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

Master Transcription Regulators02:23

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
Master Transcription Regulators02:23

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...

You might also read

Related Articles

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

Sort by
Same author

Context-aware sequence-to-function model of human gene regulation.

Nature communications·2026
Same author

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same author

Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs.

Communications biology·2026
Same author

Early neutrophil infiltration promotes TRIMELVax-induced antitumor immunity by linking local inflammation to tumor control.

Oncoimmunology·2026
Same author

Modeling strategies for <i>in vivo</i> transcription factor binding predictions.

Bioinformatics advances·2026
Same author

The measurement method matters.

IUCrJ·2026

Related Experiment Video

Updated: Jun 12, 2026

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets
03:37

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets

Published on: March 1, 2024

TransFind--predicting transcriptional regulators for gene sets.

Szymon M Kiełbasa1, Holger Klein, Helge G Roider

  • 1Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany. kielbasa@molgen.mpg.de

Nucleic Acids Research
|June 1, 2010
PubMed
Summary

Researchers developed TransFind, a web server for analyzing transcription factor binding sites. This tool aids in understanding gene expression by combining prediction methods with phylogenetic analysis for regulatory network characterization.

More Related Videos

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
07:23

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Related Experiment Videos

Last Updated: Jun 12, 2026

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets
03:37

Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets

Published on: March 1, 2024

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
07:23

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Analyzing transcription factor binding sites in gene promoters helps infer regulatory factors driving gene expression changes.
  • In-silico characterization of transcriptional regulatory networks is crucial but lacks user-friendly tools combining advanced methods.

Purpose of the Study:

  • To develop a web server, TransFind, that integrates state-of-the-art prediction methods, phylogenetic analysis, and multiple testing corrected statistics.
  • To provide a fast and accessible platform for the in-silico analysis of transcription factor binding sites in coregulated genes.

Main Methods:

  • Development of the TransFind web server (http://transfind.sys-bio.net/).
  • Integration of advanced prediction algorithms for transcription factor binding sites.
  • Incorporation of phylogenetic analysis and robust statistical correction methods.

Main Results:

  • TransFind offers a user-friendly interface for analyzing promoter regions.
  • The server combines multiple prediction tools with phylogenetic analysis.
  • It provides statistically corrected results for identifying transcription factors.

Conclusions:

  • TransFind addresses the need for an efficient and comprehensive web server for regulatory network analysis.
  • The tool facilitates the inference of transcription factors from gene expression data.
  • It is freely available to researchers for in-silico characterization of transcriptional regulation.