Max-Planck-Institut für Informatik
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Workflow 1


Installing DomainGraph

Installing the DomainGraph database (WITH internet connection)

Installing the DomainGraph database (on a machine WITHOUT internet connection)

General analysis of differential expression computed by AltAnalyze

This step requires a probeset statistics file produced by AltAnalyze (the appropriate file can be found in the results folder of AltAnalyze, called "YOUR_DATASET_NAME-DomainGraph.txt"). You can download a sample results file via right-click here. This sample file compares human embryonic stem cells (control group) to cardiac progenitor cells (experimental group). Save the file to your disk.

Analysis of a single gene

Analysis of a WikiPathway pathway

Transforming a WikiPathway pathway into a gene interaction Domain Graph

Analysis of a Reactome pathway

  • Sort the table according to Reactome pathways by clicking on the 'Reactome pathway(s)' header.
  • Scroll to an entry containing 'Apoptosis' in the Reactome column.
  • Click on 'Apoptosis'.
  • A new window opens displaying all pathways associated with the probeset's gene. Click on 'Apoptosis' in this window and then on the 'Submit' button.
  • Wait for the Reactome pathway to be loaded. Please note that you need to have an internet connection to load pathways!
  • The resulting pathway should look similar to this screenshot.
  • Pathway nodes associated with differentially expressed probeset are highlighted.
  • The table in the results panel shows the node ids, UniProt proteins and gene names for regulated nodes.
  • Please note that you can import this pathway into DomainGraph if you want to further analyze it (see workflows 2 and 3).

Transforming a Reactome pathway into a protein interaction Domain Graph

  • Go to the plugins menu, select DomainGraph -> Start DomainGraph.
  • Select 'Create domain graph for gene or protein interaction network'.
  • Click the Start button.
  • Select 'Visualize protein interaction network'.
  • Click on the drop-down menu to select/import protein interactions.
  • Select 'Apoptosis'. (This is the Reactome pathway that you just loaded).
  • Click on the second drop-down menu to select domain interactions. Choose 'InterDom' as domain interaction dataset.
  • Leave the network view on 'extended' and identifier on 'UniProt'.
  • Click the Submit button.
  • A window pops up asking which node attribute contains the gene ids. Select 'biopax.xref.UniProt' and click OK.
  • The resulting domain graph consists of the input proteins and protein interactions and is enriched by the domain compositions and domain interactions occurring according to InterDom.
  • Your resulting network should look similar to this screenshot.
  • If you want to overlay the network with your AltAnalyze results and further analyze your data, continue here ("Integrating Affymetrix Exon Array data produced by AltAnalyze for analyzing differential exon expression").