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Bioinformatics Advance Access originally published online on October 21, 2008
Bioinformatics 2008 24(24):2918-2920; doi:10.1093/bioinformatics/btn542
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data

Matteo Cesaroni 1,*, Davide Cittaro 2, Alessandro Brozzi 1, Pier Giuseppe Pelicci 1 and Lucilla Luzi 3,*

1Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano, 2Cogentech, Consortium for Genomic Technologies, Via Adamello 16, 20139 Milano and 3IFOM, FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milano, Italy

*To whom correspondence should be addressed.


  Abstract

Summary: CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.

Availability: http://bio.ifom-ieo-campus.it/galaxy

Contacts: matteo.cesaroni{at}ifom-ieo-campus.it; lucilla.luzi{at}ifom-ieo-campus.it

Associate Editor: Alfonso Valencia

Received on April 11, 2008; revised on August 29, 2008; accepted on October 17, 2008

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