geWorkbench Highlights

caBIG® Molecular Analysis Tools

Knowledge Center

AACR Annual Meeting, April 3, 2011

Customizable

Load needed modules on demand.

Visualize microarray data

Available viewers include tabular, expression profile, color mosaic and scatter plot components.

Differential Expression

Hierarchical Clustering – Dendrogram heatmap display with subtree selection

Query interactomes in the Cellular Network Knowledge Base…

…and visualize molecular interaction networks using the Cytoscape plugin

Gene Ontology Enrichment Analysis

Enrichment calculations performed using Ontologizer2.0

BioCarta Pathway Diagrams

BioCarta diagrams are supplied by the NCI’s caBIO service.

Cancer Gene Index

Query for curated cancer-related literature references including context sentence and Pubmed links. Data via NCI’s caBIO data service.

Retreive genomic and protein sequences

Scan sequence with promoter motifs

Full NCBI BLAST interface with integrated result browser

Retrieve data from caArray

Direct download of data from the NCI’s caArray microarray data repository

View molecular structures in Jmol

1e09.pdb - Major Cherry Allergen PRU AV 1

Invoke GenePattern Analytical Routines…

…then test and apply generated classifiers

Test the classifier via cross-validation

Apply the classifier to a test set of arrays

Query SkyBase Homology Models

Finds pre-built NESG homology models with similarity to a sequence supplied by the user.

Homology Modeling using Pudge

Pudge integrates numerous model building and evaluation methods.

Protein Structure Functional Annotation using MarkUs

Calculates and displays electrostatic, cavity, conservation, and many other properties

Online Resources for geWorkbench

Molecular Analysis Tools Knowledge Center

https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench

geWorkbench User Forum

https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3

Tool Landing Page https://cabig.nci.nih.gov/tools/geWorkbench

geWorkbench Project and Documentation Site

http://www.geworkbench.org

NCICBApplications Support

Email: ncicb@pop.nci.nih.gov Phone: 301-451-4384Toll-free: 888-478-4423Web: http://ncicb.nci.nih.gov/NCICB/support