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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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The direct motor pathways, also known as the pyramidal tracts, are a group of neural pathways that originate in the brain and descend through the spinal cord. They control the voluntary movement of the body. There are two major direct motor pathways: the corticospinal and the corticobulbar tracts.
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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.
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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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Mitogen-activated protein kinase, or MAPK pathway, activates three sequential kinases to regulate cellular responses such as proliferation, differentiation, survival, and apoptosis. The canonical MAPK pathway starts with a mitogen or growth factor binding to an RTK. The activated RTKs stimulate Ras, which recruits Raf or MAP3 Kinase (MAPKKK), the first kinase of the MAPK signaling cascade. Raf further phosphorylates and activates MEK or MAP2 Kinases (MAPKK), which in turn phosphorylates MAP...
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Pathguide: a pathway resource list.

Gary D Bader1, Michael P Cary, Chris Sander

  • 1Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10021, USA.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary
This summary is machine-generated.

Pathguide is a meta-database listing over 190 biological pathway and network databases. It serves as a starting point for pathway analysis and data aggregation in biological information systems.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Biological pathway and network data are fragmented across numerous specialized databases.
  • Integrating information from diverse sources is crucial for comprehensive biological analysis.

Purpose of the Study:

  • To present Pathguide, a meta-database consolidating information from over 190 biological pathway and network resources.
  • To provide a unified starting point for exploring biological pathways and networks.

Main Methods:

  • Aggregated information from 190+ web-accessible databases.
  • Categorized databases by type, including metabolic, signaling, gene regulatory, and protein interaction networks.

Main Results:

  • Pathguide offers a centralized overview of diverse biological pathway and network databases.
  • The meta-database includes resources covering metabolic pathways, signaling pathways, transcription factor targets, gene regulatory networks, genetic interactions, protein-compound interactions, and protein-protein interactions.

Conclusions:

  • Pathguide facilitates biological pathway analysis by providing a comprehensive starting point.
  • It aids in content aggregation for integrated biological information systems.