Tutorials - Revision history

Smith at 16:12, 29 April 2015

2015-04-29T16:12:48Z

2015-04-29T16:12:15Z

2015-03-11T19:46:22Z

‎T-Test

2015-03-11T19:45:53Z

2014-01-23T22:52:59Z

2014-01-23T22:51:12Z

‎Hierarchical Clustering

2014-01-23T22:46:24Z

‎Master Regulator Analysis

2014-01-23T22:33:46Z

‎SkyLine

2014-01-23T22:33:02Z

‎SkyLine

2014-01-23T22:28:54Z

‎Individual analysis and visualization components

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 The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench.
-For the web version of geWorkbench, please see [[GeWorkbench-web/Tutorials | GeWorkbench-web Tutorials]]
+For the '''web version''' of geWorkbench, please see [[GeWorkbench-web/Tutorials | GeWorkbench-web Tutorials]]
 ==Using the basic framework of geWorkbench==

← Older revision		Revision as of 16:12, 29 April 2015
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−	The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench~~. Additional information can be found in the User Guide and in the Online Help section of the program~~.	+	The tutorials shown on this page provide a quick introduction to the most important features of geWorkbench.

		+	For the web version of geWorkbench, please see [[GeWorkbench-web/Tutorials \| GeWorkbench-web Tutorials]]

	==Using the basic framework of geWorkbench==		==Using the basic framework of geWorkbench==

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 Classification using Support Vector Machines.
-===[[T-Test | T-Test]]===
+===[[T-test | T-Test]]===
 Several variants of the Student's t-Test for Differential expression are available.
 ===[[Viper_Analysis]]===

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 The DeMAND (Drug Mode of Action through Network Dysreguation) algorithm measures dysregulation between the expression of two genes in a network caused by e.g. a drug perturbation. The list of top dysregulated gene pairs can reveal details of a drug's mode of action in the tested cellular system or tissue.
 ===[[Expression Value Distribution | Expression Value Distribution]]===
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 ===[[SVM | SVM]]===
 Classification using Support Vector Machines.
 ===[[Viper_Analysis]]===

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 ===[[Hierarchical Clustering | Hierarchical Clustering]]===
 geWorkbench implements its own agglomerative hierarchical clustering algorithm.
 ===[[IDEA]]===
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 ===[[Pattern Discovery | Pattern Discovery]]===
 Upstream seqeunce can be analyzed for conserved sequence patterns.
 ===[[PCA| Principle Component Analysis (PCA)]]===

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 ===[[Master Regulator Analysis | Master Regulator Analysis]]===
-The Master Regulator Analysis (MRA) component attempts  to identify transcription factors which control the regulation of a set  of differentially expressed target genes (TGs).  Differential expression  is determined using a t-test on microarray gene expression profiles from  2 cellular phenotypes, e.g. experimental and control.
+Master Regulator analysis [Lefebvre et al., 2010] is an algorithm used to identify transcription factors whose targets (e.g., as represented in an ARACNe-generated interactome) are enriched for a particular gene signature (e.g. a list of differentially expressed genes).
 ====[[MRA-FET]]====

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 ===[[SkyLine]]===
-SlyLine is a pipeline for large-scale protein homology modeling.
+SlyLine is a pipeline for large-scale protein homology modeling.  [[SkyBase]] provides access to precomputed models generated using SkyLine.
 ===[[SOM | SOM]]===

← Older revision		Revision as of 22:33, 23 January 2014
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	===[[SkyLine]]===		===[[SkyLine]]===
		+	SlyLine is a pipeline for large-scale protein homology modeling.

	===[[SOM \| SOM]]===		===[[SOM \| SOM]]===

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 This component provides for query and display of data generated by the Columbia LINCS Technology U01 and Computation U01 Centers. It provides experimental and computational results for drug mode of action and similarity calculations, and for synergy experiments.
 ===[[MarkUs | MarkUs]]===
 The MarkUs component assists in the assessment  of the biochemical function for a given protein structure.  The component in geWorkbench provides an interface to the MarkUs web server at Columbia.  MarkUs identifies related protein structures and sequences, detects  protein cavities, and calculates the surface electrostatic potentials  and amino acid conservation profile.
 ===[[Master Regulator Analysis | Master Regulator Analysis]]===
 The Master Regulator Analysis (MRA) component attempts  to identify transcription factors which control the regulation of a set  of differentially expressed target genes (TGs).  Differential expression  is determined using a t-test on microarray gene expression profiles from  2 cellular phenotypes, e.g. experimental and control.
 ===[[MatrixREDUCE | MatrixREDUCE]]===
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 ===[[SAM|SAM]]===
-Significance Analysis of Microarrays
+===[[Sequence_Retriever | Sequence Retriever]]===
-===[[Sequence_Retriever | Sequence Retriever]]===
+===[[SkyLine]]===
 ===[[SOM | SOM]]===
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 ===[[SVM | SVM]]===
 Classification using Support Vector Machines.