Max-Planck-Institut für Informatik
max planck institut
mpii logo Minerva of the Max Planck Society

Workflow 3


Installing DomainGraph

Installing the DomainGraph database (WITH internet connection)

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

Importing a gene interaction network into DomainGraph

This step requires a gene interaction network, given with Ensembl or Entrez gene ids. You can download a toy gene interaction network containing human genes via right-click here. Save the file to your disk.

Integrating Affymetrix Exon Array data produced by AltAnalyze for analyzing differential exon expression

This step requires a results file produced by AltAnalyze (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.

  • Go to the plugins menu, select DomainGraph -> Integrate Affymetrix exon expression data.
  • Select the 'AltAnalyze data' tab.
  • Click the Import button.
  • Select the sample data for import.
  • Type in a name for this dataset and click on Import.
  • Once the data is imported, it is shown in the drop-down menu.
  • Click the OK button and wait for the data integration.
  • In the resulting domain graph, all genes, proteins and domains containing differentially expressed probeset are highlighted in yellow.
  • Your resulting network should look similar to this screenshot.
  • In the results panel on the right you can see the genes, proteins, domains, and probesets that are differentially expressed in the two samples together with their splicing indices.
  • Click on a row in the results panel to select the respective node in the network.

Viewing proteins, domains, exons, probesets, and miRNA binding sites as graphics

  • Double-click on the gene node labelled 'FYN' (you might have to zoom in to be able to read the node labels).
  • The graphics is displayed in the data panel and should look similar to this screenshot.
  • The top row of an entry shows the protein with its contained domains (colored rectangles).
  • Below is the exon structure including 5' and 3' UTRs. Identical exon numbers in different transcripts indicate identical exons.
  • Below are the probesets. White coloring means the probeset was not statistically analyzed by AltAnalyze due to pre-filtering steps. Gray probesets are expressed at similar levels in both groups of samples. Differentially expressed probesets are shown in red (up-regulated in the experimental group) and green (down-regulated in the experimental group).
  • Scroll down the graphics. Please note the down-regulated (highlighted by green-colored probesets) exon no 14. This result indicates that protein isoforms containing exon no 14 are down-regulated in cardiac progenitor cells.
  • Blue rectangles below some probesets indicate microRNA binding sites.
  • Move the mouse over the domains, exons, probesets, and miRNAs. Tooltips providing additional information are shown.
  • Move the mouse over the green-colored probesets annotated to exon no 14. The tooltips display that exon no 14 is known to be a cassette exon, supporting the potential alternative splicing event. The Cross-hybridization information shows that both these probesets are 'unique'. This means, the probesets were specifically designed for this genomic locus and (at design-time of the microarray) did not align to any other transcript.
  • Right-click somewhere in the data panel. A menu will pop up for customizing and saving the graphics.
  • Click on an exon. This will open the corresponding Ensembl website for further information.