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

CellWhere: graphical display of interaction networks organized on subcellular localizations.

Author information

1
Bioinformatics Department, Bielefeld University, Bielefeld, D-33501, Germany Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
2
Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
3
Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France Orthopaedics and Musculoskeletal Science, University College London, London, WC1E 6BT, UK.
4
Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, SE-17177, Sweden.
5
Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France william.duddy@upmc.fr.

Abstract

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.

PMID:
25883154
PMCID:
PMC4489307
DOI:
10.1093/nar/gkv354
[Indexed for MEDLINE]
Free PMC Article

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