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

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,...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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...
Gene Flow02:39

Gene Flow

Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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,...

You might also read

Related Articles

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

Sort by
Same author

Rhizoplane microbiome: niche-specific recruitment and plant defense priming against bacterial wilt disease.

Plant physiology·2026
Same author

Neoadjuvant Immunotherapy-Based Treatment Versus Chemotherapy Alone in Resectable Locally Advanced dMMR/MSI-H Gastric Cancer: A Real-World Study with Meta-Analysis.

Cancers·2026
Same author

Quantitative Analysis of the Association between Clinical Antimicrobial Use and Healthcare-associated Infections: A Multicentre Case-Control Study.

The Journal of hospital infection·2026
Same author

Artesunate does not prevent cardiac hypertrophy but inhibits heart failure progression in mice.

The Journal of pharmacology and experimental therapeutics·2026
Same author

FPGA-Based Low-Latency Semantic Feedback System for Real-Time Instrument Localization in Telesurgery.

The international journal of medical robotics + computer assisted surgery : MRCAS·2026
Same author

Secreted frizzled-related protein 1 augments vascular smooth muscle cell calcification via activating the Wnt/β-catenin/Runx2 axis.

International urology and nephrology·2026

Related Experiment Video

Updated: May 15, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

Hufeng Zhou1, Jingjing Jin, Haojun Zhang

  • 1NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore.

BMC Systems Biology
|January 4, 2013
PubMed
Summary
This summary is machine-generated.

We developed IntPath, an integrated pathway gene relationship database, overcoming data incompatibility and inconsistency issues. IntPath provides richer, unified pathway-gene data for model organisms and pathogens, enhancing biological research.

More Related Videos

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Related Experiment Videos

Last Updated: May 15, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Area of Science:

  • Bioinformatics and Computational Biology
  • Systems Biology
  • Genomics and Molecular Biology

Background:

  • Pathway data are crucial for understanding molecular relationships in organisms, aiding fields like biochemistry, computational biology, and medicine.
  • Existing pathway databases (e.g., KEGG, WikiPathways, BioCyc) face challenges with data format incompatibility, inconsistent representations, and incomplete information.
  • These limitations hinder the effective utilization of pathway data for research and applications.

Purpose of the Study:

  • To address the limitations of existing pathway databases by creating a unified and comprehensive resource.
  • To integrate pathway gene relationship data from multiple public databases into a single, accessible repository.
  • To provide a normalized and consistent dataset that facilitates computational analysis and referencing.

Main Methods:

  • Extraction, normalization, and integration of pathway data from major public databases (KEGG, WikiPathways, BioCyc, etc.).
  • Development of the Integrated Pathway gene relationship database (IntPath) using a "full unification" approach to ensure data integrity.
  • Inclusion of data for four key organisms: S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens, and M. musculus.
  • Application of moderate manual curation to resolve errors and noise from source data.

Main Results:

  • IntPath offers significantly richer pathway-gene and pathway-gene pair relationships compared to single-source databases.
  • The database contains a larger number of non-redundant genes and gene pairs, with enhanced gene relationships per pathway.
  • Data are presented in a normalized, unified format (tab-delimited text and MySQL tables) for convenient computational use and analysis.
  • IntPath provides web services and an interface for data retrieval and analysis, along with supporting tools.

Conclusions:

  • IntPath successfully overcomes compatibility, consistency, and comprehensiveness issues in pathway databases.
  • The current release includes four organisms, with a methodology applicable to expanding to more species.
  • IntPath is regularly updated and freely available, serving as a valuable resource for the scientific community.