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Open Access Technical Note

The PinkThing for analysing ChIP profiling data in their genomic context

Fiona G Nielsen12*, Maarten Kooyman1, Philip Kensche1, Hendrik Marks2, Henk Stunnenberg2 and Martijn Huynen1

Author Affiliations

1 CMBI - Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, PO box 9101, 6500HB Nijmegen, Netherlands

2 Department of Molecular Biology, Radboud University Nijmegen, Nijmegen Centre for Molecular Life Sciences, PO box 9101, 6500HB Nijmegen, Netherlands

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BMC Research Notes 2013, 6:133  doi:10.1186/1756-0500-6-133

Published: 4 April 2013

Abstract

Background

Current epigenetic research makes frequent use of whole-genome ChIP profiling for determining the in vivo binding of proteins, e.g. transcription factors and histones, to DNA. Two important and recurrent questions for these large scale analyses are: 1) What is the genomic distribution of a set of binding sites? and 2) Does this genomic distribution differ significantly from another set of sites?

Findings

We exemplify the functionality of the PinkThing by analysing a ChIP profiling dataset of cohesin binding sites. We show the subset of cohesin sites with no CTCF binding have a characteristic genomic distribution different from the set of all cohesin sites.

Conclusions

The PinkThing is a web application for fast and easy analysis of the context of genomic loci, such as peaks from ChIP profiling experiments. The output of the PinkThing analysis includes: categorisation of position relative to genes (intronic, exonic, 5’ near, 3’ near 5’ far, 3’ far and distant), distance to the closest annotated 3’ and 5’ end of genes, direction of transcription of the nearest gene, and the option to include other genomic elements like ESTs and CpG islands. The PinkThing enables easy statistical comparison between experiments, i.e. experimental versus background sets, reporting over- and underrepresentation as well as p-values for all comparisons. Access and use of the PinkThing is free and open (without registration) to all users via the website: http://pinkthing.cmbi.ru.nl webcite