to paper

• 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

• Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C. (2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 37(1):43-53. PubMed 15016385

• Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147(2):370-81. doi: 10.1016/j.cell.2011.09.041 (PubMed 22000015).

• 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

• Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes (2006) Lecture Notes in Computer Science 3909:348-362. link to paper

• 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