geWorkbench

Revision as of 16:21, 31 January 2006

Plugins are sets of pluggable components for geWorkbench.

Below is the list of available plugins.

Plugin	Description	Compatibility
Color Mosaic	Displays heat maps for microarray expression data, organized by phenotypic or gene groupings.	Verified to work on 3.0
Dendrogram	A tree-structured diagrams reflecting the results of hierarchical clustering analysis.	TBD
Dot Matrix	Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions[[.<A - I'm not sure if I should move this to Sequence Analysis]]>	tbd
Expression Profiles	Expression of genes across several arrays/ hybridizations.	TBD
Expression Value Distribution	A distribution plot of the expression values for one or more microarrays.	TBD
Marker Annotations	Supports the retrieval of CGAP annotations for genes within a marker panel.	TBD
Microarray Panel	Color-coded levels of gene expression using a color scale varying gradually from red (up-regulated) through black (no change) to green (down-regulated).	TBD
Scatter Plot	Expression data is plotted with one marker or microarray on the x-axis and the other on the y-axis (on up to six plots).	TBD
SOM Clusters	<A should I leave here or place in analysis>	TBD
Tabular Microarray Panel	The numerical values of the expression measurements displayed in a table format; each row represents an individual probe and the columns display the signal and background intensities and intensity ratios.	TBD

Plugin	Description	Compatibility
Gene Panel	A subselection of markers which define data views by restricting number of markers shown.	TBD
Phenotype Panel	A subselection of microarrays which define data views by restricting number of arrays shown.	TBD

Plugin	Description	Compatibility
Array-Based Centering	Subtracts the mean (median) measurement of a microarray from every measurement in that microarray.	TBD
Marker-Based Centering	Subtracts the mean (median) measurement of a marker profile from every measurement in the profile.	TBD
Mean-Variance Normalizer	For every marker profile, the mean measurement of the entire profile is subtracted from each measurement in the profile and the resulting value is divided by the standard deviation.	TBD
Missing Value Calculation	Replaces every missing value with either the mean value of that marker across all microarrays or with the mean measurement of all markers in the microarray.	TBD
Threshold Normalizer	All data points whose value is less than (or greater than) a user-specified minimum (maximum) value are raised (reduced) to that minimum (maximum) value.	TBD
Quantile	Expression measurements in each microarray is adjusted to reflect the same expression value distribution for all microarrays.	TBD
Housekeeping	Normalization based on the average expression of all markers corresponding to user selected housekeeping genes.	TBD

Plugin	Description	Compatibility
Dataset History	Lists data transformations induced by data-modifying operations.	?
Dataset Annotation	A free text format box used by users to annotate data files, projects and images.	?
Experiment Information	Displays available experiment information associated with a Microarray dataset.	?
Marker Annotation	Retrieves CGAP annotations for selected genes.	?
caBIO Pathway Listing	Displays BioCarta pathway diagrams for selected genes.	TBD
Go Terms	Categorization of selected genes provided by the Gene Ontology Consortium (http://www.geneontology.org) displayed in a tree structure.	TBD

Plugin	Description	Compatibility
Reverse Engineering	Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer the underlying gene regulatory network.	?
Cytoscape	Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 2.0 http://www.cytoscape.org/.	?

Plugin	Description	Compatibility
Hierarchical Clustering	Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.	?
Self Organizing Map (SOM)	An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.	?
T Test	The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform http://www.tm4.org/mev.html	?

Plugin	Description	Compatibility
Synteny	A utility for comparison of extended genomic regions.-	?

Plugin	Description	Compatibility
Promoter Panel	This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).	?
Sequence Alignment	--.	?
Sequence Panel	Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.	?
Position Histogram	Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.	?

Plugin	Description	Compatibility
Affy Detection Call	(Affymetrix data only) Sets all measurements whose detection status is any user-defined combination of A, P or M as missing.	TBD
Deviation	Sets all markers whose measurements deviate below a given value across all microarrays as missing.	?
Expression Threshold	Sets all markers whose measurements are inside (or outside) a user-defined range as missing.	?
Genepix Flag Filter	(Genepix data only)Designate as “missing” measurements whose Flags column assume specific user selected values.	?
Missing Values	Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate.	TBD
2-channel Threshold	(Genepix data only) Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing.	TBD

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-|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform http://www.tm4.org/mev.html.||?
+|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform http://www.tm4.org/mev.html ||?
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-|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ).  The promoter panel can be used to visualize transcription factor binding sites (TFBS.||?
+|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ).  The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?
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