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Related Concept Videos

Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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C4 Pathway and CAM01:27

C4 Pathway and CAM

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Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
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Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

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Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
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IP3/DAG Signaling Pathway01:11

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Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
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Enzyme-linked Receptors01:00

Enzyme-linked Receptors

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Enzyme-linked receptors are proteins that act as both receptor and enzyme, activating multiple intracellular signals. This is a large group of receptors that include the receptor tyrosine kinase (RTK) family. Many growth factors and hormones bind to and activate the RTKs.
Neurotrophin (NT) receptors are a family of RTKs, including trkA, trkB, and trkC (tropomyosin-related kinase) receptors. TrkA is specific for nerve growth factor (NGF), neurotrophin-6, and neurotrophin-7. TrkB binds...
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Updated: Feb 20, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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A Web Tool for Generating High Quality Machine-readable Biological Pathways

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Reactome enhanced pathway visualization.

Konstantinos Sidiropoulos1, Guilherme Viteri1, Cristoffer Sevilla1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.

Bioinformatics (Oxford, England)
|October 28, 2017
PubMed
Summary
This summary is machine-generated.

Reactome enhances its pathway visualization system with interactive SVG diagrams for high-level pathways and editable PPTX for detailed ones. These updates improve navigation and allow easier reuse of pathway data in research and publications.

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Area of Science:

  • Biomolecular pathways
  • Bioinformatics
  • Systems biology

Background:

  • Reactome is a curated, open-source knowledge base of biomolecular pathways.
  • Pathways are organized hierarchically, aligning with Gene Ontology (GO) biological processes.
  • The system facilitates navigation from broad concepts to detailed molecular events.

Purpose of the Study:

  • To present new developments in the Reactome visualization system.
  • To improve navigation through the pathway hierarchy.
  • To enable efficient reuse of Reactome visualizations for research and publications.

Main Methods:

  • Development of scalable, interactive textbook-style diagrams in Scalable Vector Graphics (SVG) format.
  • Creation of a library of reusable graphic elements for common pathway components.
  • Provision of detailed lower-level diagrams in editable PowerPoint (PPTX) format.

Main Results:

  • High-level pathway diagrams are now interactive, scalable, and downloadable in SVG format.
  • A library of reusable diagram elements (e.g., mitochondrion, receptor) is available.
  • Detailed pathway diagrams can be downloaded as editable sets of interconnected objects in PPTX format.

Conclusions:

  • The enhanced Reactome visualization system offers improved navigation and data reusability.
  • New features support researchers in presentations and publications.
  • The updates make complex pathway information more accessible and adaptable.