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

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Transcription Factors02:16

Transcription Factors

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...
Transcription Factors02:16

Transcription Factors

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...
General Transcription Factors01:30

General Transcription Factors

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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Combinatorial Gene Control02:33

Combinatorial Gene Control

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...

You might also read

Related Articles

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

Sort by
Same author

Extracting adverse event nature, severity, timelines and resulting interventions from clinical notes of patients receiving CAR-T therapy using large language models.

medRxiv : the preprint server for health sciences·2026
Same author

HIV-seq reveals gene expression differences between HIV-transcribing cells from viremic and suppressed people with HIV.

Nature communications·2026
Same author

Investigating CAR-T Treatment Access for Multiple Myeloma Patients Using Real-World Evidence.

Cancers·2026
Same author

Integrating expert knowledge into large language models improves performance for psychiatric reasoning and diagnosis.

Psychiatry research·2025
Same author

Extracting TNFi switching reasons and trajectories from real-world data using large language models.

JAMIA open·2025
Same author

Immunologic Profiling Suggests an Association Between Treg Cell Dysfunction and Pain in Knee Osteoarthritis.

Arthritis & rheumatology (Hoboken, N.J.)·2025

Related Experiment Video

Updated: May 10, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
09:58

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

Published on: June 27, 2020

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

Raymond K Auerbach1, Bin Chen, Atul J Butte

  • 1Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, Room X-163 MS-5415, Stanford, CA 94305, USA.

Bioinformatics (Oxford, England)
|June 5, 2013
PubMed
Summary
This summary is machine-generated.

Biomedical scientists can now easily identify enriched transcription factors in gene lists using the ENCODE ChIP-Seq Significance Tool. This web application leverages public ENCODE data for comparative functional analyses.

More Related Videos

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Published on: April 19, 2013

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Related Experiment Videos

Last Updated: May 10, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
09:58

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

Published on: June 27, 2020

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Published on: April 19, 2013

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Biological analysis is evolving from gene identification to functional mapping.
  • The ENCODE Project provides extensive ChIP-Seq data, but accessible analysis tools are limited.
  • Existing tools often lack flexibility for broad biological questions.

Purpose of the Study:

  • To present a flexible web application for analyzing ENCODE ChIP-Seq data.
  • To enable identification of enriched transcription factors in gene or transcript lists.
  • To facilitate comparative analyses for biomedical scientists.

Main Methods:

  • Developed the ENCODE ChIP-Seq Significance Tool as a web application.
  • Utilized client-side JavaScript and server-side PHP, R, and MySQL.
  • Ensured cross-browser compatibility (Chrome, Safari, Firefox).

Main Results:

  • The tool successfully leverages public ENCODE ChIP-Seq data.
  • It identifies enriched transcription factors within user-provided gene or transcript lists.
  • The application supports comparative analyses of functional genomics data.

Conclusions:

  • The ENCODE ChIP-Seq Significance Tool offers a flexible solution for analyzing large-scale ChIP-Seq datasets.
  • It empowers biomedical scientists to explore transcription factor enrichment and functional relationships.
  • This tool enhances the utility of public ENCODE data for biological discovery.