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

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...
Diversity in Cell Signaling Responses01:22

Diversity in Cell Signaling Responses

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...
Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...
Amplifying Signals via Enzymatic Cascade01:22

Amplifying Signals via Enzymatic Cascade

When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze the...
Intracellular Signaling Cascades01:24

Intracellular Signaling Cascades

Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. The continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell, such as DNA. Only internal receptors can interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the...
Chemical Signaling in the Endocrine System01:08

Chemical Signaling in the Endocrine System

A signaling cascade is a series of events that facilitates the transmission of information within or between cells, culminating in a targeted response in the recipient cell. As chemical messengers, hormones are pivotal in initiating and modulating these intricate signaling cascades based on their solubility.
Lipid-soluble hormones, such as steroid hormones, demonstrate an intracellular action. These hormones traverse cell membranes due to their lipid nature. Once inside the target cell, they...

You might also read

Related Articles

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

Sort by
Same author

Early neutrophil infiltration promotes TRIMELVax-induced antitumor immunity by linking local inflammation to tumor control.

Oncoimmunology·2026
Same author

Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.

Biomolecules·2026
Same author

The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8<sup>+</sup> T cells.

EMBO reports·2026
Same author

Inhibition of USP7 Destabilizes the Noncanonical PRC1.1 Complex and Induces Neuroblastoma Differentiation.

Molecular cancer research : MCR·2026
Same author

Overcoming EGFR resistance by monovalent and bident inhibitors targeting Cys775.

bioRxiv : the preprint server for biology·2026
Same author

Structure-Guided Design of Potent and Selective Covalent Inhibitors Targeting the SARS-CoV-2 Papain-like Protease.

Journal of medicinal chemistry·2026
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: Jun 12, 2026

Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres
06:52

Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres

Published on: July 22, 2020

Discovering causal signaling pathways through gene-expression patterns.

Jignesh R Parikh1, Bertram Klinger, Yu Xia

  • 1Bioinformatics Program, Boston University, Boston, MA 02115, USA.

Nucleic Acids Research
|May 25, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces SPEED, a novel web server and algorithm for identifying upstream signaling pathways that regulate gene expression. It helps uncover the root causes of differential gene expression in biological research.

More Related Videos

Optogenetic Signaling Activation in Zebrafish Embryos
07:18

Optogenetic Signaling Activation in Zebrafish Embryos

Published on: October 27, 2023

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Related Experiment Videos

Last Updated: Jun 12, 2026

Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres
06:52

Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres

Published on: July 22, 2020

Optogenetic Signaling Activation in Zebrafish Embryos
07:18

Optogenetic Signaling Activation in Zebrafish Embryos

Published on: October 27, 2023

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Area of Science:

  • Systems Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput gene-expression studies generate lists of differentially expressed genes.
  • Current meta-analyses often focus on protein membership in signaling pathways, not upstream regulators.
  • Existing methods lack insight into the causative signaling pathways driving gene expression changes.

Purpose of the Study:

  • To develop an intuitive approach for discovering upstream signaling pathways responsible for differential gene expression.
  • To identify consistently regulated signature genes specific to signal transduction pathways.
  • To create a web server resource for this novel algorithm.

Main Methods:

  • Perturbation experiments were used to identify signature genes specific to single signal transduction pathways.
  • An algorithm was developed to detect overrepresentation of these signature genes in gene groups of interest.
  • A web server, SPEED (Signaling Pathway Enrichment using Experimental Data sets), was created to host the resource and algorithm.

Main Results:

  • Successfully identified signature genes specific to various signal transduction pathways.
  • Developed and validated an algorithm for inferring upstream signaling pathways based on signature gene overrepresentation.
  • Launched the SPEED web server, providing a freely accessible resource for researchers.

Conclusions:

  • The SPEED approach offers a novel method for inferring upstream signaling pathways regulating gene expression.
  • This tool provides deeper insights into the regulatory mechanisms underlying differential gene expression.
  • SPEED facilitates a more comprehensive understanding of signaling pathway involvement in biological processes.