PUBLICATION
Ion Channel Gene Expression in the Inner Ear
- Authors
- Gabashvili, I.S., Sokolowski, B.H., Morton, C.C., and Giersch, A.B.
- ID
- ZDB-PUB-070625-1
- Date
- 2007
- Source
- Journal of the Association for Research in Otolaryngology : JARO 8(3): 305-328 (Journal)
- Registered Authors
- Keywords
- hearing, ionic currents, ion channels, genome, EST mapping, expressed sequence tags, splice variants, alternative transcripts
- MeSH Terms
-
- Amino Acid Sequence
- Animals
- DNA, Complementary/genetics
- Ear, Inner/metabolism*
- Expressed Sequence Tags
- Gene Expression Profiling
- Gene Expression Regulation
- Genome/genetics
- Humans
- Ion Channels/genetics*
- Ion Channels/metabolism*
- Mice
- Molecular Sequence Data
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Rats
- Signal Transduction
- Zebrafish
- PubMed
- 17541769 Full text @ J. Assoc. Res. Otolaryngol.
Citation
Gabashvili, I.S., Sokolowski, B.H., Morton, C.C., and Giersch, A.B. (2007) Ion Channel Gene Expression in the Inner Ear. Journal of the Association for Research in Otolaryngology : JARO. 8(3):305-328.
Abstract
The ion channel genome is still being defined despite numerous publications on the subject. The ion channel transcriptome is even more difficult to assess. Using high-throughput computational tools, we surveyed all available inner ear cDNA libraries to identify genes coding for ion channels. We mapped over 100,000 expressed sequence tags (ESTs) derived from human cochlea, mouse organ of Corti, mouse and zebrafish inner ear, and rat vestibular end organs to Homo sapiens, Mus musculus, Danio rerio, and Rattus norvegicus genomes. A survey of EST data alone reveals that at least a third of the ion channel genome is expressed in the inner ear, with highest expression occurring in hair cell-enriched mouse organ of Corti and rat vestibule. Our data and comparisons with other experimental techniques that measure gene expression show that every method has its limitations and does not per se provide a complete coverage of the inner ear ion channelome. In addition, the data show that most genes produce alternative transcripts with the same spectrum across multiple organisms, no ion channel gene variants are unique to the inner ear, and many splice variants have yet to be annotated. Our high-throughput approach offers a qualitative computational and experimental analysis of ion channel genes in inner ear cDNA collections. A lack of data and incomplete gene annotations prevent both rigorous statistical analyses and comparisons of entire ion channelomes derived from different tissues and organisms.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping