Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

7.4K
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...
7.4K
C4 Pathway and CAM01:27

C4 Pathway and CAM

49.3K
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.
C4 Pathway
The C4 pathway is used by plants such as...
49.3K
Other Glycolytic Pathways01:24

Other Glycolytic Pathways

990
The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
990
Respiration Pathways01:26

Respiration Pathways

795
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...
795
Auditory Pathway01:15

Auditory Pathway

7.5K
Auditory pathways constitute the complex neural circuits responsible for transmitting and interpreting auditory information from the peripheral auditory system to the brain. Sound waves are initially captured by the outer ear, funneled through the ear canal, and reach the tympanic membrane (eardrum). These vibrations are transmitted via the middle ear's ossicles to the inner ear's cochlea.
When viewed cross-sectionally, the cochlea reveals the scala vestibuli and scala tympani flanking...
7.5K
ER Retrieval Pathway01:45

ER Retrieval Pathway

4.9K
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.
The ER uses many checkpoints to prevent the entry of incorrectly folded or a resident protein as cargo onto a transport vesicle. These mechanisms...
4.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.

Nature communications·2026
Same author

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.

Nucleic acids research·2025
Same author

SMART v10: three decades of the protein domain annotation resource.

Nucleic acids research·2025
Same author

InterPro: the protein sequence classification resource in 2025.

Nucleic acids research·2024
Same author

Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool.

Nucleic acids research·2024
Same author

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Nucleic acids research·2023
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Feb 11, 2026

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

589

iPath3.0: interactive pathways explorer v3.

Youssef Darzi1, Ivica Letunic2, Peer Bork3,4,5,6

  • 1Department of Biological Information, Tokyo Institute of Technology, Tokyo 152-8550, Japan.

Nucleic Acids Research
|May 3, 2018
PubMed
Summary
This summary is machine-generated.

iPath3.0 offers a customizable, interactive web application for visualizing and analyzing cellular metabolic networks. This tool aids in exploring multi-omics data, uncovering biological insights, and streamlining research workflows.

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.8K
Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology
09:39

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology

Published on: March 31, 2022

3.7K

Related Experiment Videos

Last Updated: Feb 11, 2026

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

589
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.8K
Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology
09:39

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology

Published on: March 31, 2022

3.7K

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Metabolomics

Background:

  • Cellular pathways are crucial for understanding biological processes.
  • Analyzing complex metabolic networks requires specialized tools.
  • Existing pathway analysis tools may lack comprehensive integration and user customization.

Purpose of the Study:

  • To introduce iPath3.0, a web application for visualizing and analyzing cellular pathways.
  • To provide a manually curated, interconnected metabolic network based on KEGG data.
  • To facilitate the exploration of multi-omics data and uncover novel biological insights.

Main Methods:

  • Development of a web application integrating KEGG global maps, pathway maps, and modules.
  • Implementation of a redesigned, fast, and lightweight user interface for interactive exploration.
  • Incorporation of features for multi-omics data visualization, highlighting metabolic trends.
  • Support for multiple experimental conditions and time-series datasets.

Main Results:

  • iPath3.0 provides a comprehensive, manually curated metabolic network.
  • The application enables interactive exploration and visualization of cellular pathways.
  • It effectively highlights metabolic trends in multi-omics data.
  • New features streamline data customization, programmatic access, and user account management.

Conclusions:

  • iPath3.0 enhances the analysis of cellular metabolic networks.
  • The tool facilitates the discovery of novel biological insights from complex datasets.
  • Its user-friendly interface and advanced features support streamlined research workflows.