MARINa - Revision history

Smith: /* Main Tab */

2015-03-06T23:45:32Z

‎Main Tab

Smith: /* Setting the MARINa Parameters */

2015-03-06T23:44:47Z

‎Setting the MARINa Parameters

Smith: /* Main Tab */

2015-03-06T23:44:10Z

‎Main Tab

Smith: /* Setting the MARINa Parameters */

2015-03-06T23:43:35Z

‎Setting the MARINa Parameters

Smith: /* MARINa Parameters */

2015-03-06T23:40:48Z

‎MARINa Parameters

Smith: /* References */

2014-07-28T21:06:10Z

‎References

Smith: /* References */

2014-07-28T21:04:12Z

‎References

Smith: /* Overview */

2014-07-28T21:01:09Z

‎Overview

Smith: /* Network alternative 5-column file format */

2014-05-12T17:39:52Z

‎Network alternative 5-column file format

Smith at 18:44, 22 April 2014

2014-04-22T18:44:44Z

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 * In the Main tab of the MRA component, select or load a network.
 * Set the desired GSEA p-value.
 ====Selecting the MARINa grid service====

← Older revision		Revision as of 23:44, 6 March 2015
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−	[[Image:MARINa_Parameters_Main.png]]	+	[[Image:MARINa_Parameters_Main.png\|{{ImageMaxWidth}}]]

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 * Set the desired GSEA p-value.
-Please see the description of this tab in the [[Master_Regulator_Analysis#Main| Master Regulator Analysis]] chapter.
+Please see additional details in the [[Master_Regulator_Analysis#Main| Master Regulator Analysis]] chapter.
 ====Selecting the MARINa grid service====

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 ====Main Tab====
 * In the Main tab of the MRA component, select or load a network.
 * Set the desired GSEA p-value.

← Older revision		Revision as of 23:40, 6 March 2015
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−	[[Image:~~MARINa_Parameters~~.png\|{{ImageMaxWidth}}]]	+	[[Image:MARINa_Parameters_Parameters.png\|{{ImageMaxWidth}}]]
−

	====MARINa Parameters - Retrieve prior result====		====MARINa Parameters - Retrieve prior result====

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 * Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005). Reverse engineering of regulatory networks in human B cells. Nat Genet 37(4):382-390 ([http://www.nature.com/ng/journal/v37/n4/abs/ng1532.html link to paper]).
 <span id="Lefebvre2010"></span>
 * Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A  (2010)  The transcriptional network for mesenchymal transformation of brain tumors.  Nature 463(7279):318-25.
-* Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010)  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.  Mol Syst Biol.  6:377. PMID: 20531406 ([http://www.ncbi.nlm.nih.gov/pubmed/20531406 link to paper]).
 <span id="Lim2009"></span>
 * Lim WK, Lyashenko E, Califano A (2009) Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. 2009:504-15.  PMID [http://www.ncbi.nlm.nih.gov/pubmed/19209726 19209726], ([http://psb.stanford.edu/psb-online/proceedings/psb09/lim.pdf link to paper]).
-* Subramanian A1, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.  Proc Natl Acad Sci U S A. 102(43):15545-50.  PMID: 16199517 ([http://www.ncbi.nlm.nih.gov/pubmed/16199517 link to paper]).

← Older revision		Revision as of 21:04, 28 July 2014
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	<span id="Lim2009"></span>		<span id="Lim2009"></span>
	* Lim WK, Lyashenko E, Califano A (2009) Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. 2009:504-15. PMID [http://www.ncbi.nlm.nih.gov/pubmed/19209726 19209726], ([http://psb.stanford.edu/psb-online/proceedings/psb09/lim.pdf link to paper]).		* Lim WK, Lyashenko E, Califano A (2009) Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. 2009:504-15. PMID [http://www.ncbi.nlm.nih.gov/pubmed/19209726 19209726], ([http://psb.stanford.edu/psb-online/proceedings/psb09/lim.pdf link to paper]).
		+	* Subramanian A1, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 102(43):15545-50. PMID: 16199517 ([http://www.ncbi.nlm.nih.gov/pubmed/16199517 link to paper]).

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 This chapter details the MARINa (MAster Regulator INference algorithm) method of [[Master_Regulator_Analysis|Master Regulator Analysis]].  Please see the [[Master_Regulator_Analysis|Master Regulator Analysis]] chapter for a higher-level introduction.
-MARINa uses gene set enrichment analysis (GSEA) to calculate if the regulon of a TF is enriched for genes that are differentially expressed among 2 classes of microarrays.  Please note that this does not involve any of the special gene lists available for use with the GSEA algorithm, such as [http://www.broadinstitute.org/gsea/msigdb/index.jsp. MSigDB]. Following the GSEA runs, MARINa performs an additional "shadow" analyses.  The "Synergy" analysis option is not currently supported.
+MARINa uses gene set enrichment analysis (GSEA)(Subramanian et al, 2005) to calculate if the regulon of a TF is enriched for genes that are differentially expressed among 2 classes of microarrays.  Please note that this does not involve any of the special gene lists available for use with the GSEA algorithm, such as [http://www.broadinstitute.org/gsea/msigdb/index.jsp. MSigDB]. Following the GSEA runs, MARINa performs an additional "shadow" analyses.  The "Synergy" analysis option is not currently supported.
 The MARINa algorithm runs on a computational cluster at Columbia and access is restricted.  It is run from geWorkbench using a grid service, selected using the "Services" tab.

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 * '''Spearman's correlation''': The Spearman's correlation for the edge, computed on the original microarray set that gave rise to the ARACNe network (a real number). If not known/available, the value 1 can be entered here.
 * '''P-value for Spearman's correlation'''. The p-value associated with Spearman's correlation found in the previous column (a real number between 0 and 1). It this p-value is not known/available, a value of 0 can be entered here.
 ==Example data files for running MARINa==

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 *If the "Retrieve prior results" box is checked, all other parameter fields will be disabled and disregarded.
 * In this case, it is not necessary to activate "case" and "control" sets.  They will be retrieved from the server for use in generating the "bar-code" display.
-* Enter the MARINa runID from a previous run of MARINa (this runID is found in the name of the MARINa result node in the Workspace, e.g. "mra30980", see an example in the Results section below).
+* Enter the MARINa runID from a previous run of MARINa (this runID is found in the name of the MARINa result node in the [[Workspace]], e.g. "mra30980", see an example in the Results section below).
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 ==Viewing MARINa Results==
-The MARINa calculation result is placed in the Workspace as a new data node.  The name of the node takes the form "MARINa Result: mra''num'', where ''num'' is a job id assigned on the server.
+The MARINa calculation result is placed in the [[Workspace]] as a new data node.  The name of the node takes the form "MARINa Result: mra''num'', where ''num'' is a job id assigned on the server.
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-'''Note''' - if no significant MRs are found, an empty result node is returned to the Workspace. The MRA viewer will appear but be empty.
+'''Note''' - if no significant MRs are found, an empty result node is returned to the [[Workspace]]. The MRA viewer will appear but be empty.