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

Published on: February 8, 2017

Reactome knowledgebase of human biological pathways and processes.

Peter D'Eustachio1

  • 1Department of Biochemistry, New York University School of Medicine, New York, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 18, 2010
PubMed
Summary
This summary is machine-generated.

The Reactome Knowledgebase offers a curated view of human molecular processes, from metabolism to signaling. It enables data mining and analysis of large-scale biological datasets.

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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Biological processes are complex and interconnected.
  • Understanding these processes requires integrated data resources.
  • Existing resources may lack comprehensive coverage or consistent data models.

Purpose of the Study:

  • To present the Reactome Knowledgebase as a comprehensive resource for human biological processes.
  • To highlight its manually curated data and integrated view.
  • To emphasize its utility for data mining, modeling, and analysis.

Main Methods:

  • Manual curation of molecular pathway data.
  • Development of a consistent data model for diverse biological processes.
  • Integration of information on metabolism, DNA replication, repair, and signaling cascades.

Main Results:

  • The Reactome Knowledgebase provides an integrated view of human molecular biology.
  • Data is consistently represented, facilitating diverse applications.
  • It covers a wide range of biological processes, including metabolism, DNA repair, and signaling.

Conclusions:

  • Reactome serves as a valuable online resource for researchers.
  • Its integrated and curated data supports various analytical approaches.
  • It aids in understanding the complexity of human biological systems.