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

Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.7K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.7K

You might also read

Related Articles

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

Sort by
Same author

Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).

Scientific reports·2025
Same author

A dominant SRCAP truncating mutation promotes squamous cell carcinoma progression.

Oncogenesis·2025
Same author

Developmentally cascading structures do not lose evolutionary potential, but compound developmental instability in rat molars.

bioRxiv : the preprint server for biology·2025
Same author

Nucleoporin downregulation modulates progenitor differentiation independent of nuclear pore numbers.

Communications biology·2023
Same author

NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization.

Communications biology·2023
Same author

Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study.

Sexually transmitted diseases·2023

Related Experiment Video

Updated: Oct 16, 2025

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.4K

GPSmatch: an R package for comparing Genomic-binding Profile Similarity among transcriptional regulators using

Amy Dong1, Xiaomin Bao2,3,4

  • 1Hinsdale Central High School, Hinsdale, IL 60521, USA.

Bioinformatics (Oxford, England)
|October 21, 2021
PubMed
Summary

GPSmatch is a new R package that compares ChIP-Seq data to identify shared genomic-binding sites between transcriptional regulators. This tool helps researchers understand gene regulation mechanisms by analyzing binding profile similarities.

More Related Videos

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
10:44

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

1.6K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.1K

Related Experiment Videos

Last Updated: Oct 16, 2025

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.4K
In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
10:44

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

1.6K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.1K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Eukaryotic gene expression involves complex coordination of numerous transcriptional regulators.
  • Understanding how these regulators interact at genomic sites is crucial for deciphering gene regulation mechanisms.
  • The increasing volume of chromatin immunoprecipitation assays with sequencing (ChIP-Seq) data necessitates efficient analysis tools.

Purpose of the Study:

  • To develop a computational tool for comparing ChIP-Seq data to identify shared genomic-binding sites among transcriptional regulators.
  • To provide a method for assessing the statistical significance of binding profile similarities.

Main Methods:

  • Development of the R package GPSmatch (Genomic-binding Profile Similarity match).
  • Utilizing the Jaccard index to quantify the similarity between ChIP-Seq peak sets.
  • Implementing a nonparametric Monte Carlo procedure for statistical significance evaluation.

Main Results:

  • GPSmatch effectively calculates the Jaccard index to compare ChIP-Seq experiments.
  • The package can identify and rank transcriptional regulators based on shared genomic-binding profiles.
  • Statistical significance of shared binding sites can be reliably assessed.

Conclusions:

  • GPSmatch is a valuable tool for analyzing ChIP-Seq data to uncover functional relationships between transcriptional regulators.
  • The software facilitates the discovery of potential mechanistic actions in gene regulation.
  • The package aids in the integration and analysis of diverse genomic binding data.