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Interactions Between Signaling Pathways01:19

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
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
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...
Amplifying Signals via Enzymatic Cascade01:22

Amplifying Signals via Enzymatic Cascade

When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze the...
Indirect Motor Pathways01:22

Indirect Motor Pathways

The indirect motor or extrapyramidal pathways originate in the brainstem, the lower portion of the brain that connects it to the spinal cord. They consist of several distinct tracts, each with specialized functions. The four main tracts of the indirect motor pathways are the vestibulospinal tract, the reticulospinal tract, the tectospinal tract, and the rubrospinal tract.
The vestibulospinal tract originates in the vestibular nuclei of the brainstem. The vestibular system detects changes in...
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,...

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Related Experiment Video

Updated: Jun 1, 2026

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

LinkinPath: from sequence to interconnected pathway.

Supawadee Ingsriswang1, Sunai Yokwai, Duangdao Wichadakul

  • 1Information Systems Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani 12120, Thailand. supawadee@biotec.or.th

Bioinformatics (Oxford, England)
|June 4, 2011
PubMed
Summary
This summary is machine-generated.

LinkinPath is a novel pathway mapping tool for analyzing gene and protein sequences. It visualizes data on KEGG pathway maps, functional compositions, and molecular networks, aiding biological discovery.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • LinkinPath is a freely available web-based tool.
  • It addresses the need for comprehensive pathway analysis of gene and protein sequence data.

Purpose of the Study:

  • To introduce LinkinPath, a versatile tool for pathway mapping and analysis.
  • To enable exploration and visualization of gene/protein sequence datasets.

Main Methods:

  • Utilizes Flash-driven interactive web interfaces.
  • Supports analysis of single or multiple gene/protein sequence datasets.
  • Incorporates KEGG pathway maps, TreeMaps, and network visualizations.

Main Results:

  • Enables visualization of gene/protein co-occurrence and co-absence on KEGG maps.
  • Facilitates comparison of functional compositions within and among datasets using TreeMaps.
  • Supports analysis of statistically enriched pathways and construction of pathway-to-pathway networks.

Conclusions:

  • LinkinPath provides a comprehensive platform for exploring complex biological pathways.
  • The tool aids in identifying molecular interactions, reactions, and common pathway networks.
  • It empowers researchers to gain deeper insights from gene and protein sequence data.