Revision as of 17:36, 22 February 2010

geWorkbench Configuration

=Component Configuration Manager

Individual components can be loaded as needed.

Microarray Data Displays

Microarray Viewer

The Microarray Viewer displaying marker values for selected array.

Tabular Microarray Viewer

The Tabular Microarray Viewer displays expression values in spreadsheet format.

CEL Image Viewer

Allows viewing of Affyemtrix CEL files.

Color Mosaic

The Color Mosaic component displaying selected arrays, group designation and marker names.

Expression Profile

Expression Profile plotting values for selected markers and arrays.

TP53 (31618) and PTTG2 (31631_f_at)

Expression Value Distribution

Scatter Plot

Compare multiple markers or arrays with the standard Scatter Plot analysis.

Array vs Array

Marker vs Marker

Gene and Pathway Annotations

Marker Annotations

Retrieve and display gene and pathway information from CGAP and Cancer Gene Index (CGI).

Marker Annotations - BioCarta Pathways

Displays BioCarta images retrieved from caBIO.

Marker Annotations - Cancer Gene Index

Displays literature citations from the Cancer Gene Index project.

Statistical tests and clustering

Gene Ontology Term Over-representation Analysis

T Test

Volcano Plot

A t-test result display on a "volcano plot": Log significance vs log fold change.

Color Mosaic

The t-test result can also be displayed as a color mosaic.

(Visualization preference setting: Relative)

Analysis of Variance (ANOVA)

Detects markers for which a statistically significant difference exists in a data set containing multiple classes of samples.

(Visualization preference setting: Absolute)

Hierarchical Clustering Dendrogram

A Dendrogram displays the results of the Hierarchical clustering analysis.

SOM Clustering

Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.

Sequence Analysis / Pattern Discovery

Sequence Retriever

Retrieve genomic and protein sequences for selected markers. Retrieved sequences can be individually selected and added to the project as new data nodes.

BLAST Queries

The Sequence Alignment component submits BLAST jobs to the NCBI server and displays the results such that individual hits can be used in further analysis steps.

Pattern Discovery

Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.

Motif discovery and display

The Pattern Discovery component itself with results displayed in the sequence viewer.

Position Histogram

The Pattern Discovery component with results displayed as histogram of support for selected discovered motifs across the sequence data set. Support indicates what fraction of the seqeunces are matched by the motif at a within a sliding window about a given location.

Promoter

Individual motifs from the JASPAR Transcription Factor Binding Profile Database can be scanned against loaded genomic sequences.

Motif selection and Logo display

Result of a scan against a single sequence

Sequence-level display of match

Network Discovery and Visualization

Cytoscape - ARACNe Network display

The adjacency matrix generated by an ARACNe network reverse engineering run displayed in Cytoscape.

Cellular Network Knowledge Base

Results of queries against the CNKB can be filtered based on confidence values using the throttle graph.

Query results and Throttle Graph

CNKB query results displayed in Cytoscape

Display of protein-DNA interactions produced with throttle graph set at 75% confidence in above picture.

Master Regulator Analysis

Molecular Structure

JMOL Structure Viewer

Mark-Us - Protein Functional Annotation