Strategies for Enhanced Annotation of a Microarray Probe Set
TuShun R. Powers, Selene M. Virk and
Elba E. Serrano
We aim to determine the biological relevance of genes identified through
microarray-mediated transcriptional profiling
of Xenopus sensory organs and brain tissue. Genetic data analysis
depends on how, and to what extent, the probe sets for genes
represented on the microarray are characterized. Difficulties can
arise when probe set annotation is used to interpret expression
data because of limitations to the amount of available information
and the lack of a universal gene nomenclature. To address
these potential impediments, we used three curation strategies to
augment the annotation of probe sets on a commercially available
microarray by using sequence based and semantic linking
methods in combination with computational approaches. Our
curation efforts enabled linkage of our probe sets and expression
data to public access databases. We found that each curation
process contributed to the enhancement of the vendor supplied
annotation and also assisted with the tentative identification of
previously unidentified probe set IDs. Our methods provide an
alternative to the use of proprietary data analysis software to gain
biological significance from microarray data. These approaches
may be especially useful for laboratories investigating less studied
organisms and species whose genomes have not been sequenced.
Index Terms
Bioinformatics, data mining, gene identification, inner ear, mechanosensory hair cell.
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