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

Diversity in Cell Signaling Responses01:22

Diversity in Cell Signaling Responses

6.3K
The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity. 
Graded and Abrupt Responses
Some signaling systems generate...
6.3K
Overview of Cell Signaling01:23

Overview of Cell Signaling

20.0K
Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
20.0K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

6.2K
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...
6.2K
What is Cell Signaling?02:03

What is Cell Signaling?

112.7K
Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.
112.7K
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

11.8K
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...
11.8K
PI3K/mTOR/AKT Signaling Pathway01:22

PI3K/mTOR/AKT Signaling Pathway

3.4K
The mammalian target of rapamycin  (mTOR) is a serine/threonine kinase that regulates growth, proliferation, and cell survival in response to hormones, growth factors, or nutrient availability. This kinase exists in two structurally and functionally distinct forms: mTOR complex 1  (mTORC1) and mTOR complex 2  (mTORC2). The first form (mTORC1) is composed of a rapamycin-sensitive Raptor and proline-rich Akt substrate, PRAS40. In contrast,  mTORC2 consists of a...
3.4K

You might also read

Related Articles

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

Sort by
Same author

Modeling human B cell development with pluripotent stem cells.

bioRxiv : the preprint server for biology·2026
Same author

Transient anti-interferon autoantibodies in the airways are associated with recovery from COVID-19.

Science translational medicine·2024
Same author

Craniofacial chondrogenesis in organoids from human stem cell-derived neural crest cells.

iScience·2024
Same author

Stromal STAT5-Mediated Trophic Activity Regulates Hematopoietic Niche Factors.

Stem cells (Dayton, Ohio)·2023
Same author

Understanding heterogeneity of human bone marrow plasma cell maturation and survival pathways by single-cell analyses.

Cell reports·2023
Same author

Profiling the peripheral immune response to ex vivo TNF stimulation in untreated juvenile idiopathic arthritis using single cell RNA sequencing.

Pediatric rheumatology online journal·2023
Same journal

Genetic Impacts on Variability of Body Fat Distribution Uncover Gene-Environment and Gene-Gene Interactions.

bioRxiv : the preprint server for biology·2026
Same journal

16S ribosomal RNA modification drives transcript-specific translation efficiency.

bioRxiv : the preprint server for biology·2026
Same journal

FlcE latches onto the FliL-stator complex to turbocharge flagellar motility in <i>Borrelia burgdorferi</i>.

bioRxiv : the preprint server for biology·2026
Same journal

Synaptic pruning, myelination and the emergence of psychiatric disorders in late adolescence.

bioRxiv : the preprint server for biology·2026
Same journal

Structural and functional insights into the Rcs phosphorelay.

bioRxiv : the preprint server for biology·2026
Same journal

The structural basis of RanGAP1 regulation and catalysis in nuclear transport.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: May 27, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.1K

Cell signaling pathways discovery from multi-modal data.

Changhan He1, Claire Simpson2, Ian Cossentino2

  • 1Department of Mathematics, University of California, Irvine, California, 92697, USA.

Biorxiv : the Preprint Server for Biology
|February 20, 2025
PubMed
Summary
This summary is machine-generated.

Incytr integrates multi-omics data to discover cell signaling pathways, aiding disease research and drug discovery. This computational tool enhances understanding of cell communication and disease mechanisms.

More Related Videos

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts
08:51

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Published on: September 20, 2024

1.1K
Author Spotlight: Advancing Alzheimer's Research &#8211; Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

940

Related Experiment Videos

Last Updated: May 27, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.1K
Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts
08:51

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Published on: September 20, 2024

1.1K
Author Spotlight: Advancing Alzheimer's Research &#8211; Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

940

Area of Science:

  • Computational biology
  • Systems biology
  • Genomics and Proteomics

Background:

  • Understanding cell signaling pathways is crucial for biology and medicine.
  • Multi-omics technologies provide rich data but are complex for interpretation.
  • Existing computational tools for inferring signaling pathways from multi-omics data are limited.

Purpose of the Study:

  • To develop a computational method for efficient cell signaling pathway discovery from multi-omics data.
  • To address the challenge of interpreting complex, high-dimensional omics data.
  • To facilitate target and drug discovery by identifying novel signaling pathways.

Main Methods:

  • Developed Incytr, a novel computational method.
  • Integrated diverse data modalities: transcriptomics, proteomics, phosphoproteomics, and kinomics.
  • Applied Incytr to study cell signaling in COVID-19, Alzheimer's disease, and cancer.

Main Results:

  • Incytr successfully rediscovered known disease-associated subpathways.
  • Generated novel hypotheses for cell-type-specific signaling pathways supported by multi-modal data.
  • Demonstrated utility in facilitating target and drug discovery through integration with databases.

Conclusions:

  • Incytr is an effective tool for discovering cell signaling pathways from integrated multi-omics data.
  • The method aids in understanding disease mechanisms and identifying therapeutic targets.
  • AI-driven pathway analysis can deepen insights into cell-cell communication and co-evolution.