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Related Concept Videos

IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

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 produces two-second...
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Interactions Between Signaling Pathways

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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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.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
ER Retrieval Pathway01:45

ER Retrieval Pathway

In the secretory pathway, vesicles transport proteins from one cellular compartment to another in forward transport to deliver the protein to its correct location. Occasionally, misfolded proteins and incorrect proteins escape their original compartments, and a retrieval pathway is used to return the escaped proteins to their original compartment.
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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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Published on: February 8, 2017

PID: the Pathway Interaction Database.

Carl F Schaefer1, Kira Anthony, Shiva Krupa

  • 1National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA. schaefec@mail.nih.gov

Nucleic Acids Research
|October 4, 2008
PubMed
Summary
This summary is machine-generated.

The Pathway Interaction Database (PID) offers curated human molecular signaling pathways for researchers. It provides tools for pathway exploration, data analysis, and downloads, aiding cancer research and other biological fields.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Cellular processes and molecular signaling are fundamental to biological functions.
  • Understanding complex molecular interactions is crucial for disease research, particularly in oncology.
  • Existing pathway databases vary in scope and curation standards.

Purpose of the Study:

  • To introduce the Pathway Interaction Database (PID) as a comprehensive resource for human molecular signaling and regulatory events.
  • To highlight PID's utility as a research tool for cancer research and other biological disciplines.
  • To detail the features and data accessibility offered by PID.

Main Methods:

  • Curated collection of human molecular signaling and regulatory events.
  • Development of search and visualization tools for pathway exploration.
  • Provision of data download options in XML and BioPAX formats.

Main Results:

  • PID provides a freely accessible, curated collection of molecular pathways.
  • Features include pathway browsing, network map creation, and batch query tools for analyzing large datasets (e.g., from microarrays).
  • Users can download pathway components, citations, and full database content.

Conclusions:

  • PID serves as a valuable, up-to-date resource for researchers investigating cellular pathways.
  • The database supports diverse research areas including cancer, neuroscience, developmental biology, and immunology.
  • Regular updates and supplementary articles enhance PID's practical application and discoverability.