Revision as of 16:01, 17 October 2013 by Smith (talk | contribs) (Master Regulator Analysis)

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The geWorkbench graphical interface with a CNKB query result dislayed in Cytoscape.

GeWorkbench Main Cytoscape no frame.png

geWorkbench Configuration

Component Configuration Manager

Individual components can be loaded as needed.

CCM Main.png

Workspace and Data Management


Data sets are loaded into the Workspace. Individual analysis results are stored under their parent dataset.

Workspace with results.png


Sets of arrays can be defined and included or excluded from particular analyses (via checkboxes). Sets can be individually marked as belonging to case (here indicated with a red thumbtack) or control groups.

T-test Set selection BCell.png


Sets of arrays can be defined and included or excluded from particular analyses (via checkboxes).

Marker Sets Example.png

In addition, routines such as ANOVA or t-test return lists of significant markers to the Markers component.

ANOVA Example Markers.png

Retrieval from caArray

Microarray data can be retrieved directly from instances of caArray.

Open File Remote caArray show arrays.png

Microarray Data Displays

Microarray Viewer

The Microarray Viewer displaying marker values for selected array.

Microarray Viewer.png

Tabular Microarray Viewer

The Tabular Microarray Viewer displays expression values in spreadsheet format.

Tabular Microarray Viewer.png

CEL Image Viewer

Allows viewing of Affyemtrix CEL files.

T CEL viewer.png

Color Mosaic

The Color Mosaic component displaying a result from ANOVA analysis. It can also directly display the loaded expression data, or subsets of that data created using Marker and Array sets.

Color Mosaic ANOVA.png

Expression Profile

Expression Profile plotting values for selected markers and arrays. Individual values can be seen by hovering over a desired data point.

Expression Profiles.png

Expression Value Distribution

The dataset has been quantile normalized and log2 transformed.

Expression Value Distribution.png

Scatter Plot

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

Array vs Array

Scatter Plot array vs array.png

Marker vs Marker

Scatter Plot marker vs marker.png

Gene and Pathway Annotations

Marker Annotations

Retrieve and display gene and pathway information from bioDBNet.

Marker Annotations bioDBNet.png

Marker Annotations - BioCarta Pathways

Displays BioCarta images retrieved via bioDBNet.

Marker Annotations Pathway bioDBNet.png

Statistical tests, clustering and classification

Gene Ontology Term Over-representation Analysis

GO Terms Table Browser.png

T Test

Volcano Plot

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

Volcano Plot.png

Color Mosaic

The t-test result can also be displayed in the Color Mosaic component.

(Visualization preference setting: Relative)

Color Mosaic.png

Analysis of Variance (ANOVA)

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

Color Mosaic View

(Visualization preference setting: Relative)

Color Mosaic ANOVA.png

Tabular View

ANOVA Tabular View.png

Hierarchical Clustering Dendrogram

A Dendrogram displays the results of the Hierarchical clustering analysis.

T HC Dendrogram display.png

SOM Clustering

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

T SOM result.png

Consensus Clustering (GenePattern)

Consensus clustering result color mosaic.png

Classification (GenePattern)

GenePattern components that perform classification on microarray datasets have been adapted to geWorkbench.

K-Nearest Neighbors (KNN)

KNN Parameters.png

Example of classifier result

The classifiers return groups of markers to the Markers component:

Tutorial-GP KNN-ClassPredictions.png

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.

T SequenceRetriever AfterRetrieval.png

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.

T SequenceAlignment BLAST results.png

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.

PatternDiscovery Basic histone result exact seqs.png

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.

PatternDiscovery Basic Histones Result exact 3 histogram.png


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

Motif selection and Logo display

T Promoter CDH2 AP2 2000updn setup logo.png

Result of a scan against a single sequence

T Promoter CDH2 AP2 2000updn scan.png

Sequence-level display of match

T Promoter CDH2 AP2 2000updn scan fullseq.png


MatrixREDUCE is a tool for inferring the binding specificity and nuclear concentration of transcription factors from microarray data.

T MatrixREDUCE PSAM view.png

Network Discovery and Visualization

Cytoscape - ARACNe Network display

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

T ARACNE result1.png

Cellular Network Knowledge Base (CNKB)

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

Query results and Throttle Graph

CNKB Result Display 3types threshold0.75 v2.2.png

CNKB query results displayed in Cytoscape

Display of CNKB interactions in Cytoscape.

CNKB Result Cytoscape 3types v2.2.png

Master Regulator Analysis

MRA viewer GBM FOSL2 v3.png

Molecular Structure

JMOL Structure Viewer

JMOL is a viewer for PDB protein structure files.

T JMOL Viewer.png

Mark-Us - Protein Functional Annotation

Mark-Us is a web server to assist the assessment of the biochemical function for a given protein structure. MarkUs identifies related protein structures and sequences, detects protein cavities, and calculates the surface electrostatic potentials and amino acid conservation profile.

T MarkUs Web result.png


Pudge is a server for the prediction of the 3D structures of proteins. While the server can be run without any user intervention, it is primarily designed to be interactive and to allow functional information to be used as a guide to the modeling.

PUDGE allows a pipeline of modeling and evaluation steps, depicted below, to be set up and run.

T Pudge Parameters.png

Pudge has a number of output types, the following illustrates a sequence alignment:

T Pudge Alignment example.png