Visual Comparison of Organism-Specific Metabolic Pathways

Information

• Publication Type: Student Project
• Workgroup(s)/Project(s):
  • Visual Information Foraging on the Desktop
• Date: 2019
• Date (Start): October 2018
• Date (End): February 2019
• Matrikelnummer: 01325652
• First Supervisor: Manuela Waldner
• Keywords: pathways, web-based visualization

Abstract

The Kyoto Encyclopaedia of Genes and Genomes (KEGG) resource is a combination of multiple databases, containing information about biochemical compounds, reactions, pathways, genes and much more. This database is one of the main resources for bioinformaticians and biologists to gain an understanding of molecular functionality inside organisms. The Orthology (KO) database from KEGG assigns pathways and genes with identical functionality to the same ortholog groups (KO entries). Therefore it is possible to map genes onto the pathway maps and obtain organism-specific visualizations. KEGG offers a web-based graph visualization to explore these pathways, however, the interaction possibilities are restricted and the rendering is inefficient. It is possible to visualize organism-specific pathways but a visual analysis tool to compare ortholog groups of multiple organisms is missing. In this work, we present an efficient interactive web application to compare ortholog groups of multiple organisms in the metabolic reference pathway. We introduce a graph overlay technique to mark the differences and similarities between multiple organisms and demonstrate it with two use cases. Additionally, we compare it against an existing point set membership visualization.

Additional Files and Images

Weblinks

• Online tool
  Best to be used with Chrome. Enter the organisms to be compared by entering them as a string like this: "eco+hsa+mmu" (compares E-Coli, Homo Sapiens, and Mus Musculus).
• List of KEGG organisms
  List of organisms available in KEGG.
• CESCG paper
  Paper presented at the Central European Seminar on Computer Graphics 2019.

BibTeX

@studentproject{unger-2019_vcp,
  title =      "Visual Comparison of Organism-Specific Metabolic Pathways",
  author =     "Katharina Unger",
  year =       "2019",
  abstract =   "The Kyoto Encyclopaedia of Genes and Genomes (KEGG) resource
               is a combination of multiple databases, containing
               information about biochemical compounds, reactions,
               pathways, genes and much more. This database is one of the
               main resources for bioinformaticians and biologists to gain
               an understanding of molecular functionality inside
               organisms. The Orthology (KO) database from KEGG assigns
               pathways and genes with identical functionality to the same
               ortholog groups (KO entries). Therefore it is possible to
               map genes onto the pathway maps and obtain organism-specific
               visualizations. KEGG offers a web-based graph visualization
               to explore these pathways, however, the interaction
               possibilities are restricted and the rendering is
               inefficient. It is possible to visualize organism-specific
               pathways but a visual analysis tool to compare ortholog
               groups of multiple organisms is missing. In this work, we
               present an efficient interactive web application to compare
               ortholog groups of multiple organisms in the metabolic
               reference pathway. We introduce a graph overlay technique to
               mark the differences and similarities between multiple
               organisms and demonstrate it with two use cases.
               Additionally, we compare it against an existing point set
               membership visualization.",
  month =      feb,
  keywords =   "pathways, web-based visualization",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/unger-2019_vcp/",
}