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

Reconstruction of Signal using Interpolation01:10

Reconstruction of Signal using Interpolation

699
Signal processing techniques are essential for accurately converting continuous signals to digital formats and vice versa. When a continuous signal is sampled with a period T, the resulting sampled signal exhibits replicas of the original spectrum in the frequency domain, spaced at intervals equal to the sampling frequency. To handle this sampled signal, a zero-order hold method can be applied, which creates a piecewise constant signal by retaining each sample's value until the next...
699
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

7.2K
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...
7.2K
Notch Signaling Pathway03:14

Notch Signaling Pathway

6.5K
The Notch signaling pathway is a major intracellular signaling pathway that is highly conserved over a broad spectrum of metazoan species. It stands unique from other intracellular signaling mechanisms in animals because notch protein itself acts as the receptor as well as the primary signaling molecule.
The Notch gene came into the limelight in 1914 after the discovery that its mutation in Drosophila melanogaster leads to a serrated (or "notched") wing margin phenotype. It was not...
6.5K
Hedgehog Signaling Pathway02:33

Hedgehog Signaling Pathway

9.8K
The Hedgehog gene (Hh) was first discovered due to its control of the growth of disorganized, hair-like bristles phenotype in Drosophila, much like hedgehog spines. Hh plays a crucial role in the development of organs and the maintenance of homeostasis in both invertebrates and vertebrates. However, while Drosophila has only one Hh protein, mammals have multiple functional Hedgehog proteins - Sonic (Shh), Desert (Dhh), and Indian Hedgehog (Ihh). All of these homologous proteins have adapted to...
9.8K
Insulin: The Receptor and Signaling Pathways01:28

Insulin: The Receptor and Signaling Pathways

2.8K
Insulin action is mediated through a receptor tyrosine kinase, akin to the IGF-1 receptor. The number of receptors per cell varies significantly, from 40 on erythrocytes to 300,000 on adipocytes and hepatocytes. The insulin receptor consists of linked α/β subunit dimers, forming a heterotetramer glycoprotein with two extracellular α subunits and two β subunits spanning the membrane. The α subunits inhibit the inherent tyrosine kinase activity of the β subunits, but...
2.8K
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

14.3K
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...
14.3K

You might also read

Related Articles

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

Sort by
Same author

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

Cell press blue·2026
Same author

Spatial proteomic analysis in human Alzheimer's disease brains enables identification of microenvironment-dependent microglial cell states.

Nature neuroscience·2026
Same author

Varying Perfusate Hemoglobin During Normothermic Ex Situ Heart Perfusion: Elevated Hemoglobin Exacerbates Functional Decline Through Hemolysis.

Transplantation direct·2026
Same author

Preservation of pediatric donor hearts via subnormothermic machine perfusion: Comparison to cold storage.

JHLT open·2026
Same author

Provenance Tracing in Network Diffusion Algorithms.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2026
Same author

Improving metabolic support during normothermic <i>ex-situ</i> heart perfusion.

Frontiers in cardiovascular medicine·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jan 19, 2026

Reconstruction of Signal using Interpolation
01:10

Reconstruction of Signal using Interpolation

699

Reconstructing signaling pathways using regular language constrained paths.

Mitchell J Wagner1, Aditya Pratapa1, T M Murali1

  • 1Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.

Bioinformatics (Oxford, England)
|September 13, 2019
PubMed
Summary
This summary is machine-generated.

RegLinker automates the identification of new protein interactions for signaling pathways. This computational approach enhances pathway annotation accuracy and efficiency.

More Related Videos

Interactions Between Signaling Pathways
01:19

Interactions Between Signaling Pathways

7.2K
Regulation of Notch Signaling Pathway and Stem Cells&#039; Fate
03:14

Regulation of Notch Signaling Pathway and Stem Cells' Fate

6.5K

Related Experiment Videos

Last Updated: Jan 19, 2026

Reconstruction of Signal using Interpolation
01:10

Reconstruction of Signal using Interpolation

699
Interactions Between Signaling Pathways
01:19

Interactions Between Signaling Pathways

7.2K
Regulation of Notch Signaling Pathway and Stem Cells&#039; Fate
03:14

Regulation of Notch Signaling Pathway and Stem Cells' Fate

6.5K

Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Manual curation of signaling pathways is time-consuming and often incomplete.
  • Many experimentally detected protein interactions remain unassigned to specific pathways.
  • Automated methods are needed to expand pathway knowledge.

Purpose of the Study:

  • To develop and evaluate an algorithm for automatically identifying new protein interactions within signaling pathways.
  • To leverage existing pathway annotations to improve the completeness of pathway databases.

Main Methods:

  • RegLinker algorithm computes short paths between pathway receptors and transcription factors in a network.
  • Regular language constraints are used to filter non-pathway interactions within computed paths.
  • Systematic evaluation against 15 signaling pathways and comparison with alternative methods.

Main Results:

  • RegLinker demonstrated superior precision and recall in recovering withheld pathway proteins and interactions.
  • The algorithm successfully proposed novel extensions to existing signaling pathways.
  • Literature review supported the biological relevance of the proposed pathway additions.

Conclusions:

  • Automated analysis, exemplified by RegLinker, can significantly alleviate the challenges of manual pathway curation.
  • RegLinker offers a powerful tool for expanding and refining signaling pathway knowledge.
  • This approach holds broad potential for advancing systems biology research.