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Abstract:
Microarray technologies are established approaches for high throughput
gene expression, methylation and genotyping analysis. An accurate
mapping of the array probes is essential to generate reliable biological
findings. However, manufacturers of the microarray platforms typically
provide incomplete and outdated annotation tables, which often rely on
older genome and transcriptome versions that differ substantially from
up-to-date sequence databases. Here, we present the Re-Annotator, a
re-annotation pipeline for microarray probe sequences. It is primarily
designed for gene expression microarrays but can also be adapted to
other types of microarrays. The Re-Annotator uses a custom-built mRNA
reference database to identify the positions of gene expression array
probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4
microarray platform and found that about one quarter (25%) of the probes
differed from the manufacturer's annotation. In further computational
experiments on experimental gene expression data, we compared
Re-Annotator to another probe re-annotation tool, ReMOAT, and found that
Re-Annotator provided an improved re-annotation of microarray probes. A
thorough re-annotation of probe information is crucial to any microarray
analysis. The Re-Annotator pipeline is freely available at
http://sourceforge.net/projects/reannotator along with re-annotated
files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.
