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,...
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,...
Amino Acid Biosynthetic Pathways01:29

Amino 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...
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...
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,...
Positive Regulator Molecules02:39

Positive Regulator Molecules

Mitotic cell division results in daughter cells that exactly resemble the parent cell. However, errors in the DNA replication or distribution of genetic material may lead to genetic mutations that may be passed down to every new cell formed from the resulting abnormal cell. Propagation of such mutant cells is restricted through checkpoint mechanisms present at different stages of the cell cycle. These checkpoints involve regulator molecules that either promote or demote cell cycle events.

You might also read

Related Articles

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

Sort by
Same author

CIROZ is dispensable in ancestral vertebrates but essential for left-right patterning in humans.

American journal of human genetics·2025
Same author

Uncharacterized yeast gene <i>YBR238C</i>, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via <i>HAP4</i>- and <i>RMD9</i>-dependent mechanisms.

eLife·2024
Same author

Targeting the GPI transamidase subunit GPAA1 abrogates the CD24 immune checkpoint in ovarian cancer.

Cell reports·2024
Same author

Correction: Cserző et al. The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method. <i>Int. J. Mol. Sci.</i> 2023, <i>24</i>, 14016.

International journal of molecular sciences·2024
Same author

Global longitudinal strain and plasma biomarkers for prognosis in heart failure complicated by diabetes: a prospective observational study.

BMC cardiovascular disorders·2024
Same author

PICLS with human cells is the first high throughput screening method for identifying novel compounds that extend lifespan.

Biology direct·2024

Related Experiment Video

Updated: Jun 15, 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

Biomolecular pathway databases.

Hong Sain Ooi1, Georg Schneider, Teng-Ting Lim

  • 1Bioinformatics Institute, Agency for science, Technology, and Research, Singapore.

Methods in Molecular Biology (Clifton, N.J.)
|March 12, 2010
PubMed
Summary
This summary is machine-generated.

This chapter reviews biomolecular pathway databases, focusing on their scope, reliability, and classification. The trend is towards quantitative data for predictive modeling and enhanced analytical capabilities.

More Related Videos

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Related Experiment Videos

Last Updated: Jun 15, 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

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Molecular Biology

Background:

  • Biomolecular pathways are crucial for biological functions, involving complex interactions of biomacromolecules and compounds.
  • These pathways are often linked to specific subcellular compartments, influencing cellular processes.
  • Understanding these pathways is essential for deciphering biological outcomes and disease mechanisms.

Purpose of the Study:

  • To analyze major public biomolecular pathway databases.
  • To evaluate database scope, completeness, annotation reliability, and classification systems.
  • To review information retrieval systems and gene set mapping tools for pathway analysis.

Main Methods:

  • Comparative analysis of prominent biomolecular pathway databases.
  • Assessment of data quality, including annotation reliability and scope.
  • Review of existing tools for pathway data retrieval and gene set mapping.

Main Results:

  • Identification of key features and limitations across major pathway databases.
  • Evaluation of current approaches for pathway classification and data organization.
  • Overview of tools facilitating the integration of user-specific gene data with pathway information.

Conclusions:

  • Pathway databases are evolving, with a growing need for quantitative descriptions of interactions.
  • The future of pathway databases lies in enabling predictive modeling and serving as analytical workbenches.
  • Enhanced data quality and advanced analytical tools will improve biological research applications.