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Related Concept Videos

Respiration Pathways01:26

Respiration Pathways

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...
Protein Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...
Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which provide...
Primary Active Transport01:29

Primary Active Transport

In contrast to passive transport, active transport involves a substance being moved through membranes in a direction against its concentration or electrochemical gradient. There are two types of active transport: primary active transport and secondary active transport. Primary active transport utilizes chemical energy from ATP to drive protein pumps embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction they would not...
cAMP-dependent Protein Kinase Pathways01:25

cAMP-dependent Protein Kinase Pathways

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
08:01

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

Published on: February 8, 2017

Reactome knowledgebase of human biological pathways and processes.

Lisa Matthews1, Gopal Gopinath, Marc Gillespie

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Nucleic Acids Research
|November 5, 2008
PubMed
Summary
This summary is machine-generated.

Reactome is a comprehensive, peer-reviewed knowledgebase of human biological pathways and reactions. It offers enhanced tools for data mining and pathway visualization, supporting research across multiple species.

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Bioinformatics

Background:

  • Reactome is an expert-authored, peer-reviewed knowledgebase detailing human reactions and pathways.
  • It serves as a valuable resource for data mining and as an electronic textbook.
  • The current release encompasses 2975 human proteins, 2907 reactions, and 4455 literature citations.

Purpose of the Study:

  • To enhance the utility of the Reactome knowledgebase for researchers.
  • To improve tools for searching, visualizing, and analyzing pathway data.
  • To expand pathway inference capabilities to model organisms.

Main Methods:

  • Development of a new entity-level pathway viewer.
  • Implementation of improved search and data mining functionalities.
  • Enhancement of orthology prediction methods for cross-species pathway inference.

Main Results:

  • The updated Reactome release facilitates searching and visualization of pathway data.
  • New tools enable the analysis of user-supplied high-throughput datasets.
  • Pathway inference is now possible for 22 species, including model organisms like Arabidopsis and Drosophila.
  • Collaborations have led to curated pathway datasets for multiple species.

Conclusions:

  • Reactome provides a robust and expanding resource for biological pathway information.
  • Enhanced tools and cross-species capabilities increase its value for diverse research applications.
  • The open-source nature of Reactome promotes widespread use and redistribution.