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Chromatin Immunoprecipitation (ChIP) using Drosophila tissue
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The PinkThing for analysing ChIP profiling data in their genomic context.

Fiona G Nielsen1, Maarten Kooyman, Philip Kensche

  • 1CMBI-Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, PO Box 9101, 6500HB Nijmegen, Netherlands. fnielsen@cmbi.ru.nl

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|April 6, 2013
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Summary

The PinkThing web application analyzes genomic loci, such as ChIP-seq binding sites. It reveals that cohesin binding sites without CTCF show a distinct genomic distribution compared to all cohesin sites.

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • Whole-genome ChIP-profiling is crucial for epigenetic research, determining in vivo protein-DNA binding.
  • Key questions involve analyzing the genomic distribution of binding sites and comparing distributions between datasets.

Purpose of the Study:

  • To introduce PinkThing, a web application for analyzing the genomic context of loci.
  • To demonstrate PinkThing's utility in comparing ChIP-profiling datasets.

Main Methods:

  • Utilized PinkThing to analyze a ChIP-profiling dataset of cohesin binding sites.
  • Compared the genomic distribution of cohesin sites with and without CTCF binding.

Main Results:

  • PinkThing provides detailed categorization of genomic loci relative to genes (intronic, exonic, etc.).
  • Analysis showed cohesin sites lacking CTCF exhibit a characteristic genomic distribution distinct from all cohesin sites.

Conclusions:

  • PinkThing offers fast, free, and open web-based analysis of genomic loci.
  • The tool facilitates statistical comparisons between experimental and background sets, reporting over/underrepresentation and p-values.