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Bioinformatics Advance Access originally published online on April 27, 2009
Bioinformatics 2009 25(15):1978-1979; doi:10.1093/bioinformatics/btp279
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome

Lasse Folkersen 1,*, Diego Diez 2, Craig E. Wheelock 3, Jesper Z. Haeggström 3, Susumu Goto 2, Per Eriksson 1 and Anders Gabrielsen 1

1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden

* To whom correspondence should be addressed.


  Abstract

Summary: Whole-genome microarrays allow us to interrogate the entire transcriptome of a cell. Affymetrix microarrays are constructed using several probes that match to different regions of a gene and a summarization step reduces this complexity into a single value, representing the expression level of the gene or the expression level of an exon in the case of exon arrays. However, this simplification eliminates information that might be useful when focusing on specific genes of interest. To address these limitations, we present a software package for the R platform that allows detailed analysis of expression at the probe level. The package matches the probe sequences against a target gene sequence (either mRNA or DNA) and shows the expression levels of each probe along the gene. It also features functions to fit a linear regression based on several genetic models that enables study of the relationship between gene expression and genotype.

Availability and implementation: The software is implemented as a platform-independent R package available through the Bioconductor repository at http://www.bioconductor.org/. It is licensed as GPL 2.0.

Contact: lasse.folkersen{at}ki.se

Supplementary Information: Supplementary data are available at Bioinformatics online.

Associate Editor: David Rocke

Received on March 13, 2009; revised on April 6, 2009; accepted on April 20, 2009

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