SHIELD: an integrative gene expression database for inner ear research

Abstract

The inner ear is a highly specialized mechanosensitive organ responsible for hearing and balance. Its small size and difficulty in harvesting sufficient tissue has hindered the progress of molecular studies. The protein components of mechanotransduction, the molecular biology of inner ear development and the genetic causes of many hereditary hearing and balance disorders remain largely unknown. Inner-ear gene expression data will help illuminate each of these areas. For over a decade, our laboratories and others have generated extensive sets of gene expression data for different cell types in the inner ear using various sample preparation methods and high-throughput genome-wide approaches. To facilitate the study of genes in the inner ear by efficient presentation of the accumulated data and to foster collaboration among investigators, we have developed the Shared Harvard Inner Ear Laboratory Database (SHIELD), an integrated resource that seeks to compile, organize and analyse the genomic, transcriptomic and proteomic knowledge of the inner ear. Five datasets are currently available. These datasets are combined in a relational database that integrates experimental data and annotations relevant to the inner ear. The SHIELD has a searchable web interface with two data retrieval options: viewing the gene pages online or downloading individual datasets as data tables. Each retrieved gene page shows the gene expression data and detailed gene information with hyperlinks to other online databases with up-to-date annotations. Downloadable data tables, for more convenient offline data analysis, are derived from publications and are current as of the time of publication. The SHIELD has made published and some unpublished data freely available to the public with the hope and expectation of accelerating discovery in the molecular biology of balance, hearing and deafness.

Figure 1.

Architecture of the SHIELD. The URLs to external resources are HGNC, HUGO Gene Nomenclature Committee (http://www.genenames.org/); HHH, the Hereditary Hearing loss Homepage (http://hereditaryhearingloss.org/); NCBI, National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/); MGI, Mouse Genome Informatics (http://www.informatics.jax.org/); OMIM Online Mendelian Inheritance in Man (http://www.omim.org/), UCSC, UCSC Genome Bioinformatics (https://genome.ucsc.edu/) and UniProt, the Universal Protein Resource (http://www.uniprot.org/). ‘TM pred.’ refers to manually annotated transmembrane domain prediction. Abbreviations for the datasets are explained in Table 1. ‘+’ and ‘*’ indicate unpublished data and unpublished statistical analysis available in the SHIELD. The line under ‘Annotation w/ hyperlinks’ represents clickable hyperlinks to other resources.

Figure 2.

The Web Portal of the SHIELD. The homepage of the SHIELD shows the site logo, the menu, a brief introduction to the site, and news. At the bottom are the logos of the participating institutions and funding agencies.