1. geWorkbench Highlights caBIG ® Molecular Analysis Tools Knowledge Center AACR Annual Meeting, April 3, 2011

2. Customizable Load needed modules on demand.

3. Visualize microarray data Available viewers include tabular, expression profile, color mosaic and scatter plot components.

4. Differential Expression

5. Hierarchical Clustering – Dendrogram heatmap display with subtree selection

6. Query interactomes in the Cellular Network Knowledge Base…

7. …and visualize molecular interaction networks using the Cytoscape plugin

8. Gene Ontology Enrichment Analysis Enrichment calculations performed using Ontologizer2.0

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

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

11. Retreive genomic and protein sequences

12. Scan sequence with promoter motifs

13. Full NCBI BLAST interface with integrated result browser

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

15. View molecular structures in Jmol 1e09.pdb - Major Cherry Allergen PRU AV 1

16. Invoke GenePattern Analytical Routines…

17. …then test and apply generated classifiers Test the classifier via cross-validation Apply the classifier to a test set of arrays

18. Query SkyBase Homology Models Finds pre-built NESG homology models with similarity to a sequence supplied by the user.

19. Homology Modeling using Pudge Pudge integrates numerous model building and evaluation methods.

20. Protein Structure Functional Annotation using MarkUs Calculates and displays electrostatic, cavity, conservation, and many other properties

21. 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 Pagehttps://cabig.nci.nih.gov/tools/geWorkbench geWorkbench Project and Documentation Site http://www.geworkbench.org NCICB Applications Support Email: ncicb@pop.nci.nih.govncicb@pop.nci.nih.gov Phone: 301-451-4384 Toll-free: 888-478-4423 Web: http://ncicb.nci.nih.gov/NCICB/supporthttp://ncicb.nci.nih.gov/NCICB/support