Biochemical Pathway Map

Overview

Pathway Map View in Genome Projector is based on the world-famous Roche Biochemical Pathway Wallchart. This view provides a biochemical context with the reactome and metabolome. Every enzyme (in blue text) is clickable to show more detailed information. With the growing importance of systems biology approaches in molecular biology, understanding of genomic information from the context of pathway is critical, especially in terms of regulation and identifying targets for genetic engineering.

Roche Biochemical Pathway Wallchart is extremely comprehensive compared to other existing pathway databases, since it displays the reactions, enzymes, metabolites, chemical structures of compounds, activations and inhibitions, and reversibility of reactions, while displaying the entire pathways collectively within one view. Although majority of the existing pathway databases intentionally hide some of these information, Roche Biochemical Pathway Wallchart allows the system biologists to have a comprehensive understanding of cellular components at a glance. Because of the large size of the map and the details within, Roche Biochemical Pathway Wallchart is an ideal media to be viewed using zoomable user interface.

Biochemical Pathway Map

Displayed Objects

Enzymes are shown in blue letters, coenzymes are in red, and other compounds are in black. Key compounds have chemical structures shown in box bound with black borders.

Lines in black represents general pathway, red is for unicellular organisms and fungi, blue for animals, and green for higher plants. Orange lines show regulation, accompanied by + or - signs to show activation or regulation. Displayed objects

Overlay: organism-specific pathway

Roche Biochemical Pathway shows the integrated collection of biochemistry, so the enzymes and reactions depicted here are not necessarily present in all organisms. Using the semi-transparent overlay layer which can be toggled with the buttons located in the top-right corner, Genome Projector highlights only the enzymes that are present in the specified genome, and grays out the rest. Here the presence of enzymes are identified by using EC number based matching of KEGG and ExPASy ENZYME database.

Overlay

Displayed Annotations

Upon searching, search results are shown as pins on the map, or as text shown in collapsible window on the right-most side. Clicking on each of the pins or text result entries will bring up a dialogue baloon, which shows the following information:

  • enzyme name
  • Links to ExPASy ENZYME, KEGG ENZYME, and Brenda

In Biochemical Pathway Map, all enzymes (those represented by blue letters) are clickable even without the pins that are only shown when searched.

Annotations

Acknowledgements

Roche Biochemical Pathways wall chart is provided by the courtesy of Roche Diagnostics GmbH, Germany. We would like to thank the ExPASy team of Swiss Bioinformatics Institute for kindly granting the use of digital images and coordinate data for the Roche Biochemical Pathways wall chart.

biochemical_pathway_map_view.txt · Last modified: 2009/04/19 15:41 (external edit)