Difference between revisions of "Plugins"
(→Normalizers) |
(→Annotation) |
||
| Line 89: | Line 89: | ||
!Plugin||Description||Compatibility | !Plugin||Description||Compatibility | ||
|- | |- | ||
| − | |Dataset History|| | + | |Dataset History||Log of data transformations induced by data-modifying operations.||? |
|- | |- | ||
|- | |- | ||
| − | |Dataset Annotation|| | + | |Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||? |
|- | |- | ||
|- | |- | ||
| − | |Experiment Information|| | + | |Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||? |
|- | |- | ||
|- | |- | ||
| − | |Marker Annotation || | + | |Marker Annotation ||Retrieval of CGAP annotations for selected genes.||? |
|- | |- | ||
|- | |- | ||
| − | |caBIO Pathway Listing|| | + | |caBIO Pathway Listing||Visualization of BioCarta pathway diagrams.||TBD |
|- | |- | ||
| − | |Go Terms|| | + | |Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations. ||TBD |
|- | |- | ||
|- | |- | ||
Revision as of 17:50, 6 February 2006
Contents
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 | Line graph of genes expression profiles across several arrays/ hybridizations (screenshot). | TBD |
| Expression Value Distribution | Distribution plot of marker expression values across one or more microarrays. | TBD |
| Marker Annotations | Retrieval of gene and pathway information for markers on a microarray. | TBD |
| Microarray Panel | Color-gradient representation of measured gene expression values (screenshot). | TBD |
| Scatter Plot | Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values (screenshot). | TBD |
| SOM Clusters | Visualization of gene clusters produced by the self-organizing maps analysis (screenshot). | TBD |
| Tabular Microarray Panel | Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray (screenshot). |
Data Management
| Plugin | Description | Compatibility |
|---|---|---|
| Gene Panel | Definition of data views consisting of marker subgroups. The views control how much data is displayed by only using values for markers in the defined groups. | TBD |
| Phenotype Panel | Definition of data views consisting of microarray subgroups. The views control how much data is displayed by only using values for microarrays in the defined groups. | TBD |
Normalizers
| Plugin | Description | Compatibility |
|---|---|---|
| Array-Based Centering | Subtraction of the mean or median measurement of a microarray from every measurement in that microarray. | TBD |
| Marker-Based Centering | Subtraction of the mean or median measurement of a marker profile from every measurement in the profile. | TBD |
| Mean-Variance Normalizer | Transformation of expression measurements to standard units: for every marker, the mean measurement of the marker profile (across all microarrays in an experiment) is subtracted from each measurement in the profile and the resulting value is divided by the standard deviation of the profile. | TBD |
| Missing Value Calculation | Replacement of missing values with consensus values. | TBD |
| Threshold Normalizer | Adjustment of values that fall outside a user-specified threshold. | TBD |
| Quantile | Expression measurements in each microarray are adjusted so that expression value distribution is the same across all microarrays in an experiment. | TBD |
| Housekeeping | Measurements are divided by the average expression value of a (user defined) set of housekeeping genes. | TBD |
Annotation
| Plugin | Description | Compatibility |
|---|---|---|
| Dataset History | Log of data transformations induced by data-modifying operations. | ? |
| Dataset Annotation | Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook". | ? |
| Experiment Information | Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed | ? |
| Marker Annotation | Retrieval of CGAP annotations for selected genes. | ? |
| caBIO Pathway Listing | Visualization of BioCarta pathway diagrams. | TBD |
| Go Terms | Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations. | 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 |
