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


METHODS
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Folkersen
Lasse
L
Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden. lasse.folkersen@ki.se
Diez
Diego
D
Wheelock
Craig E
CE
Haeggström
Jesper Z
JZ
Goto
Susumu
S
Eriksson
Per
P
Gabrielsen
Anders
A
D003198:Computer Simulation; D030541:Databases, Genetic; D016678:Genome; D005838:Genotype; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface