CellWhere: graphical display of interaction networks organized on subcellular localizations

Nucleic Acids Res. 2015 Jul 1;43(W1):W571-5. doi: 10.1093/nar/gkv354. Epub 2015 Apr 16.


Given a query list of genes or proteins, CellWhere produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein-protein interactions or gene functional associations. Subcellular localization terms are obtained from public sources (the Gene Ontology and UniProt-together containing several thousand such terms) then mapped onto a smaller number of CellWhere localizations. These localizations include all major cell compartments, but the user may modify the mapping as desired. Protein-protein interaction listings, and their associated evidence strength scores, are obtained from the Mentha interactome server, or power-users may upload a pre-made network produced using some other interactomics tool. The Cytoscape.js JavaScript library is used in producing the graphical display. Importantly, for a protein that has been observed at multiple subcellular locations, users may prioritize the visual display of locations that are of special relevance to their research domain. CellWhere is at http://cellwhere-myology.rhcloud.com.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Graphics
  • Genes
  • Internet
  • Intracellular Space / chemistry
  • Protein Interaction Mapping*
  • Proteins / analysis*
  • Software*


  • Proteins