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Network-Ontology Visualization and Analysis
Chao ZhangComputer Science Department
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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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Importance and common drawbacks
• Function enrichment analysis– DAVID (2003) Genome biol 3,364
(3,293)– DAVID (2008) Nature protcols 1,908
(1,802)– Bingo (2005) Bioinformatics 657 (609)
• Limitations– Lack of good visualization tool– All for gene set, not network
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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Visualization (Mosaic)
• What’s the difference?
Mosaic
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Visualization (Mosaic)
• Mosaic shows slices of a given network in the visual language of biological pathways, which are familiar to any biologist and are ideal frameworks for integrating knowledge
Mosaic
Biological Process
Molecular functionCellular
components
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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)
NOA
Molecular systems biology, 2009
Normal DiseaseDisease
The same gene list
Different phenotype
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Edge-based algorithm
NOA: a novel Network Ontology Analysis method
Nucleic Acids Research, 2009
NOA
Blast2GO, GoAnnotator, Goanna, etc
FatiGO, DAVID, g:profiler,BiNGO, etc
NOA
Gene annotation
Gene list annotation
Network annotation
N e t w o r k
Network
Single genes
Single genes
G ene set
Gene set
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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
Other projects>AVALON
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Node/edge-based algorithms
Other projects>AVALON
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Batch mode
Other projects>AVALON
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Batch mode
Other projects>AVALON
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Acknowledgement
Project advisor:Alexander R. Pico (UCSF)Dong Xu (Uni. Of Missouri)
Mosaic:Kristina Hanspers (UCSF)Allan Kuchinsky (Agilent)Nathan Salomonis (UCSF)
NOA:Jiguang Wang (Columbia Uni.)Luonan Chen (CAS)Xiangsun Zhang (CAS)
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
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