Related Experiment Video
Updated: Jul 7, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
iPath: interactive exploration of biochemical pathways and networks
Ivica Letunic1, Takuji Yamada, Minoru Kanehisa
1EMBL, Meyerhofstrasse 1, Heidelberg, Germany.
Trends in Biochemical Sciences
|February 16, 2008
Summary
iPath is a free online tool for exploring metabolic pathways. It helps visualize and analyze biochemical processes, aiding in understanding host-symbiont metabolic complementarity.
Area of Science:
- Metabolic pathway visualization and analysis
- Bioinformatics tools
- Systems biology
Background:
- Metabolic pathways are crucial for understanding cellular functions.
- Analyzing complex metabolic networks requires specialized tools.
- iPath provides an open-access platform for pathway exploration.
Discussion:
- iPath facilitates interactive navigation and data integration for metabolic pathway analysis.
- The tool allows customization of pathway maps with external data, including genomic information.
- It enables the identification of metabolic complementarities between different organisms, such as hosts and symbionts.
Key Insights:
- iPath offers a user-friendly interface for visualizing and analyzing metabolic pathways.
- The platform supports the integration of diverse datasets for enhanced pathway interpretation.
- It is valuable for comparative metabolic studies, exemplified by host-symbiont interactions.
Outlook:
- Future development could involve expanding the database of metabolic pathways and associated data.
- Integration with other omics data types could further enhance iPath's analytical capabilities.
- iPath has the potential to become a central hub for metabolic network research.
Related Concept Videos
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
01:29Amino 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...
01:11IP3/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...
02:04Protein-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...
01:26Respiration 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...