Difference between revisions of "CNKB Data"

(→‎CNKB Data Summary)
 
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Line 13: Line 13:
 
!Date of release
 
!Date of release
 
!Number of interactions
 
!Number of interactions
−
!Data source
+
!Interactome source
  
 
|-style="color:black;background-color:#CCFFCC;"
 
|-style="color:black;background-color:#CCFFCC;"
Line 29: Line 29:
 
|"protein-protein"
 
|"protein-protein"
 
|open
 
|open
−
|align="center"|—
+
|2007
 
|26,931
 
|26,931
 
|Rzhetsky lab
 
|Rzhetsky lab
Line 60: Line 60:
 
|Califano lab
 
|Califano lab
  
−
|-style="color:black;background-color:#FFFFFF;"
+
|-style="color:black;background-color:#CCFFCC;"
 
|HGi_TCGA
 
|HGi_TCGA
 
|2.0
 
|2.0
 
|"TF-modulator"
 
|"TF-modulator"
−
|pending publication
+
|open
 
|03/15/2010
 
|03/15/2010
 
|15,071
 
|15,071
 
|Califano lab
 
|Califano lab
  
 +
|-style="color:black;background-color:#CCFFCC;"
 +
|HGi (TCGA)
 +
|3.0
 +
|"miRNA-mRNA"
 +
|open
 +
|9/15/2011
 +
|314,974
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#FFFFFF;"
 +
|HGi (integrates Sun, Phillips and TCGA)
 +
|4.0
 +
|"miRNA-mRNA", "protein-dna", "protein-protein"
 +
|pending publication
 +
|3/15/2012
 +
|862,643
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#FFFFFF;"
 +
|BRCA_ceRNET
 +
|1.0
 +
|"rna-rna-miRNA"
 +
|pending publication
 +
|8/1/2013
 +
|2,702,102
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#FFFFFF;"
 +
|GBM_ceRNET
 +
|1.0
 +
|"rna-rna-miRNA"
 +
|pending publication
 +
|8/1/2013
 +
|4,079,082
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#FFFFFF;"
 +
|OV_ceRNET
 +
|1.0
 +
|"rna-rna-miRNA"
 +
|pending publication
 +
|8/1/2013
 +
|4,218,414
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#FFFFFF;"
 +
|PRAD_ceRNET
 +
|1.0
 +
|"rna-rna-miRNA"
 +
|pending publication
 +
|8/1/2013
 +
|2,884,011
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#FFFFFF;"
 +
|TCGA_MCF7
 +
|1.0
 +
|"protein-dna"
 +
|pending publication
 +
|01/2013
 +
|448,457
 +
|Califano lab
 +
 +
|-style="color:black;background-color:#CCFFCC;"
 +
|PrePPI
 +
|1.0
 +
|"protein-protein"
 +
|open
 +
|10/2011
 +
|8,301,885
 +
|Honig lab
 +
 +
|-style="color:black;background-color:#CCFFCC;"
 +
|[http://www.bind.ca/ BIND]
 +
|align="center"|—
 +
|protein-protein, protein-dna
 +
|open
 +
|08/20/2010
 +
|45,454
 +
|align="center"|—
  
 
|-style="color:black;background-color:#CCFFCC;"
 
|-style="color:black;background-color:#CCFFCC;"
 
|[http://www.reactome.org/ Reactome]
 
|[http://www.reactome.org/ Reactome]
−
|31
+
|33
−
|"neighboring_reaction","reaction","direct_complex","indirect_complex"
+
|protein-protein (see note 1)
 
|open
 
|open
 +
|06/2010
 +
|86,442
 
|align="center"|—
 
|align="center"|—
−
|172,295
+
 
 +
|-style="color:black;background-color:#CCFFCC;"
 +
|[http://www.reactome.org/ Reactome]
 +
|50
 +
|protein-protein (see note 1)
 +
|open
 +
|12/2014
 +
|??
 
