CeRNA Query - Revision history

Smith: /* References */

2014-05-22T18:25:15Z

‎References

2014-05-22T18:24:27Z

‎References

2014-05-22T18:23:20Z

‎Overview

2014-01-13T21:43:37Z

2013-09-17T21:46:35Z

2013-08-02T21:53:13Z

‎Controls

2013-08-02T21:52:16Z

‎Output

2013-08-02T21:51:09Z

‎Output

2013-08-02T21:40:16Z

2013-08-02T21:36:32Z

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 ==References==
-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 link to paper]).
+* 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 link to paper]).
-[http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/HERMES Hermes website for application download]
+* [http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/HERMES Hermes website] for application download.

← Older revision		Revision as of 18:24, 22 May 2014
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	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 link to paper]).		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 link to paper]).
		+
		+	[http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/HERMES Hermes website for application download]

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 ==Overview==
-This component provides query access to a precomputed database of competitive endogenous RNA  (ceRNA) interactions, also called "sponge" interactions.  These interactions underlie a post-transcriptional layer of regulation, and were predicted using the Hermes algorithm ([http://www.ncbi.nlm.nih.gov/pubmed/22000015 Sumazin et al., 2011]) with subsequent improvements (submitted).
+This component provides query access to a precomputed database of competitive endogenous RNA  (ceRNA) interactions, also called "sponge" interactions.  These interactions underlie a post-transcriptional layer of regulation, and were predicted using the [http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/HERMES Hermes] algorithm ([http://www.ncbi.nlm.nih.gov/pubmed/22000015 Sumazin et al., 2011]) with subsequent improvements (submitted).
 Datasets for Glioblastoma (GBM), Ovarian (OV), Breast (BRCA), and Prostate (PRAD) cancer are currently available.  Each is calculated by analyzing gene expression profiles in combination with matched microRNA (miR) profiles obtained from the TCGA.

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 * '''Query Value''' - Enter the desired search term.
 * '''Submit''' - perform the query.
+* '''Export''' - Export the query result to a CSV-format file.
 ==Output==

← Older revision	Revision as of 21:46, 17 September 2013
(No difference)

← Older revision		Revision as of 21:52, 2 August 2013
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−	Querying on a miRNA ID:	+	Querying on a miRNA ID (Note - * indicates the less-used strand):

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-[[File:Hermes_ceRNA_Query_Result_mir-519d.png]]
+[[File:Hermes_ceRNA_Query_Result_mir-526bstar.png]]
 ==References==
 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 link to paper]).

← Older revision		Revision as of 21:40, 2 August 2013
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		+	==Output==

		+	Querying on a gene symbol, STAT3:

	[[File:Hermes_ceRNA_Query_Result_STAT3.png]]		[[File:Hermes_ceRNA_Query_Result_STAT3.png]]
		+
		+	The data columns returned are:
		+
		+	* '''InteractionID''' - internal record number from the CNKB database.
		+	* '''Gene1''' and '''Gene2''' - the two competing RNA molecules.
		+	* '''miRNA''' - a miRNA which is predicted to bind to both RNA molecules.
		+
		+
		+	Querying on a miRNA ID:


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		+	==References==

	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 link to paper]).		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 link to paper]).

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 This component provides query access to a precomputed database of competitive endogenous RNA  (ceRNA) interactions, also called "sponge" interactions.  These interactions underlie a post-transcriptional layer of regulation, and were predicted using the Hermes algorithm ([http://www.ncbi.nlm.nih.gov/pubmed/22000015 Sumazin et al., 2011]) with subsequent improvements (submitted).
@@ Line 5: / Line 7: @@
 Hermes predicts the intersection set (program) of miRNAs which bind to both of two different RNAs.  Variation in the level of one of the RNA species may affect the level of the second RNA via its effects on the availability of the various miRNAs.
 [[File:Hermes_ceRNA_Query_Interface.png]]