The human intermediate filament database: Comprehensive information on a gene family involved in many human diseases

Authors

Ildiko Szeverenyi, A-Star, Institute of Medical Biology
Andrew J. Cassidy, University of Dundee School of Medicine
Wang Chung Cheuk, A-Star, Bioinformatics Institute
Bernett T.K. Lee, A-Star, Bioinformatics Institute
John E.A. Common, A-Star, Institute of Medical Biology
Stephen C. Ogg, A-Star, Institute of Medical Biology
Huijia Chen, A-Star, Institute of Medical Biology
Yin Sim Shu, A-Star, Institute of Medical Biology
Walter L.P. Goh, A-Star, Institute of Medical Biology
Woei Ng Kee, A-Star, Institute of Medical Biology
John A. Simpson, University of Dundee
Lian Chee Li, A-Star, Institute of Medical Biology
Hui Eng Goi, A-Star, Institute of Medical Biology
Bin Li, A-Star, Institute of Medical Biology
Declan P. Lunny, A-Star, Institute of Medical Biology
Danny Chuon, A-Star, Bioinformatics Institute
Aparna Venkatesh, A-Star, Institute of Medical Biology
Hoe Khoo Kian, A-Star, Institute of Medical Biology
W. H.Irwin McLean, University of Dundee School of Medicine
Ping Lim Yun, A-Star, Bioinformatics Institute
E. Birgitte Lane, A-Star, Institute of Medical Biology

Document Type

Article

Publication Date

3-1-2008

Abstract

We describe a revised and expanded database on human intermediate filament proteins, a major component of the eukaryotic cytoskeleton. The family of 70 intermediate filament genes (including those encoding keratins, desmins, and lamins) is now known to be associated with a wide range of diverse diseases, at least 72 distinct human pathologies, including skin blistering, muscular dystrophy, cardiomyopathy, premature aging syndromes, neurodegenerative disorders, and cataract. To date, the database catalogs 1,274 manually-curated pathogenic sequence variants and 170 allelic variants in intermediate filament genes from over 459 peer-reviewed research articles. Unrelated cases were collected from all of the six sequence homology groups and the sequence variations were described at cDNA and protein levels with links to the related diseases and reference articles. The mutations and polymorphisms are presented in parallel with data on protein structure, gene, and chromosomal location and basic information on associated diseases. Detailed statistics relating to the variants records in the database are displayed by homology group, mutation type, affected domain, associated diseases, and nucleic and amino acid substitutions. Multiple sequence alignment algorithms can be run from queries to determine DNA or protein sequence conservation. Literature sources can be interrogated within the database and external links are provided to public databases. The database is freely and publicly accessible online at www.interfil.org (last accessed 13 September 2007). Users can query the database by various keywords and the search results can be downloaded. It is anticipated that the Human Intermediate Filament Database (HIFD) will provide a useful resource to study human genome variations for basic scientists, clinicians, and students alike. © 2007 Wiley-Liss, Inc.

Publication Source (Journal or Book title)

Human Mutation

First Page

351

Last Page

360

Recommended Citation

Szeverenyi, I., Cassidy, A., Cheuk, W., Lee, B., Common, J., Ogg, S., Chen, H., Shu, Y., Goh, W., Kee, W., Simpson, J., Li, L., Goi, H., Li, B., Lunny, D., Chuon, D., Venkatesh, A., Kian, H., McLean, W., Yun, P., & Lane, E. (2008). The human intermediate filament database: Comprehensive information on a gene family involved in many human diseases. Human Mutation, 29 (3), 351-360. https://doi.org/10.1002/humu.20652