Why do we want to add information about complexes to our networks?

1. To understand the biology!
2. To import additional proteins that are implicitly relevant
3. To simplify our networks

Sources of data about protein complexes

• Corum: The comprehensive resource of mammalian protein complexes
  • Richest data set, but no API (that I could find)
  • Data downloaded as PSI-MI, TSV, JSON

Sources of data about protein complexes

• Corum: The comprehensive resource of mammalian protein complexes
• EBI Complex Portal
  • Newer portal -- still adding data
  • Data downloaded as PSI-MI, TSV, JSON
  • Sometimes it doesn't quite work (e.g. download button doesn't always work)
  • REST API: https://www.ebi.ac.uk/intact/complex-ws/
    • Examples:
      • https://www.ebi.ac.uk/intact/complex-ws/complex/ -- view JSON data for a complex
      • https://www.ebi.ac.uk/intact/complex-ws/details/ -- view JSON data for complexes containing the sequence
      • https://www.ebi.ac.uk/intact/complex-ws/export/ -- download a complex
        • append "?format=[xml25|xml30|tsv|json]" to control the file type
      • https://www.ebi.ac.uk/intact/complex-ws/search/ -- search for a complex

Getting data into Cytoscape

1. It's not easy...
2. It's kind of clunky and definitely manual...
3. Somebody should write an app...
4. However...

Getting data into Cytoscape

• Actually, it is sort of easy...
• Cytoscape supports PSI-MI directly (File→Import→Network from File...)
• Issues:
  • The central node seems to be somewhat arbitrary
  • Links don't really indicate interaction, but indicate "membership"
  • Might want to group them together

Steps

1. Import complex from PSI-MI 2.5 (3.0 isn't supported by Cytoscape yet)
2. Add edges between all of the complex nodes (right-click Add→Edges Connecting Selected Nodes)
3. Import your network of interest
4. Merge the networks (Tools→Merge→Networks...)
   • Need to use the Advanced Merge panel
   • Select the matching columns appropriately
5. Now, in the merged network, go to the Edge Table and sort the interaction column
6. Select all of the rows that have interacts with and right-click Select edges from selected rows
7. Finally, do an Select→Nodes→Connected by Selected Edges
8. Right click on a node, Group→Group Selected Nodes

See, simple...

Like I said, somebody should write an app...

Any takers?