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
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
Authors: Nagesha A S Rao; Melysia T McCalman; Panagiotis Moulos; Kees-Jan Francoijs; Aristotelis Chatziioannou; Fragiskos N Kolisis; Michael N Alexis; Dimitra J Mitsiou; Hendrik G Stunnenberg Journal: Genome Res Date: 2011-07-12 Impact factor: 9.043
Authors: Cory Y McLean; Dave Bristor; Michael Hiller; Shoa L Clarke; Bruce T Schaar; Craig B Lowe; Aaron M Wenger; Gill Bejerano Journal: Nat Biotechnol Date: 2010-05-02 Impact factor: 54.908
Authors: Michiel Vermeulen; H Christian Eberl; Filomena Matarese; Hendrik Marks; Sergei Denissov; Falk Butter; Kenneth K Lee; Jesper V Olsen; Anthony A Hyman; Henk G Stunnenberg; Matthias Mann Journal: Cell Date: 2010-09-17 Impact factor: 41.582
Authors: David L M van der Meer; Tatjana Degenhardt; Sami Väisänen; Philip J de Groot; Merja Heinäniemi; Sacco C de Vries; Michael Müller; Carsten Carlberg; Sander Kersten Journal: Nucleic Acids Res Date: 2010-01-27 Impact factor: 16.971
Authors: Anja Nitzsche; Maciej Paszkowski-Rogacz; Filomena Matarese; Eva M Janssen-Megens; Nina C Hubner; Herbert Schulz; Ingrid de Vries; Li Ding; Norbert Huebner; Matthias Mann; Hendrik G Stunnenberg; Frank Buchholz Journal: PLoS One Date: 2011-05-12 Impact factor: 3.240
Authors: Chi-Yi Yu; Oleg Mayba; Joyce V Lee; Joanna Tran; Charlie Harris; Terence P Speed; Jen-Chywan Wang Journal: PLoS One Date: 2010-12-20 Impact factor: 3.240
Authors: Jamie M Kramer; Korinna Kochinke; Merel A W Oortveld; Hendrik Marks; Daniela Kramer; Eiko K de Jong; Zoltan Asztalos; J Timothy Westwood; Hendrik G Stunnenberg; Marla B Sokolowski; Krystyna Keleman; Huiqing Zhou; Hans van Bokhoven; Annette Schenck Journal: PLoS Biol Date: 2011-01-04 Impact factor: 8.029