Cytoscape Wiki|
← Revision 6 as of 2008-08-16 11:56:28
Size: 1953
Comment:
|
← Revision 7 as of 2008-08-16 11:58:21 →
Size: 2701
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 21: | Line 21: |
| ||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.|| |
||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. || ||<style="vertical-align: top;">Get additional information on proteins and domains ||<style="vertical-align: top;">Hover the mouse over LCP2 protein node to get tooltip information on constituent domains and to highlight neighboring nodes ||<style="vertical-align: top;"> || ||<style="vertical-align: top;"> ||<style="vertical-align: top;">Right-click on LCP2 protein node: DomainGraph Options -> Detailed Information. Displays information on protein/constituent domains, GO and OMIM annotation ||<style="vertical-align: top;"> || ||<style="vertical-align: top;"> ||<style="vertical-align: top;">Right-click on LCP2 protein node: DomainGraph Options -> UniProt description. Links to the external webpage. ||<style="vertical-align: top;"> || |
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. |
Get additional information on proteins and domains |
Hover the mouse over LCP2 protein node to get tooltip information on constituent domains and to highlight neighboring nodes |
|
|
Right-click on LCP2 protein node: DomainGraph Options -> Detailed Information. Displays information on protein/constituent domains, GO and OMIM annotation |
|
|
Right-click on LCP2 protein node: DomainGraph Options -> UniProt description. Links to the external webpage. |
|
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