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= Your Title = '''Your name ''' |
= DomainGraph: Visual Analysis of the Effects of Alternative Splicing on Protein and Domain Interaction Networks = ''''''Dorothea Emig^1^, Melissa S. Cline^2^, Thomas Lengauer^1^, and Mario Albrecht^1^''' ''' |
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| ''Your institute'' | '' 1 Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany '' |
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| '''__Biological Use Case__''': Describe a real biological problem. | ''2 Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA''' ''''' |
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| '''__Recipe__''' | __Biological Use Case__: Visualize the domain interactions that actually form a protein interaction network. Integrate exon expression data to visualize occurrences of alternative splicing events and the impact on the interactions. ''' ''' |
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| ''__Cytoscape version__'': Version number (2.6) | '''__Recipe__''' ''' ''' |
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| ''__Plugins to Load__'': Plugins and urls | __Cytoscape version__: 2.5, 2.6 ''''' ''''' |
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| ''__GUI steps__'': | ''__Plugins to Load__'': DomainGraph (http://domaingraph.bioinf.mpi-inf.mpg.de) ''''' ''''' |
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Describe each step (story), the GUI action to take, and probable remarks || ''Story'' || ''Action'' || ''Remarks'' || || || || || |
''__GUI steps__'': ''''' ''''' |
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| '''__Data / Session Files__''': Attach (preferably) a session file or else the data files used in the workflow |
Describe each step (story), the GUI action to take, and probable remarks ''''' ''''' || Story '' '' || Action '' '' || Remarks '' '' || ||Create local database ||Plugins -> DomainGraph -> Create Database ||has to be done the first time, the db is stored locally in the Cytoscape plugins directory || ||Import the sample protein network and decompose it into underlying domain interactions||Plugins -> DomainGraph -> Create Domain Graph: 1. import protein interactions: select to import your own ppi network ('sample_ppi.sif') 2. select the species of the network ('H.sapiens') 3. select the domain interaction dataset ('InterDom') 4. select initial network view ('extended') ||small subnetwork of protein interactions by Rual et al.|| |
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| '''__Presentation__''': Attach your presentation | __Data / Session Files__: Attach (preferably) a session file or else the data files used in the workflow ''' ''' |
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| '''__Webstart__''': Attach a webstart | '''__Presentation__''': Attach your presentation ''' ''' |
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| '''__Video__''': Attach a video link |
'''__Webstart__''': Attach a webstart ''' ''' '''__Video__''': Attach a video link ''' ''' |
DomainGraph: Visual Analysis of the Effects of Alternative Splicing on Protein and Domain Interaction Networks
Dorothea Emig1, Melissa S. Cline2, Thomas Lengauer1, and Mario Albrecht1
1 Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany
2 Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
Biological Use Case: Visualize the domain interactions that actually form a protein interaction network. Integrate exon expression data to visualize occurrences of alternative splicing events and the impact on the interactions.
Recipe
Cytoscape version: 2.5, 2.6
Plugins to Load: DomainGraph (http://domaingraph.bioinf.mpi-inf.mpg.de)
GUI steps:
Describe each step (story), the GUI action to take, and probable remarks
Story |
Action |
Remarks |
Create local database |
Plugins -> DomainGraph -> Create Database |
has to be done the first time, the db is stored locally in the Cytoscape plugins directory |
Import the sample protein network and decompose it into underlying domain interactions |
Plugins -> DomainGraph -> Create Domain Graph: 1. import protein interactions: select to import your own ppi network ('sample_ppi.sif') 2. select the species of the network ('H.sapiens') 3. select the domain interaction dataset ('InterDom') 4. select initial network view ('extended') |
small subnetwork of protein interactions by Rual et al. |
Data / Session Files: Attach (preferably) a session file or else the data files used in the workflow
Presentation: Attach your presentation
Webstart: Attach a webstart
Video: Attach a video link