The PinkThing for analysing ChIP profiling data in their genomic context

Fiona G Nielsen,Martijn Huynen,Henk Stunnenberg,Philip Kensche,Hendrik Marks,Maarten Kooyman

doi:10.1186/1756-0500-6-133

Abstract

BackgroundCurrent 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?FindingsWe 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.ConclusionsThe 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

Highlights

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
Transcription factor (TF) binding sites can be identified in vivo using the emerging technologies for ChIP profiling such as ChIP-on-chip and ChIP-sequencing
The PinkThing provides the option of supplying an appropriate background distribution to be used for comparisons, e.g. the set of all binding sites of a ChIP-seq experiment when examining a subset of these sites

Summary

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

Background

Methods

Conclusion

Sanderson L