Probing the <it>Xenopus laevis</it> inner ear transcriptome for biological function

<p><b>Abstract</b></p> <p><b>Background</b></p> <p>The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus <it>Xenopus</it> is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the <it>Xenopus laevis</it> inner ear transcriptome through microarray analysis.</p> <p><b>Results</b></p> <p>Microarray analysis uncovered genes within the <it>X. laevis</it> inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of <it>Xenopus</it> in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors) facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the <it>Affymetrix</it> GeneChip® <it>Xenopus laevis</it> Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization.</p> <p><b>Conclusions</b></p> <p>We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the <it>Xenopus</it> inner ear transcriptome, thereby addressing the impediment imposed by insufficient gene annotation. These findings heighten the relevance of <it>Xenopus</it> as a model organism for genetic investigations of inner ear organogenesis, morphogenesis, and regeneration.</p

MOESM1 of RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance

Additional file 1. Master table for Xenopus OMIM auditory and vestibular genes. This spreadsheet contains the list of OMIM® deafness and vestibular disorder genes, mappings to the JGI predicted proteins and Xl-PSID’S (E-value for alignment, E-value for expression, scaffold number and coordinates), RNA-Seq reads associated with each OMIM® gene and microarray GCRMA value for each OMIM® gene. The original data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and can be accessed under GEO Series accession numbers GSE69701 (RNA-Seq) and GSE73829 (microarray)