The geWorkbench platform employs a component repository infrastructure to manage a large collection of pluggable components that can be used to customize the application's graphical user interface. This (ever growing) list of plug-in components covers a wide range of fucntionality for a number of different genomic data modalities:
Microarray Visualization
| Plugin |
Description |
Compatibility
|
| Color Mosaic |
Heat maps for microarray expression data, organized by phenotypic or gene groupings (screenshot). |
Verified to work on 3.0
|
| Dendrogram |
Tree-structured diagrams reflecting the results of hierarchical clustering analysis (screenshot). |
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
|
Data Management
| 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
|
Normalizers
| 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
|
Annotation
| 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
|
Network Generation
| 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/). |
?
|
Analysis
| 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). |
?
|
Sequence Analysis
| Plugin |
Description |
Compatibility
|
| Synteny |
A utility for comparison of extended genomic regions.- |
?
|
Pattern Discovery
| 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. |
?
|
| Dot Matrix |
Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. |
tbd
|
Filters
| 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
|