|align="center"|—
 
|align="center"|—
  
−
|-style="color:black;background-color:#FFFFFF;"
+
|-style="color:black;background-color:#CCFFCC;"
 
|[http://mint.bio.uniroma2.it MINT]
 
|[http://mint.bio.uniroma2.it 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"
+
|protein-protein (see note 2)
−
|not ready
+
|open
−
|align="center"|—
+
|09/09/2010
−
|18,634
+
|18,516
 
|align="center"|—
 
|align="center"|—
  
 
|-style="color:black;background-color:#CCFFCC;"
 
|-style="color:black;background-color:#CCFFCC;"
 +
|[http://mint.bio.uniroma2.it MINT]
 +
|?
 +
|protein-protein (see note 2)
 +
|open
 +
|03/26/2013
 +
|189,962
 
|align="center"|—
 
|align="center"|—
−
|align="center"|—
+
 
−
|align="center"|—
 
−
|align="center"|—
 
−
|align="center"|—
 
−
|align="center"|—
 
−
|align="center"|—
 
 
|}
 
|}
  
−
==Local abbreviations used==
+
* 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.
+
* [http://wiki.c2b2.columbia.edu/califanolab/index.php/BCellInteractome.htm '''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:
 
* '''HGi''' - Human High-Grade Glioma interactome, produced by analysis of microarray data from several sources:
−
** '''Phillips''' - data published by Phillips et al. ...
+
** '''Phillips''' - derived from data published by Phillips et al., 2006.
−
** '''Sun''' - data published by Sun et al. ...
+
** '''Sun''' - derived from data published by Sun et al., 2006.
−
** '''TCGA''' - data obtained from The Cancer Genome Atlas project (NCI).
+
** '''TCGA''' - derived from data obtained from Cancer Genome Atlas Research Network, 2008.
 +
* '''MCF7''' - breast cancer cell line (Chiu et al., 2013)
 +
* [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PrePPI '''PrePPI'''] - Predicting Protein-Protein Interactions by Combining Structural and non-Structural Information.  See Zhang et al., 2012, 2013.
  
 +
===External Interaction Databases===
 +
* [http://www.bind.ca/ '''BIND'''] - The Biomolecular Interaction Network Database. Bader et al., 2001.
 +
* [http://mint.bio.uniroma2.it '''MINT'''] - MINT: a Molecular INTeraction database. Zanzoni et al., 2002.
 +
* [http://www.reactome.org/ '''Reactome'''] - Croft et al., 2011, Matthews et al., 2009.
  
 
==Notes==
 
==Notes==
Line 111: Line 218:
 
* '''HGi version 1.0''' - interactome derived from ARACNe runs (transcriptional).
 
* '''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).
 
* '''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. [http://www.ncbi.nlm.nih.gov/pubmed/11125103 PubMed 11125103]
 +
 +
* Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways.  Nature 455(7216):1061-8 [http://www.ncbi.nlm.nih.gov/pubmed/18772890 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 [http://www.ncbi.nlm.nih.gov/pubmed/21067998 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 [http://cancerres.aacrjournals.org/cgi/content/meeting_abstract/73/8_MeetingAbstracts/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. [http://chianti.ucsd.edu/recombsysbio06/pages/abstractslist.html 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. [http://www.ncbi.nlm.nih.gov/pubmed/18981052 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 [http://www.ncbi.nlm.nih.gov/pubmed/16530701 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. [http://www.ncbi.nlm.nih.gov/pubmed/15016385 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 ([http://www.ncbi.nlm.nih.gov/pubmed/22000015 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 [http://www.ncbi.nlm.nih.gov/pubmed/16616334 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. [http://www.arxiv.org/abs/q-bio/0510030 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.  [http://www.ncbi.nlm.nih.gov/pubmed/11911893 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. [http://www.ncbi.nlm.nih.gov/pubmed/23023127 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. [http://www.ncbi.nlm.nih.gov/pubmed/23193263 PubMed 23193263]

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

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 (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 86,442 —
Reactome 50 protein-protein (see note 1) open 12/2014 ?? —
MINT ? protein-protein (see note 2) open 09/09/2010 18,516 —
MINT ? protein-protein (see note 2) open 03/26/2013 189,962 —
  • 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
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