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Network-Ontology Visualization and Analysis(AVALON)
Chao ZhangComputer Science Department
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Motivation
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GO annotation
Background
Up to October 26, 2010, there have been more than 2,753,338 annotations covering 48 species in GO database
annotation
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Enrichment analysis
Background
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Workflow
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
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Batch Mode
• More than 150 plugins
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Background
Annotation Network analysis
Functional analysis Visualization
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Mosaic & NOA
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Visualization (Mosaic)
• Partitioning with BP• Layout with CC• Coloring with MF• Automatic annotation• ID mapping• Overview network
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Mosaic
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1st Partitioning/decomposition
• Decompose a huge biological network to sub-networks (Biological process)
Mosaic
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2nd Layout/Pathway
• Currently only support PathVisio and WikiPathway formats (Cellular components)
Mosaic
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3rd Coloring/Highlighting
• Molecular function
Other projects>AVALON
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3rd Coloring/Highlighting
• Molecular function
Other projects>AVALON
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Overview network
Mosaic
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Analysis (NOA)
• Edge-base algorithm• Batch mode• Heatmap• Overview network• Interaction with Mosaic
NOA
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Node/edge-based algorithms
NOA
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Node/edge-based algorithms
NOA
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Batch mode
NOA
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Example
400HumanPathways
NOA
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Future works
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Novel algorithms development
• Meta-analysis and multiply network integration
• Functional module detection and decomposition
Future Works
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Current plugin improvement
• Extending CyThesaurus• OBO/pathway file parsing• Functional annotation• Database file management
Future Works
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Customized pipeline
Future Works
MCODEBingo
MosaicNOA
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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
Acknowledgement
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Question?
Mosaic:http://nrnb.org/tools/mosaic/
NOA:http://nrnb.org/tools/noa/
Chao Zhang:[email protected]
Acknowledgement
