Nucleic Acids Research, 2001, Vol. 29, No. 1 327-328
© 2001 Oxford University Press
The KMDB/MutationView: a mutation database for human disease genes
Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan, 1Department of Environmental Health Science and 2Department of Biochemistry, Setsunan University, Hirakata-shi, Osaka 573-0101, Japan
Received October 4, 2000; Accepted October 5, 2000.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONDATA CONTENTDISTRIBUTION OF THE DATABASEACCESSIBILITY AND AVAILABILITYREFERENCES |
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The KMDB/MutationView is a graphical database of mutations in human disease-causing genes and its current version consists of nine category-based sub-databases including diseases of eye, heart, ear, brain, cancer, syndrome, autoimmunity, muscle and blood. The KMDB/MutationView stores mutation data of 97 genes involved in 87 different disease and is accessible through http://mutview.dmb.med.keio.ac.jp.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONDATA CONTENTDISTRIBUTION OF THE DATABASEACCESSIBILITY AND AVAILABILITYREFERENCES |
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We previously developed the KMDB for mutation data in human disease-causing genes using a database software called MutationView, which was designed to serve as a distributed database system (1). The previous KMDB contained six category-based sub-databases such as KMeyeDB, KMheartDB, KMbrainDB, KMearDB, KMaiDB and KMcancerDB. Here, we report a more advanced version of KMDB (v. 1.2), which now includes three additional sub-databases such as KMsyndromeDB, KMmuscleDB and KMbloodDB with a substantial increase in genes and mutations.
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DATA CONTENT |
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TOPABSTRACTINTRODUCTIONDATA CONTENTDISTRIBUTION OF THE DATABASEACCESSIBILITY AND AVAILABILITYREFERENCES |
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The KMDB/MutationView has collected 3092 mutation entries from 606 literature sources, dealing with 97 genes involved in 87 distinct diseases (Fig. 1, top left; Table 1). The KMsyndromeDB deals with the syndromes such as Waardenburg syndrome, which is caused by single gene mutations. The KMaiDB collects mutations in the hereditary autoimmune diseases such as APECED (autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy). The KMmuscleDB deals with various neuromuscular diseases such as Duchenne muscular dystrophy and the KMbloodDB is designed for the genetic diseases of blood cells such as chronic myeloid leukemia and the genetic deficiencies in serum components such as albumin.
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Figure 1 shows the entrance window of KMDB/MutationView. Clicking a part of the body will show up a list of the associated diseases and genes (not shown). Choosing a genetic disease will bring up its mutation data displayed in the ‘gene structure window’. Figure 1 (top right) shows the gene structure of PARKIN which is a pathogenic gene for ARJP (autosomal recessive juvenile parkinsonism) (2). The gene structure can easily be switched to the nucleotide sequence and/or amino acid sequence. The frequency of each mutation type is shown as a histogram along with the genomic exon/intron strucutre. Details for each mutation can be seen by clicking the appropriate symbol listed in the ‘Help’ menu. Figure 1 (bottom right) shows the mutation detail for a large deletion mutation DelEx3-4 in the PARKIN gene.
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DISTRIBUTION OF THE DATABASE |
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TOPABSTRACTINTRODUCTIONDATA CONTENTDISTRIBUTION OF THE DATABASEACCESSIBILITY AND AVAILABILITYREFERENCES |
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The software MutationView was designed to manage and coordinate multiple category-based sub-databases located at different web sites. Currently, the coordinating server for KMDB/MutationView is located at Keio University, Tokyo, while a category-based KMcancerDB dealing with E-cadherin and ß-catenin mutations in cancer is located at Setsunan University, Osaka. Users can access all the data in KMDB/MutationView through Keio University.
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ACCESSIBILITY AND AVAILABILITY |
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TOPABSTRACTINTRODUCTIONDATA CONTENTDISTRIBUTION OF THE DATABASEACCESSIBILITY AND AVAILABILITYREFERENCES |
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The KMDB/MutationView employs Java1.1 interpreter for entire function and hence most Internet browsing softwares can be used except Netscape on a Macintosh (Apple computer, Inc.). The coordinating server of KMDB/MutationView is located at Keio University School of Medicine (URL: http://mutview.dmb.med.keio.ac.jp). The user ID and password are issued upon formal application through the above URL. The software MutationView is made available to any research groups that are interested in establishing a world-wide distributed database for disease gene mutations. For inquiries, contact the first author (mino{at}dmb.med.keio.ac.jp).
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ACKNOWLEDGEMENTS |
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We thank Chi Co., Ltd. for their extensive collaboration. This work was supported in part by a fund for the ‘Research for the Future’ Program from the Japan Society for the Promotion of Science (JSPS) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. We also thank The Nikkei Science Co. for the permission to use an illustration of the human body (3)
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FOOTNOTES |
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* To whom correspondence should be addressed. Tel: +81 3 5363 3755; Fax: +81 3 3351 2370; Email: shimizu{at}dmb.med.keio.ac.jp
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REFERENCES |
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TOPABSTRACTINTRODUCTIONDATA CONTENTDISTRIBUTION OF THE DATABASEACCESSIBILITY AND AVAILABILITYREFERENCES |
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1 Minoshima,S., Mitsuyama,S., Ohno,S., Kawamura,T. and Shimizu,N. (2000) Keio Mutation Database (KMDB) for human disease gene mutations. Nucleic Acids Res., 28, 364–368.
2 Kitada,T., Asakawa,S., Hattori,N., Matsumine,H., Yamamura,Y., Minoshima,S., Yokochi,M., Mizuno,Y. and Shimizu,N. (1998) Deletion mutation in a novel ubiquitin-like protein (PARKIN) gene causes autosomal recessive juvenile Parkinsonism (AR-JP). Nature, 392, 605–608,[Medline]
3 Welsh,M.J. and Smith,A.E. (1996) Cystic fibrosis. Nikkei Science, 26 (2), 90–99.
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