Cupid - Revision history

Smith at 21:43, 13 January 2014

2014-01-13T21:43:07Z

Smith at 21:42, 13 January 2014

2014-01-13T21:42:15Z

Smith: /* The Cupid Service */

2014-01-13T18:24:26Z

‎The Cupid Service

Smith: /* Results */

2014-01-13T18:22:11Z

‎Results

Smith: /* Parameters and Controls */

2014-01-13T18:21:20Z

‎Parameters and Controls

Smith: /* Using the Cupid Interface */

2014-01-13T18:20:54Z

‎Using the Cupid Interface

Smith: /* Using the CUPID Interface */

2014-01-13T18:20:42Z

‎Using the CUPID Interface

Smith: /* Overview */

2014-01-13T18:20:00Z

‎Overview

Smith: /* Overview */

2014-01-13T18:18:36Z

‎Overview

Smith: /* References */

2014-01-13T18:17:47Z

‎References

← Older revision		Revision as of 21:43, 13 January 2014
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−	{{TutorialsTopNav]]	+	{{TutorialsTopNav}}

← Older revision		Revision as of 21:42, 13 January 2014
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		+	{{TutorialsTopNav]]
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	==Overview==		==Overview==

← Older revision		Revision as of 18:24, 13 January 2014
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	==The Cupid Service==		==The Cupid Service==
		+
		+	The CUPID servlet takes two parameters for a query, type and value.
		+	* '''type''' –a string value of "RefSeq ID" or "miRNA ID".
		+	* '''value''' – a string containing the RefSeq or miRNA ID on which to query.
		+

	Below are example lines from the output file produced by the Cupid code:		Below are example lines from the output file produced by the Cupid code:

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 # '''Conservation Score''' - Conservation score of the sequence region of the miRNA match (computed against conservation across 46 vertebrate genomes).
 # '''Gold Standard Classification''' - "Yes" means that the site is classified as a gold standard; "No" that it is not).
 Below are example lines from the output file produced by the Cupid code:

@@ Line 21: / Line 21: @@
 ===Parameters and Controls===
-* '''Server URL''' - The URL of the CUPID service (at Columbia).  The user should not need to change this.
+* '''Server URL''' - The URL of the Cupid service (at Columbia).  The user should not need to change this.
-* '''Query Type''' - CUPID results can be queried either by RefSeq ID or miRNA id.
+* '''Query Type''' - Cupid results can be queried either by RefSeq ID or miRNA id.
 ** RefSeq ID - query by RefSeq ID.
 ** miRNA ID - query by miRNA ID.

@@ Line 12: / Line 12: @@
 The Cupid interface is a standalone component in geWorkbench.  Unlike many components which are available only when a relevant dataset type has been loaded in the Workspace, the Cupid interface is available as long as it has been loaded in the [[Component_Configuration_Manager|Component Configuration Manager]].
-===Using the Cupid  Interface===
+==Using the Cupid  Interface==
 ===Prerequisites===

@@ Line 1: / Line 1: @@
 ==Overview==
-CUPID (Sumazin et al. 2011) generates information that can help predict if a gene is a target of a specific miRNA.  The Cupid service provides a simple query interface to a database of precalculated Cupid results.  The results can be searched either by '''miRNA ID''' or by '''RefSeq gene ID'''.
+Cupid (Sumazin et al. 2011) generates information that can help predict if a gene is a target of a specific miRNA.  The Cupid service provides a simple query interface to a database of precalculated Cupid results.  The results can be searched either by '''miRNA ID''' or by '''RefSeq gene ID'''.
 For each miRNA M the algorithm uses TargetScan (Lewis et al., 2005), PITA (Kertesz et al., 2007), and MIRANDA (Enright et al., 2003), at their default settings, to predict target sites of M in 3' UTRs of REFseq (hg19) transcripts. Each predicted site seed is scored according to its conservation across [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way 46 vertebrate genomes]. Site distances from 5' and 3' ends of the 3'UTR are also annotated. Scores are normalized and input into a support vector machine tool (LIBSVM, Chang and Lin, 2011)  to train against 684 validated miRNA targets (the “gold standard”), procured from http://mirecords.biolead.org and TRANSFAC. Site seeds classified by LIBSVM together with the gold standard interaction set are considered positive, otherwise they are considered negative. The output produced by ideal includes:
@@ Line 10: / Line 10: @@
 ** An overall probability of being a true target site (integrating all the above scores).
-The CUPID interface is a standalone component in geWorkbench.  Unlike many components which are available only when a relevant dataset type has been loaded in the Workspace, the CUPID interface is available as long as it has been loaded in the [[Component_Configuration_Manager|Component Configuration Manager]].
+The Cupid interface is a standalone component in geWorkbench.  Unlike many components which are available only when a relevant dataset type has been loaded in the Workspace, the Cupid interface is available as long as it has been loaded in the [[Component_Configuration_Manager|Component Configuration Manager]].
 ===Using the CUPID Interface===
 ===Prerequisites===
-The CUPID component must be loaded in the [[Component_Configuration_Manager|Component Configuration Manager]]
+The Cupid component must be loaded in the [[Component_Configuration_Manager|Component Configuration Manager]]
@@ Line 31: / Line 31: @@
 ===Results===
-The CUPID output lists all the sites where an miRNA is predicted to match the 3’ UTR region of a REFseq gene.
+The Cupid output lists all the sites where an miRNA is predicted to match the 3’ UTR region of a REFseq gene.
-Each result line represents how well a miRNA (identified by the third column of a line) is predicted to match the 3’ UTR region of a gene (identified by the second column of the line, via its refSeq id). More precisely, each column in a line captures the following info (columns below are listed in the order in which they appear in the CUPID output file):
+Each result line represents how well a miRNA (identified by the third column of a line) is predicted to match the 3’ UTR region of a gene (identified by the second column of the line, via its refSeq id). More precisely, each column in a line captures the following info (columns below are listed in the order in which they appear in the Cupid output file):
 # '''Interaction Probability''' - overall probability that the miRNA matches the 3' UTR region of the gene.
 # '''refSeq id''' - refSeq idof the target gene.
@@ Line 44: / Line 44: @@
 # '''Gold Standard Classification''' - "Yes" means that the site is classified as a gold standard; "No" that it is not).
-Below are example lines from the output file produced by the CUPID code:
+Below are example lines from the output file produced by the Cupid code:
 .805531	NM_000034	hsa-miR-122	0.16	0.84	0.92 0.74	 0.93	0.78	1
 .897525	NM_000034	hsa-miR-122	0.17	0.83	0.92	0.74	0.93	1.00	1

← Older revision		Revision as of 18:17, 13 January 2014
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	* Lewis, B.P., C.B. Burge, and D.P. Bartel (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1): p. 15-20.		* Lewis, B.P., C.B. Burge, and D.P. Bartel (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1): p. 15-20.
		+
		+	* 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]

	* http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/		* http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/