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Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...
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The cross-sectional anatomy of the spinal cord offers a detailed view of its complex structure and function within the central nervous system. At the core of the spinal cord lies the gray matter, characterized by its butterfly or "H"-shaped appearance in cross-section. This central region is enveloped by white matter, with the overall structure divided into symmetrical halves by the dorsal median sulcus and the ventral median fissure.
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Each cerebral hemisphere can be divided into three main regions. The outermost region, the cerebral cortex, is a thin layer (2 to 4 millimeters thick) made up of gray matter, consisting of neuron cell bodies, dendrites, glial cells, and blood vessels. The middle region, or white matter, is primarily composed of myelinated nerve fibers organized into three types of large tracts: association fibers, commissures, and projection fibers. Association fibers connect different areas within the same...
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COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies.

Dmitrii Travin1, Iaroslav Popov1, Arzu Tugce Guler2

  • 1Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 119234 Moscow, Russian Federation.

Journal of Proteome Research
|October 31, 2017
PubMed
Summary

COMICS is a new web platform that visualizes molecular expression data in zebrafish, carp, and mouse anatomograms. It maps omics data using anatomical ontologies, enabling clear visualization of gene and protein expression across experiments.

Keywords:
anatomical ontologiesmodel systemsomics data integrationvisualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Molecular expression data analysis often lacks standardized visualization across different model systems.
  • Integrating and visualizing omics data within anatomical contexts is crucial for biological interpretation.
  • Existing tools may not effectively handle spatially resolved omics data or offer user-friendly anatomical mapping.

Purpose of the Study:

  • To develop an interactive, open-access web platform (COMICS) for integrating and visualizing molecular expression data.
  • To enable mapping of omics data across experiments and between data and anatomical visualizations using ontologies.
  • To provide a user-friendly tool for generating publication-quality visualizations of gene and protein expression.

Main Methods:

  • Utilized anatomical ontologies and the ontoCAT R package for data aggregation and mapping.
  • Employed QGIS geographical information system libraries with R packages ('maps', 'maptools') for visualization.
  • Developed a web platform allowing users to upload their own omics data with controlled vocabulary (CV) terms for anatomical regions and developmental stages.

Main Results:

  • COMICS integrates and visualizes molecular expression data in anatomograms of zebrafish, carp, and mouse.
  • The platform maps omics data using anatomical ontologies, facilitating cross-experiment comparisons.
  • It generates clear anatomical representations of spatially resolved omics data, moving beyond data tables.

Conclusions:

  • COMICS offers a novel approach to visualizing spatially resolved omics data in model organisms.
  • The platform enhances the integration and interpretation of molecular expression data through anatomical context.
  • COMICS provides an easy-to-use interface for generating publication-quality visualizations, supporting biological discovery.