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

Matteo Cesaroni, Davide Cittaro, Alessandro Brozzi, Pier Giuseppe Pelicci, Lucilla Luzi

Research output: Contribution to journalArticle

22 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2918-2920
Number of pages3
JournalBioinformatics
Volume24
Issue number24
DOIs
Publication statusPublished - Dec 2008

Fingerprint

Boidae
Tiling
Quality Control
Web-based
Chip
Genes
Genome
Gene Expression
Quality control
Data acquisition
Experiments
Python
Normalization
Genomics
Annotation
Experimental Data
Gene
Graph in graph theory

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

CARPET : A web-based package for the analysis of ChIP-chip and expression tiling data. / Cesaroni, Matteo; Cittaro, Davide; Brozzi, Alessandro; Pelicci, Pier Giuseppe; Luzi, Lucilla.

In: Bioinformatics, Vol. 24, No. 24, 12.2008, p. 2918-2920.

Research output: Contribution to journalArticle

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