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J Proteome Res. 2018 Jan 5;17(1):739-744. doi: 10.1021/acs.jproteome.7b00615. Epub 2017 Nov 13.

COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies.

Author information

1
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 119234 Moscow, Russian Federation.
2
Center for Proteomics and Metabolomics, Leiden University Medical Center , PO Box 9600, 2300 RC, Leiden The Netherlands.
3
Institute of Biology, Leiden University , PO Box 9502, 2300 RA, Leiden The Netherlands.

Abstract

COMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages "maps" and "maptools" to visualize and interact with molecular expression data in anatomical drawings of the model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided additional support. COMICS can be used to generate publication-quality visualizations of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data.

KEYWORDS:

anatomical ontologies; model systems; omics data integration; visualization

PMID:
29083911
PMCID:
PMC5772887
DOI:
10.1021/acs.jproteome.7b00615
[Indexed for MEDLINE]
Free PMC Article

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