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Amino Acid Biosynthetic Pathways

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Cellular respiration is a fundamental metabolic process that enables organisms to generate energy from organic molecules. One of its central pathways is the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, which plays a crucial role in energy production and biosynthetic processes.Conversion of Pyruvate to Acetyl-CoAThe pyruvate generated from glycolysis undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex, producing acetyl-CoA, one molecule of NADH, and one...
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Cyclic Adenosine Monophosphate (cAMP) is an essential second messenger that activates protein kinase A (PKA) and regulates various biological processes. A single epinephrine molecule binds to GPCR and activates several heterotrimeric G proteins, each stimulating multiple adenylyl cyclase, amplifying the signal, and synthesizing large numbers of cAMP molecules. Small changes in cAMP concentration affect PKA activity. The binding of four cAMP molecules induces a conformational change in PKA,...
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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The reactome pathway knowledgebase.

Bijay Jassal1, Lisa Matthews2, Guilherme Viteri3

  • 1Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.

Nucleic Acids Research
|November 7, 2019
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Summary
This summary is machine-generated.

Reactome is a knowledgebase of cellular processes, now enhanced with drug annotations for cardiovascular diseases. New features improve expert collaboration and pathway visualization for biological research.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics and Computational Biology
  • Systems Biology

Background:

  • The Reactome knowledgebase archives molecular details of cellular processes, including signal transduction, metabolism, and DNA replication.
  • It serves as a tool for discovering functional relationships in biological data, such as gene expression profiles and tumor cell mutation data.

Purpose of the Study:

  • To extend the annotation of human disease processes within the Reactome knowledgebase.
  • To enhance the usability and accessibility of Reactome for researchers and domain experts.

Main Methods:

  • Implementation of a new drug class for annotating drugs, initially focusing on cardiovascular disease-related medications.
  • Development of new web pages to recruit and manage community experts, enabling contribution tracking and ORCID integration.
  • Introduction of a new tool for automatic layout of reaction components and improved visualization of the event hierarchy.

Main Results:

  • Successful annotation of drugs relevant to cardiovascular disease using the new drug class.
  • Facilitation of community expert recruitment and contribution management.
  • Improved visualization tools for reaction diagrams and pathway analysis results.

Conclusions:

  • Reactome's new features enhance its utility as a resource for understanding cellular processes and diseases.
  • The knowledgebase is better equipped to support collaborative annotation and data interpretation in biomedical research.
  • Enhanced visualization and expert-driven annotation improve the discoverability and application of Reactome data for disease research.