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

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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
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...

You might also read

Related Articles

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

Sort by
Same author

Cross-chemical and cross-species toxicity prediction: benchmarking and a novel 3D-structure-based deep learning model.

Environmental toxicology and chemistry·2026
Same author

AKI-twinX: explainable organ structured digital twin for sepsis AKI trajectory forecasting.

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

Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction.

bioRxiv : the preprint server for biology·2026
Same author

FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra.

Nature communications·2025
Same author

Koina: Democratizing machine learning for proteomics research.

Nature communications·2025
Same author

Predicting the trend of SARS-CoV-2 mutation frequencies using historical data.

Bioinformatics (Oxford, England)·2025

Related Experiment Video

Updated: Jul 14, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis.

Seung-Hee Bae1, Haixu Tang, Jing Wu

  • 1Department of Computer Science, Indiana University - Bloomington, IN 47404, USA.

Bioinformatics (Oxford, England)
|June 7, 2007
PubMed
Summary

Identifying transcription factor binding sites (TFBSs) is challenging due to their short length. This study improves TFBS detection accuracy by integrating gene expression data with a novel search approach.

More Related Videos

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

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

Related Experiment Videos

Last Updated: Jul 14, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

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

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Transcription factor binding sites (TFBSs) are short DNA sequences recognized by transcription factors.
  • Traditional TFBS search methods using profile models often yield numerous false positives.
  • Integrating gene expression data can enhance the accuracy of TFBS identification.

Purpose of the Study:

  • To improve the sensitivity and specificity of TFBS detection.
  • To develop a computational tool for identifying TFBSs in gene promoter regions.
  • To leverage gene expression data for more accurate TFBS searches.

Main Methods:

  • Modification of the existing REFINEMENT approach.
  • Development of a new tool named dPattern.
  • Application of dPattern to search for TFBSs in promoter regions of differentially expressed and random genes.

Main Results:

  • The dPattern tool was developed based on the REFINEMENT approach.
  • dPattern effectively searches for TFBS occurrences in promoter regions.
  • The study demonstrates improved TFBS search accuracy by incorporating gene expression data.

Conclusions:

  • Combining gene expression data with profile models significantly enhances TFBS search accuracy.
  • The dPattern tool offers a more specific and sensitive method for TFBS identification.
  • This approach aids in understanding gene regulation by improving the identification of functional TFBSs.