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

4.6K
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,...
4.6K
Protein Networks02:26

Protein Networks

2.9K
2.9K
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

7.4K
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...
7.4K
C4 Pathway and CAM01:27

C4 Pathway and CAM

49.6K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
49.6K
Canonical Wnt Signaling Pathway02:54

Canonical Wnt Signaling Pathway

10.8K
The gene encoding the main signaling molecules of the Wnt signaling pathways (the Wnt proteins) was discovered almost four decades ago by Nüsslein-Volhard and Wieschaus. They identified and originally named the gene "wingless" (wg) after a phenotype discovered during their landmark genetic screen in Drosophila for body pattern defects. At around the same time, another researcher named Harold Varmus found that a murine tumor virus activates the mammalian wg homolog, Int-1, which...
10.8K
Cell Signaling in Plants01:25

Cell Signaling in Plants

6.8K
Plant cells communicate to coordinate their cycle of growth, flowering and fruiting, and activities in roots, shoots, and leaves in response to the changing environmental conditions. Plant signaling is distinct from animal signaling. Plants primarily utilize enzyme-linked receptors, whereas the largest class of cell-surface receptors in animals are G-protein coupled receptors (GPCRs). Unlike animals, receptor tyrosine kinases are rare in plants. Instead, plants have a diverse class of...
6.8K

You might also read

Related Articles

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

Sort by
Same author

Identification and functional analysis of class 3 lipases associated with triacylglycerol metabolism in Nannochloropsis oceanica (Eustigmatophyceae).

Journal of phycology·2026
Same author

CRISPR/Cas9-mediated genome editing reveals the involvement of a polyphenol oxidase in the shikonin-specific biosynthesis in Lithospermum erythrorhizon.

Plant & cell physiology·2026
Same author

Revisiting the Oxidation State of [Cu(HIO<sub>6</sub>)<sub>2</sub>]<sup>5-</sup>: A Copper(III) Complex between Classical Werner-Type and Inverted Ligand Fields.

Inorganic chemistry·2026
Same author

S-alk(en)yl-cysteine sulfoxides in Allium species are excellent acrolein scavengers: implications for secondary antioxidants in plants.

Bioscience, biotechnology, and biochemistry·2025
Same author

Stress-induced brain extracellular vesicles ameliorate anxiety behavior.

Translational psychiatry·2025
Same author

Activation of Anionic Redox for Stoichiometric and Li-Excess Metal Sulfides through Structural Disordering: Joint Experimental and Theoretical Study.

Journal of the American Chemical Society·2025

Related Experiment Video

Updated: Mar 1, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

20.6K

Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene.

Takafumi Narise1, Nozomu Sakurai1, Takeshi Obayashi2

  • 1Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan.

BMC Genomics
|June 7, 2017
PubMed
Summary

This study introduces a new tomato gene co-expression database that improves gene function prediction by analyzing all co-expressed genes, not just strongly co-expressed ones. A novel percentile (p)-score enhances pathway relevance identification.

Keywords:
Co-expression databaseGene set enrichment analysisOver-representation analysisPathwayPercentile-score

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.8K
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

1.0K

Related Experiment Videos

Last Updated: Mar 1, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

20.6K
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

3.8K
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

1.0K

Area of Science:

  • Plant genomics
  • Bioinformatics
  • Functional genomics

Background:

  • Gene co-expression analysis is crucial for inferring gene function and relationships.
  • Existing co-expression databases often rely on over-representation analysis (ORA) of strongly co-expressed genes, limiting functional predictions.
  • A key limitation is the inability to leverage information from weakly co-expressed genes.

Purpose of the Study:

  • To develop an improved co-expression database for tomato gene function prediction.
  • To incorporate analysis of all co-expressed genes, not solely strongly co-expressed ones.
  • To introduce a novel metric for evaluating gene-pathway relationships that accounts for internal pathway correlations.

Main Methods:

  • Utilized over-representation analysis (ORA) with varying thresholds and gene set enrichment analysis (GSEA) on ranked co-expression lists.
  • Developed a new metric, the percentile (p)-score, to assess gene-pathway relationships.
  • Validated the approach using receiver operating characteristic (ROC) curves.

Main Results:

  • Identified that internal pathway correlations can impact enrichment analysis significance.
  • The developed percentile (p)-score effectively predicts functionally relevant pathways, mitigating the influence of internal pathway correlations.
  • The p-score demonstrated improved performance compared to traditional ORA.

Conclusions:

  • Introduced the Co-expressed Pathways DataBase for Tomato (CPDBT).
  • CPDBT enables prediction of relevant pathways for query genes, aiding in function inference.
  • The database and the p-score offer a more comprehensive approach to understanding gene function through co-expression analysis.