Strategies for enhanced annotation of a microarray probe set

Powers, TuShun R.; Virk, Selene; Serrano, Elba E.

doi:10.1504/ijbra.2010.032119

Cited by 1 publication

(4 citation statements)

References 17 publications

(19 reference statements)

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“…Powers et al [55] implemented manual and large-scale computational approaches to expand annotation of the X. laevis GeneChip® Xl-PSIDs by linkage to ion channel genes, HGNC symbols identified via UniGene cluster IDs, or Swiss-Prot proteins from multiple species (human, mouse, fly and worm). Similar manual approaches were used to link X. laevis GeneChip® Xl-PSIDs to five categories of genes with expected inner ear function: (1) inner ear tissue genes, IET; (2) genes implicated in human deafness, DF; (3) genes for ion channels, IC, (4) genes for ion transport, IT; and (5) genes for transcription factors, pTF (see Additional file 2).…”

Section: Methodsmentioning

confidence: 99%

“…Consequently, the IT category of 370 genes was represented by 180 IT/Xl-PSIDs. Manual curation efforts as described in Powers et al [55] ensured that all IT/Xl-PSIDs identified by keyword query of the X. laevis GeneChip® annotation file were linked to ion transport in primary literature or other online databases. Several ion transport genes were found to be represented by multiple Xl-PSIDs on the X. laevis GeneChip®.…”

Section: Methodsmentioning

confidence: 99%

“…Protein sequences from IET, DF, and IC gene lists were collected from Ensembl [92] with the Biomart data-mining tool as described in Powers et al [55]. BLAST algorithms (standalone BLAST version 2.2.15; TBLASTN and BLASTP, [93]) were used to compare sequences from the gene lists to X. laevis GeneChip® Xl-PSID consensus sequences [61] and to predicted proteins from the X. tropicalis genome assembly (4.1; proteins.Xentr4.fasta.gz, Xt4.1 predicted proteins [94,95]).…”

Section: Methodsmentioning

confidence: 99%

“…In order to relate prior knowledge of genes with predicted inner ear function to the X. laevis inner ear transcriptome, we focused our X. laevis GeneChip® annotation efforts on five inner ear gene categories: genes that encode ion channels (IC), ion transporters (IT), and transcription factors (pTF); genes found in inner ear tissue (IET); and genes with mutations that cause deafness (DF). Sequence similarity mapping, semantic keyword querying and the XenEnhance relational database [55] enabled linkage of the more informative official gene symbols from the HUGO Gene Nomenclature Committee (HGNC, [56]) to a subset of Xl-PSIDs on the X. laevis GeneChip® [54,55]. Throughout this paper we use the HGNC nomenclature to refer to genes of interest.…”

Section: Introductionmentioning

confidence: 99%

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Probing the Xenopus laevis inner ear transcriptome for biological function

et al. 2012

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BackgroundThe 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 Xenopus 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 Xenopus laevis inner ear transcriptome through microarray analysis.ResultsMicroarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus 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 Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization.ConclusionsWe 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 Xenopus inner ear transcriptome, thereby addressing the impediment imposed by insufficient gene annotation. These findings heighten the relevance of Xenopus as a model organism for genetic investigations of inner ear organogenesis, morphogenesis, and regeneration.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%