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 Experiment Videos

Mining ChIP-chip data for transcription factor and cofactor binding sites.

Andrew D Smith1, Pavel Sumazin, Debopriya Das

  • 1Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. asmith@cshl.edu

Bioinformatics (Oxford, England)
|June 18, 2005
PubMed
Summary

We developed a new method to find DNA binding motifs and their interactions using ChIP-chip data. This approach accurately predicts transcription factor localization and gene expression in specific tissues.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage.

Nature communications·2026
Same author

Catalytic Enantioselective Dearomatizing [2,3]-Wittig Rearrangements Allow Divergent [2,3]-, [1,2]-, and Sommelet-Hauser-Type Products.

Journal of the American Chemical Society·2026
Same author

The acylative kinetic resolution of 1,2-azaborine naphthols.

Chemical science·2026
Same author

Association Between Gastroesophageal Reflux Disease and Frequency of Asthma Exacerbations: A Systematic Review and Meta-Analysis.

Cureus·2026
Same author

The catalytic enantioselective [1,2]-Wittig rearrangement cascade of allylic ethers.

Nature chemistry·2026
Same author

Aspirin Use in Secondary Prevention of Myocardial Infarction: A Systematic Review and Meta-Analysis.

Cureus·2025

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying regulatory elements in DNA is crucial for understanding gene expression.
  • Transcription factor binding site motifs are key to gene regulation.
  • ChIP-chip data provides insights into where transcription factors bind to DNA.

Purpose of the Study:

  • To develop a novel computational methodology for de novo identification of individual and interacting transcription factor binding site motifs.
  • To integrate transcription factor localization data directly into the motif discovery process.
  • To evaluate the predictive power of identified motifs for both transcription factor localization and gene expression.

Main Methods:

  • A de novo motif discovery algorithm was developed, combining matrix-enumeration with multivariate regression.

Related Experiment Videos

  • The algorithm integrates transcription factor localization data directly into the motif discovery process.
  • Candidate motifs and their interactions were evaluated for their ability to predict localization and gene expression.

    • Main Results:

    • The methodology successfully identified novel and improved known motifs from ChIP-chip data.
    • Interaction models of HNF1 and CDP motifs demonstrated excellent prediction of HNF1 localization and gene expression in liver tissue.
    • The study confirmed that ChIP-chip data can be effectively utilized to discover interacting binding site motifs.

    Conclusions:

    • The developed computational approach enables the identification of interacting binding site motifs from ChIP-chip data.
    • This method enhances the prediction of transcription factor localization and tissue-specific gene expression.
    • The findings highlight the importance of considering motif interactions in regulatory element identification.