Abstract
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.
INTRODUCTION
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.
DATA CONTENT
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.
Figure 1.
Features of the KMDB/MutationView. (Top left) Entrance window. (Bottom left) Anatomy window of MutationView. (Bottom middle) Anatomy window of KMearDB. (Top right) Gene structure window of KMbrainDB showing PARKIN gene with a histogram of mutation frequencies. (Bottom right) Mutation details window showing DelEx3-4 mutation in the PARKIN gene. See text for details.
Table 1. Mutation data in the KMDB/MutationView.
| Category |
Number of diseases |
Number of genes |
Number of
mutation entries |
Number of literature references compiled |
| Eye | 24 | 23a | 385 | 112 |
| Heart | 7 | 7 | 79 | 19 |
| Ear | 3 | 11a | 49 | 21 |
| Brain/nerve | 10 | 11a | 227 | 77 |
| Cancer-related | 8 | 8 | 1303 | 164 |
| Syndrome | 15 | 17a | 855 | 159 |
| Autoimmunity | 2 | 2 | 96 | 13 |
| Muscle | 3 | 3 | 42 | 15 |
| Blood | 4 | 4 | 13 | 7 |
| Miscellaneous | 11 | 11 | 43 | 19 |
| Total | 87 | 97 | 3092 | 606 |
aThe number of diseases does not necessarily match with the number of genes because it has been known that some diseases with different clinical symptoms are caused by different mutation types in the same gene and other diseases with a common clinical phenotype are caused by multiple different genes involved in a certain physiological pathway.
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.
DISTRIBUTION OF THE DATABASE
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 β-catenin mutations in cancer is located at Setsunan University, Osaka. Users can access all the data in KMDB/MutationView through Keio University.
ACCESSIBILITY AND AVAILABILITY
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@dmb.med.keio.ac.jp).
Acknowledgments
ACKNOWLEDGEMENTS
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)
References
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