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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...
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hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.

Li Chen1, George Wu, Hongkai Ji

  • 1Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.

Bioinformatics (Oxford, England)
|April 1, 2011
PubMed
Summary

The hmChIP database offers a comprehensive resource for human and mouse chromatin immunoprecipitation (ChIP) data. It enables exploration of protein-DNA interactions across various experiments and samples.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin immunoprecipitation (ChIP) is crucial for understanding protein-DNA interactions.
  • Existing ChIP data is often fragmented, hindering large-scale analysis.
  • The hmChIP database consolidates human and mouse ChIP data.

Purpose of the Study:

  • To create a centralized, accessible database of genome-wide chromatin immunoprecipitation data.
  • To provide a web interface for querying and analyzing protein-DNA binding intensities.
  • To facilitate the exploration of combinatorial patterns and cell-type specificities in protein-DNA interactions.

Main Methods:

  • Compilation of 2016 samples from 492 ChIP-seq and ChIP-chip experiments.
  • Development of a web server for database access and querying.
  • Retrieval of protein-DNA binding intensities for user-defined genomic regions.

Main Results:

  • The database contains data for 170 proteins and over 11 million protein-DNA interactions.
  • Users can retrieve binding intensities to analyze sample and genomic region clusters.
  • The data supports the investigation of combinatorial binding and cross-sample variability.

Conclusions:

  • hmChIP serves as a valuable resource for researchers studying protein-DNA interactions.
  • The database facilitates the analysis of complex regulatory mechanisms.
  • It enables deeper insights into cell-type specific and combinatorial protein-DNA binding patterns.