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

Cell Specific Gene Expression01:58

Cell Specific Gene Expression

5.4K
5.4K
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

16.2K
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
16.2K
Combinatorial Gene Control02:33

Combinatorial Gene Control

9.5K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
9.5K
General Transcription Factors01:30

General Transcription Factors

6.7K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
6.7K

You might also read

Related Articles

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

Sort by
Same author

Decoding stage-specific symbiotic programs in the Rhizophagus irregularis-tomato interaction using single-nucleus transcriptomics.

Current biology : CB·2026
Same author

Ready for battle: histone modifications shape rice intergenerational memory to protect against nematode attack.

Journal of experimental botany·2026
Same author

White paper: standards for handling and analyzing plant pan-genomes.

F1000Research·2025
Same author

JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models.

Nucleic acids research·2025
Same author

Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.

Nature communications·2025
Same author

Integrative gene regulatory networks and machine learning unveil the functions of novel maize regulators.

Molecular plant·2025
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jan 13, 2026

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights
08:23

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

Published on: June 28, 2024

1.4K

MINI-EX Version 2: Cell-Type-Specific Gene Regulatory Network Inference Using an Integrative Single-Cell

Jasper Staut1,2, Nicolás Manosalva Pérez1,2, Thomas Depuydt1,2

  • 1Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

Methods in Molecular Biology (Clifton, N.J.)
|January 10, 2026
PubMed
Summary
This summary is machine-generated.

MINI-EX identifies plant cell-type-specific gene regulatory networks (GRNs) using single-cell data and transcription factor (TF) motifs. The tool aids in understanding TF functions and transcriptional cascades, even for non-model species.

Keywords:
Gene regulatory networkSingle-cell RNA-seqSystems biologyTranscription factors

More Related Videos

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies
05:45

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Published on: March 29, 2024

3.3K
Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

19.0K

Related Experiment Videos

Last Updated: Jan 13, 2026

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights
08:23

Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights

Published on: June 28, 2024

1.4K
Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies
05:45

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Published on: March 29, 2024

3.3K
Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

19.0K

Area of Science:

  • Plant biology
  • Genomics
  • Bioinformatics

Background:

  • Gene regulatory networks (GRNs) control gene expression and biological processes.
  • Understanding cell-type-specific GRNs is crucial for multicellular organisms.
  • Transcription factors (TFs) are key regulators within GRNs.

Purpose of the Study:

  • To introduce MINI-EX, an integrative tool for identifying cell-type-specific GRNs in plants.
  • To enhance the accuracy of GRN inference by integrating TF motif information.
  • To provide a method for GRN identification in non-model plant species lacking motif data.

Main Methods:

  • Leveraging single-cell transcriptomics data to construct expression-based networks.
  • Integrating transcription factor motif information to improve GRN accuracy.
  • Assigning regulatory modules to cell types and prioritizing candidate regulators using network centrality, functional annotations, and expression specificity.

Main Results:

  • MINI-EX successfully identifies cell-type-specific GRNs in plants.
  • The tool enhances understanding of TF functions and transcriptional cascades.
  • The latest version of MINI-EX supports GRN identification for non-model species.

Conclusions:

  • MINI-EX provides a powerful approach for dissecting plant gene regulation at the single-cell level.
  • The tool facilitates the study of TF roles in diverse biological processes.
  • MINI-EX offers a comprehensive pipeline for GRN analysis from data preparation to output interpretation.