= 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^''' '''

''  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. ||
||<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;"> ||
||<style="vertical-align: top;">Graphical representation of protein domain architecture ||<style="vertical-align: top;">Double-click on LCP2 protein node ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Tooltip information for graphics ||<style="vertical-align: top;">Hover the mouse over a domain box ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Customizing/ exporting graphics ||<style="vertical-align: top;">Right-click in the Data Panel (save as png, change domain colors) ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Change network view ||<style="vertical-align: top;">Plugins -> DomainGraph -> Change View. Select ppi network view. ||<style="vertical-align: top;">The ppi network view can be used to explore the domain interactions in a stepwise manner ||
||<style="vertical-align: top;">Stepwise exploration of protein and domain interaction network ||<style="vertical-align: top;">Select protein nodes LCP2 and GRAP2: Get into the options dialog (Plugins -> DomainGraph -> Options). Choose to show domains for selected proteins. ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Exon expression data integration ||<style="vertical-align: top;">Plugins -> DomainGraph -> Integrate Affymetrix exon expression data ||<style="vertical-align: top;"> ||
|| ||Import rma-sketch and dabg files for spleen and testis ||Data obtained from Affymetrix, must be downloaded from their webpage! Data is stored in the local db. ||
||<style="vertical-align: top;">Integrate testis expression data into sample network ||<style="vertical-align: top;">select testis expression and pvalue data ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Visualize domain/exon/probeset structures of proteins and present/absent probesets ||<style="vertical-align: top;">double-click on LCP2 protein ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Additional Information on domains/exons/probesets ||<style="vertical-align: top;">hover the mouse over the boxes in the graphical representation ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;">Compare similarities/dissimilarities in expression pattern across different tissues ||<style="vertical-align: top;">create a new domain graph using the same sample network, this time integrate spleen tissue data. ||<style="vertical-align: top;"> ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;">DomainGraph -> Analysis -> intersection. Choose the two domain graphs for the analysis. ||<style="vertical-align: top;">Nodes/edges with different biological types are highlighted. ||


'''__Data / Session Files__:''' [[attachment:sample_ppi.sif]], [[attachment:DomainGraph_Session.cys]] (DomainGraph features like graphical representation cannot be saved!), Affymetrix data must be downloaded from Affymetrix directly. ''' '''

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