COMICS

COMICS integrates and visualizes molecular expression data in anatomograms of zebrafish, carp, and mouse model systems using anatomical ontologies.

Key Features:

• Anatomical Ontology Mapping: Anatomical ontologies with controlled vocabulary and defined hierarchy are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner.
• Multi-Species Support: Supports zebrafish, carp, and mouse anatomical ontologies for data aggregation, comparison, and visualization.
• Flexible Data Upload: Allows users to upload their own data from omics experiments using any gene or protein nomenclature, provided controlled vocabulary terms are used to define anatomical regions or developmental stages.
• Common Nomenclature Support: Provides additional support for ZFIN gene names and UniProt accessions.
• Publication-Quality Output: Generates publication-quality visualizations of gene and protein expression across experiments.
• Spatially Resolved Data Display: Takes spatially resolved data generated by dissection or fractionation and displays this data in visually clear anatomical representations.

Scientific Applications:

• Cross-Experiment Comparison: Enables aggregation and comparison of molecular expression data across different omics experiments using anatomical ontology mappings.
• Spatial Expression Visualization: Visualizes gene and protein expression patterns in anatomical context for zebrafish, carp, and mouse model systems.
• Dissection-Based Omics Data Interpretation: Displays spatially resolved data from dissection or fractionation experiments as intuitive anatomical representations rather than large data tables.

Methodology:

COMICS uses zebrafish and mouse anatomical ontologies with the ontoCAT R package to aggregate data for comparison and visualization. QGIS geographical information system libraries are used with the R packages "maps" and "maptools" to visualize and interact with molecular expression data in anatomical drawings.