title: CellWhere: graphical display of interaction networks organized on subcellular localizations.
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.
authors.affiliation: 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.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
authors.forename: Apostolos
authors.initials: A
authors.lastname: Malatras
authors.affiliation: Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
authors.forename: Matthew
authors.initials: M
authors.lastname: Thorley
authors.affiliation: 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.
authors.forename: Idonnya
authors.initials: I
authors.lastname: Aghoghogbe
authors.affiliation: Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, SE-17177, Sweden.
authors.forename: Arvind
authors.initials: A
authors.lastname: Mer
authors.affiliation: Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Duguez
authors.affiliation: Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
authors.forename: Gillian
authors.initials: G
authors.lastname: Butler-Browne
authors.affiliation: Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Voit
authors.affiliation: 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.
authors.forename: William
authors.initials: W
authors.lastname: Duddy
mesh_terms: D003196:Computer Graphics; D005796:Genes; D020407:Internet; D042541:Intracellular Space / Q000737:chemistry; D025941:Protein Interaction Mapping; D011506:Proteins / Q000032:analysis*; D012984:Software
chemical_list: D011506:Proteins