Cytoscape stringApp exercises

Hands-on exercises using the stringApp for Cytoscape to retrieve molecular networks from the STRING and STITCH databases.

The exercises will teach you how to:

  • retrieve networks for proteins or small-molecule compounds of interest
  • retrieve networks for a disease or an arbitrary topics in PubMed
  • layout and visually style the resulting networks
  • import external data and map them onto a network
  • perform enrichment analyses and visualize the results
  • merge and compare networks
  • select proteins by attributes
  • identify functional modules through network clustering

Scientific topics: Data visualisation, Proteomics, Protein interactions, Molecular interactions, pathways and networks, Bioinformatics

Target audience: Bioinformaticians, Biologists

Difficulty level: Intermediate

Licence: Creative Commons Attribution 4.0

Authors: Lars Juhl Jensen, Nadezhda T. Doncheva, Helen V. Cook

Contributors: John "Scooter" Morris

External resources:

Cytoscape

stringApp

STRING

STITCH

DISEASES

Cytoscape stringApp exercises https://tess.elixir-europe.org/materials/cytoscape-stringapp-exercises Hands-on exercises using the stringApp for Cytoscape to retrieve molecular networks from the STRING and STITCH databases. John "Scooter" Morris Data visualisation Proteomics Protein interactions Molecular interactions, pathways and networks Bioinformatics Bioinformaticians Biologists