1. Network-Ontology Visualization and Analysis (AVALON) Chao Zhang Computer Science Department 1

2. Motivation 2

3. GO annotation 3 Background Up to October 26, 2010, there have been more than 2,753,338 annotations covering 48 species in GO database annotation

4. Enrichment analysis 4 Background

5. Workflow 5 Background Visualization + Analysis Including as more as possible functions of other software Relatively independent modules with interactions Very flexible, 4 individual plugins or 1 bundle

6. Batch Mode More than 150 plugins. 6 Background Annotation Network analysis Functional analysis Visualization

7. Mosaic & NOA 7

8. Visualization (Mosaic) Partitioning with BP Layout with CC Coloring with MF Automatic annotation ID mapping Overview network. 8 Mosaic

9. 1 st Partitioning/decomposition Decompose a huge biological network to sub-networks (Biological process) 9 Mosaic

10. 2 nd Layout/Pathway Currently only support PathVisio and WikiPathway formats (Cellular components) 10 Mosaic

11. 3 rd Coloring/Highlighting Molecular function 11 Other projects>AVALON

12. 3 rd Coloring/Highlighting Molecular function 12 Other projects>AVALON

13. Overview network 13 Mosaic

14. Analysis (NOA) Edge-base algorithm Batch mode Heatmap Overview network Interaction with Mosaic 14 NOA

15. Node/edge-based algorithms 15 NOA

16. Node/edge-based algorithms 16 NOA

17. Batch mode 17 NOA

18. Example 400 Human Pathways 18 NOA

19. Future works 19

20. Novel algorithms development Meta-analysis and multiply network integration Functional module detection and decomposition 20 Future Works

21. Current plugin improvement Extending CyThesaurus OBO/pathway file parsing Functional annotation Database file management 21 Future Works

22. Customized pipeline 22 Future Works MCODEBingoMosaicNOA

23. Acknowledgement Project advisor: Alexander R. Pico (UCSF) Mosaic: Kristina Hanspers (UCSF) Allan Kuchinsky (Agilent) Nathan Salomonis (UCSF) CyThesaurus: Jianjiong Gao(MSKCC) NOA: Jiguang Wang (Columbia Uni.) Google’ Summer of Code Program 23 Acknowledgement

24. Question? Mosaic: http://nrnb.org/tools/mosaic/ NOA: http://nrnb.org/tools/noa/ Chao Zhang: chaozhang@mizzou.edu 24 Acknowledgement