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

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Presentation transcript:

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

Motivation 2

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

Enrichment analysis 4 Background

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

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

Mosaic & NOA 7

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

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

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

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

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

Overview network 13 Mosaic

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

Node/edge-based algorithms 15 NOA

Node/edge-based algorithms 16 NOA

Batch mode 17 NOA

Example 400 Human Pathways 18 NOA

Future works 19

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

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

Customized pipeline 22 Future Works MCODEBingoMosaicNOA

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

Question? Mosaic: NOA: Chao Zhang: 24 Acknowledgement