Screenshots

Revision as of 17:45, 22 February 2010 by Smith (talk | contribs) (Sequence Analysis / Pattern Discovery)

geWorkbench Configuration

=Component Configuration Manager

Individual components can be loaded as needed.

T Component Configuration Manager.png


Microarray Data Displays

Microarray Viewer

The Microarray Viewer displaying marker values for selected array.


GeWB Microarray Viewer.png


Tabular Microarray Viewer

The Tabular Microarray Viewer displays expression values in spreadsheet format.


GeWB Tabular Microarray Viewer.png


CEL Image Viewer

Allows viewing of Affyemtrix CEL files.

T CEL viewer.png


Color Mosaic

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


GeWB Color Mosaic Viewer.png


Expression Profile

Expression Profile plotting values for selected markers and arrays.

TP53 (31618) and PTTG2 (31631_f_at)


GeWB Expression Profile 2markers.png



Expression Value Distribution

T EVD.png


Scatter Plot

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

Array vs Array

GeWB Scatter Plot array vs array.png

Marker vs Marker

GeWB Scatter Plot marker vs marker.png



Gene and Pathway Annotations

Marker Annotations

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

GeWB Marker Annotations.png


Marker Annotations - BioCarta Pathways

Displays BioCarta images retrieved from caBIO.

GeWB Marker Annotations Pathway.png


Marker Annotations - Cancer Gene Index

Displays literature citations from the Cancer Gene Index project.

GeWB Marker Annotations CGI.png


Statistical tests and clustering

Gene Ontology Term Over-representation Analysis

T GO Terms TableBrowser Gene Detail.png

T Test

Volcano Plot

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

T t-test volcano BCELL webm qldm.png

Color Mosaic

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

(Visualization preference setting: Relative)

T t-test colormosaic BCELL webm qldm.png


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)

T ANOVA ColorMosaic.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


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.

T PatternDiscovery Params 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.

T PatternDiscovery Histones Result exact Position Histogram.png


Promoter

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

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

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

Query results and Throttle Graph

T CNKB ProtDNA confidence75.png

CNKB query results displayed in Cytoscape

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

T CNKB 10at75 Cytoscape.png


Master Regulator Analysis

MRA viewer full.png


Molecular Structure

JMOL Structure Viewer

T JMOL Viewer.png


Mark-Us - Protein Functional Annotation

T MarkUs Web result.png