network-ontology visualization and analysis (avalon)
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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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