Database Commons

a catalog of worldwide biological databases

We previously isolated PARKIN (PARK2) as a gene responsible for a unique sort of Parkinson disease, namely Autosomal Recessive Juvenile Parkinsonism (ARJP). In this study, we surveyed all the available literature describing PARK2 gene/Parkin protein mutations found in Parkinson disease patients. Only carefully evaluated data were deposited in the graphical database MutationView (http://mutview.dmb.med.keio.ac.jp) to construct KM-parkin-DB, an independent sub-set database. Forty-four articles were selected for data curation regarding clinical information such as ethnic origins, manifested symptoms, onset age, and hereditary patterns as well as mutation details including base changes and zygosity. A total of 366 cases were collected from 39 ethnic origins and 96 pathogenic mutations were found. PARK2 gene mutations were found also in some general Parkinson disease patients. The majority (63%) of mutations in PARK2 were restricted to two particular domains (UBL and RING1) of the Parkin protein. In these domains, two major mutations, a large deletion (DelEx3) and a point mutation (p.Arg275Trp), were located.

It is known that cancers are caused by accumulated mutations in various genes and consequent functional alterations of proteins that are important for maintenance of normal cellular functions. The changes in nucleotide sequences and expression patterns of cancer-related genes are being extensively studied to better understand the mechanisms of tumorigenesis and to develop methods for DNA/protein [corrected] diagnosis and drug discovery. At present, a number of computer databases for molecular information on cancer-related genes are available publicly through the internet. These databases deal with familial cancer and sporadic cancer at the levels of germline mutation or somatic mutation, genomic or chromosomal abnormalities, and changes in the expression levels of relevant genes. Previously, we constructed a human gene mutation database named MutationView (http://mutview.dmb.med.keio.ac.jp/) and have accumulated mutation data for approximately 300 genes that are involved mainly in monogenic diseases. Forty-two genes are cancer-related and therefore a separate cancer database named KMcancerDB was constructed. MutationView/KMcancerDB utilizes a graphic display function for both queries and search results much more often than other existing databases, making the system quite user friendly. MutationView/KMcancerDB provides a highly sophisticated search function for all genes through a single internet URL. In the present paper, we briefly review various useful databases for cancer-related genes, and describe MutationView/KMcancerDB in more detail.

The KMeyeDB (http://mutview.dmb.med.keio.ac.jp) has been developed as a database of mutations in human eye disorder genes using software called MutationView which provides graphical presentation of various data analysis. Here, we present several display windows from the KMeyeDB for data analysis of mutations in the RB-1 gene, which is responsible for the pathogenesis of retinoblastoma, a malignant tumor in the retina.

A database of mutations in human disease-causing genes has been constructed and named as Keio Mutation Database (KMDB). This KMDB utilizes a database software called MutationView which was designed to compile various mutation data and to provide graphical presentation of data analysis. Currently, the KMDB accommodates mutation data of 38 different genes for 35 different diseases which are involved in eye, heart, ear and brain. These KMDBs are accessible through http://mutview.dmb.med.keio.ac.jp with advanced internet browsers.

A database of mutations in human eye disease genes has been constructed. This KMeyeDB employs a database software MutationView which provides graphical data presentation and analysis as a smooth user-interface. Currently, the KMeyeDB contains mutation data of 16 different genes for 18 eye diseases. The KMeyeDB is accessible through http://mutview.dmb.med.keio.ac.jp with advanced internet browsers.