0000000000072407

AUTHOR

Tatyana Goldberg

showing 3 related works from this author

CellMap visualizes protein-protein interactions and subcellular localization [version 2; referees: 2 approved]

2018

Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers.

ComputingMethodologies_PATTERNRECOGNITIONBioinformaticslcsh:Rlcsh:Medicinelcsh:Qlcsh:ScienceChemical Biology of the CellF1000Research
researchProduct

CellMap visualizes protein-protein interactions and subcellular localization

2018

Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers.

0301 basic medicineBioinformaticssubcellular locationContext (language use)BiologyJavaScriptGeneral Biochemistry Genetics and Molecular BiologyChemical Biology of the CellProtein–protein interactionprotein-protein interaction03 medical and health sciencesUploadHuman–computer interactionGeneral Pharmacology Toxicology and Pharmaceuticscomputer.programming_languagebiological visualization030102 biochemistry & molecular biologyGeneral Immunology and MicrobiologySoftware Tool ArticleNoveltyArticlesGeneral MedicineSubcellular localizationddc:ComputingMethodologies_PATTERNRECOGNITION030104 developmental biologyNeurosciencecomputerF1000Research
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Visualizing Human Protein‐Protein Interactions and Subcellular Localizations on Cell Images Through CellMap

2020

Visualizing protein data remains a challenging and stimulating task. Useful and intuitive visualization tools may help advance biomolecular and medical research; unintuitive tools may bar important breakthroughs. This protocol describes two use cases for the CellMap (http://cellmap.protein.properties) web tool. The tool allows researchers to visualize human protein-protein interaction data constrained by protein subcellular localizations. In the simplest form, proteins are visualized on cell images that also show protein-protein interactions (PPIs) through lines (edges) connecting the proteins across the compartments. At a glance, this simultaneously highlights spatial constraints that prot…

0303 health sciencesgenetic structuresComputer scienceCells030305 genetics & heredityProteinsA proteinComputational biologyBiochemistryWeb toolProtein subcellular localization predictionVisualizationProtein–protein interaction03 medical and health sciencesImaging Three-DimensionalStructural BiologyProtein Interaction MappingHumansProtocol (object-oriented programming)SoftwareSubcellular Fractions030304 developmental biologyCurrent Protocols in Bioinformatics
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