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

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray

Victor X Jin1, Alina Rabinovich, Sharon L Squazzo

  • 1Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

Genome Research
|October 21, 2006
PubMed
Summary

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

High-resolution Hi-C profiling of human breast tissues using an optimized protocol for clinical samples.

STAR protocols·2026
Same author

Single-dose cathepsin L CRISPR nanotherapy mitigates PASC-like lung damage in hamsters.

Nano research·2025
Same author

Editorial Expression of Concern: Bcl-6 mediates the germinal center B cell phenotype and lymphomagenesis through transcriptional repression of the DNA-damage sensor ATR.

Nature immunology·2025
Same author

WITHDRAWN: Phosphorylation of EZH2 by AMPK Suppresses PRC2 Methyltransferase Activity and Oncogenic Function.

Molecular cell·2025
Same author

Phosphorylation of EZH2 by AMPK Suppresses PRC2 Methyltransferase Activity and Oncogenic Function.

Molecular cell·2025
Same author

Amprenavir Mitigates Pepsin-Induced Transcriptomic Changes in Normal and Precancerous Esophageal Cells.

International journal of molecular sciences·2025

We developed ChIPModules, a computational genomics method to identify gene regulatory modules. This approach accurately predicts transcription factor binding sites and reveals novel regulatory interactions, such as E2F1 and AP-2alpha colocalization.

Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • High-throughput technologies like ChIP-chip and completed genome sequences enable systems-level analysis of gene regulation.
  • Understanding transcriptional regulatory modules is crucial for deciphering gene expression mechanisms.

Purpose of the Study:

  • To develop a computational genomics approach (ChIPModules) for identifying transcriptional regulatory modules.
  • To integrate experimental binding site data with computational methods for enhanced accuracy.
  • To discover novel regulatory modules and interactions for transcription factors like E2F1.

Main Methods:

  • Developed the ChIPModules computational genomics approach.
  • Integrated ChIP-chip data, positional weight matrices, comparative genomics, and statistical learning.

Related Experiment Videos

  • Utilized E2F1 binding site information from ENCODE regions in HeLa and MCF7 cells.
  • Validated predictions using ChIP-chip assays on a large human promoter array.

    • Main Results:

    • ChIPModules distinguished transcription factor targets from non-targets with high specificity.
    • Identified five novel regulatory modules for E2F1.
    • Predicted and experimentally validated colocalization of E2F1 and AP-2alpha on target promoters.
    • Developed a database of computationally identified and experimentally verified E2F1 target promoters.

    Conclusions:

    • The ChIPModules approach is a powerful, sequence-based, unbiased, and universal protocol for identifying transcriptional regulatory modules.
    • Demonstrated the utility of computational genomics in uncovering complex gene regulatory networks.
    • The developed database provides a valuable resource for researchers studying E2F1-mediated gene regulation.