Zhu Lu, Malatras Apostolos, Thorley Matthew, Aghoghogbe Idonnya, Mer Arvind, Duguez Stéphanie, Butler-Browne Gillian, Voit Thomas, Duddy William
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.
Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, 75013 Paris, France.
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.
给定一个基因或蛋白质的查询列表，CellWhere会生成一个交互式图形显示，它模仿细胞结构，展示组织成亚细胞位置的局部相互作用网络。这个用户友好的工具通过使实验生物学家能够同时探索功能背景的两个要素，来帮助形成机制假说：（i）蛋白质亚细胞定位和（ii）蛋白质-蛋白质相互作用或基因功能关联。亚细胞定位术语从公共来源（基因本体论和UniProt，总共包含数千个此类术语）获取，然后映射到较少数量的CellWhere定位。这些定位包括所有主要的细胞区室，但用户可以根据需要修改映射。蛋白质-蛋白质相互作用列表及其相关的证据强度得分从Mentha相互作用组服务器获取，或者高级用户可以上传使用其他一些相互作用组学工具生成的预制网络。Cytoscape.js JavaScript库用于生成图形显示。重要的是，对于在多个亚细胞位置观察到的蛋白质，用户可以对与其研究领域特别相关的位置的视觉显示进行优先级排序。CellWhere可在http://cellwhere-myology.rhcloud.com上获取。
