Cellular Networks KnowledgeBase - Revision history

Smith at 22:36, 17 March 2015

2015-03-17T22:36:18Z

Smith: /* Create Network */

2015-03-16T21:47:43Z

‎Create Network

Smith: /* Preferences */

2015-03-16T21:33:16Z

‎Preferences

Smith: /* Create Network */

2015-03-16T21:28:57Z

‎Create Network

Smith: /* Create Network */

2015-03-16T21:23:33Z

‎Create Network

Smith: /* Create Network */

2015-03-16T21:23:11Z

‎Create Network

Smith: /* Requirements */

2015-03-16T19:53:52Z

‎Requirements

Smith: /* Export Interactome */

2015-01-27T21:05:49Z

‎Export Interactome

Smith: /* References for Outside Data Sources */

2014-05-22T17:35:46Z

‎References for Outside Data Sources

Smith: /* References for Outside Data Sources */

2014-05-22T16:59:33Z

‎References for Outside Data Sources

← Older revision		Revision as of 22:36, 17 March 2015
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	=Overview=		=Overview=
		+	For the '''geWorkbench web''' version of CNKB please see [[Cellular_Networks_KnowledgeBase_web]].
		+
		+
	The Cellular Network Knowledge Base (CNKB) is a repository of molecular interactions, including ones both computationally and experimentally derived. Sources for interactions include both publicly available databases such as BIND, MINT, and Reactome, as well as reverse-engineered cellular context-specific regulatory interactomes developed in the lab of Dr. Andrea Califano at Columbia University.		The Cellular Network Knowledge Base (CNKB) is a repository of molecular interactions, including ones both computationally and experimentally derived. Sources for interactions include both publicly available databases such as BIND, MINT, and Reactome, as well as reverse-engineered cellular context-specific regulatory interactomes developed in the lab of Dr. Andrea Califano at Columbia University.

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 Create a network based on the query results, and as filtered by the throttle graph setting.   The new network is placed in the [[Workspace|Workspace]] in the form of an adjacency matrix.  The network will be displayed in the Cytoscape component if it is loaded.
-* '''Note on network size''' - If the network created is larger than it may be possible to display in Cytoscape, Cytoscape will offer the user the option to use a non-graphic display instead.
+* '''Note on network size''' - If the network created is larger than it may be possible to display in Cytoscape, Cytoscape will offer the user the option to use a tabular display instead.
 Networks created in the CNKB are represented in the adjacency matrix at the gene level.

@@ Line 171: / Line 171: @@
 ====Interactions Database====
-The preferences panel shows a description (if available) of the chosen interactome, and in a separate pane a description (if available) of the interactome version.
+The preferences panel shows a description (if available) of the chosen interactome, and in a separate pane a description of the interactome version.
@@ Line 180: / Line 180: @@
 ====Select Interactome====
-A list of all interactomes available in the CNKB is presented.  The number of interactions present in each is shown in parantheses after the name.  See also the [[CNKB_Data | CNKB data sources]] page.
+A list of all interactomes available in the CNKB is presented.  The number of interactions present in each is shown in parentheses after the name.  See also the [[CNKB_Data | CNKB data sources]] page.
 ====Interactome Description====
-When an interatome is highlighted, its description, if available, will be presented in this window.
+When an interactome is highlighted, its description, if available, will be presented in this window.
 ====Select Version====
@@ Line 191: / Line 191: @@
 ====Version Description====
-If available, a description of the selected version is displayed here.
+A description of the selected version is displayed here.
 ====Column Display Preferences====

@@ Line 157: / Line 157: @@
 * '''Note on network size''' - If the network created is larger than it may be possible to display in Cytoscape, Cytoscape will offer the user the option to use a non-graphic display instead.
-Networks created in the CNKB are represented in the adjacency matrix at the gene level, using the identifiers used in the original interactome, e.g. Entrez IDs or Gene Symbols.
+Networks created in the CNKB are represented in the adjacency matrix at the gene level.
 ===Cancel===

@@ Line 157: / Line 157: @@
 * '''Note on network size''' - If the network created is larger than it may be possible to display in Cytoscape, Cytoscape will offer the user the option to use a non-graphic display instead.
-Networks created in the CNKB are represented in the adjacency matrix at the gene level, using the identifiers used in the original interactome, e.g. Entrez IDs or Gene Names.
+Networks created in the CNKB are represented in the adjacency matrix at the gene level, using the identifiers used in the original interactome, e.g. Entrez IDs or Gene Symbols.
 ===Cancel===

← Older revision		Revision as of 19:53, 16 March 2015
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−	=~~Requirements~~=	+	=Prerequisites=

	* To use the CNKB component, first check that it has been loaded in the [[Component_Configuration_Manager \| Component Configuration Manager]].		* To use the CNKB component, first check that it has been loaded in the [[Component_Configuration_Manager \| Component Configuration Manager]].

@@ Line 234: / Line 234: @@
 ===Export Interactome===
+'''Note''' - due to the large size of many of the interactomes, currently only three smaller interactomes can be exported.  The others will report a message that they can not be exported. Work to allow export of larger interactomes is underway.
 * '''Restrict to genes present in microarray set''' - The check box '''Restrict to genes present in microarray set''', described above, can also apply to the export of an interactome.  However, because of the options offered for interactome export, its effect is somewhat different than for network generation and display as described above.

← Older revision		Revision as of 17:35, 22 May 2014
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	For some ids used in the CNKB database, there may a matching marker which however does not have a gene symbol. In the Affymetrix annotation file, these are indicated with a gene symbol of "---". These results are included in the CNKB results table.		For some ids used in the CNKB database, there may a matching marker which however does not have a gene symbol. In the Affymetrix annotation file, these are indicated with a gene symbol of "---". These results are included in the CNKB results table.
−
−
−	~~=References for Outside Data Sources=~~
−
−
−	* [BIND]
−	** 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]
−
−	* [http://www.reactome.org Reactome]
−	** 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]
−	** 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]
−
−
−	* [http://mint.bio.uniroma2.it MINT]
−	** 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]

@@ Line 423: / Line 423: @@
 ** 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]
 * [http://mint.bio.uniroma2.it MINT]
 ** 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]