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Network-Ontology Visualization and Analysis (AVALON)

Network-Ontology Visualization and Analysis (AVALON). Chao Zhang Computer Science Department. Motivation. GO annotation. annotation. Up to October 26, 2010, there have been more than 2,753,338 annotations covering 48 species in GO database. Background. Enrichment analysis. Background.

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Network-Ontology Visualization and Analysis (AVALON)

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

  2. Motivation

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

  4. Enrichment analysis • Background

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

  6. Batch Mode • More than 150 plugins . • Background

  7. Mosaic & NOA

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

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

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

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

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

  13. Overview network • Mosaic

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

  15. Node/edge-based algorithms • NOA

  16. Node/edge-based algorithms • NOA

  17. Batch mode • NOA

  18. Example 400 Human Pathways • NOA

  19. Future works

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

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

  22. Customized pipeline Future Works

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

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

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