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Review
. 2007 Mar;98(3):259-67.
doi: 10.1111/j.1349-7006.2007.00405.x. Epub 2007 Jan 12.

MutationView/KMcancerDB: a database for cancer gene mutations

Nobuyoshi Shimizu  1 , Masafumi Ohtsubo, Shinsei Minoshima
Affiliations
Review

MutationView/KMcancerDB: a database for cancer gene mutations

Nobuyoshi Shimizu et al. Cancer Sci. 2007 Mar.

Erratum in

  • Cancer Sci. 2007 May;98(5):764-5

Abstract

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.

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Figures

Figure 1
Figure 1
Access to genes. (a) Chromosome detail window. Clicking each chromosome schema opens a disease and gene list. (b) Disease and gene list of chromosome 3 opened by clicking chromosome 3 in (a). (c) Chromosome overview window. Cancer‐related genes are shown in red. The pointer indicates the VHL gene, which is in green color. Clicking each gene symbol shows a gene structure window (Fig. 2). (d) Anatomy window. Clicking on organ‐tissue names shows a list of diseases and causative genes. (e) Gene/disease details window, opened by clicking (right button) the VHL gene in (c). (f) Protein model window for the nucleotide excision repair complex. Clicking each member of the protein complex shows a gene structure window (Fig. 2).
Figure 2
Figure 2
Gene structure window. (a) Default gene structure window of the VHL gene. A histogram of mutation frequency, exon boundaries and protein domain structure is shown. Inset: a mutation symbol table. (b) Exon/intron structure of the VHL gene shown by switching from cDNA/coding region mode to genomic mode. (c) Mutation details window of mutation R167W. (d) Probe window showing polymerase chain reaction (PCR) primer pairs to amplify various parts of the VHL gene. (e) Probe detail window showing the nucleotide sequence of PCR primers and reaction conditions.
Figure 3
Figure 3
Classify function of MutationView. (a) A raw data file of the mutation description table of the VHL gene in Excel format. (b) Classify window. (c) A histogram with mutation data filtered by only ‘germline’. (c1) A part of the classify window to filter the mutations to only ‘germline’. (c2) The classify window after filtering by only ‘germline’. (d) A histogram with mutation data filtered by only ‘somatic’. (d1) A part of the classify window to filter the mutations to only ‘somatic’. (d2) The classify window after filtering by only ‘somatic’.
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References

    1. HUGO MDI. HUGO‐mutation database initiative newsletter no. 18. 2001. [Cited 27 November 2001.] Available from URL: http://www.hgvs.org/newsletters/news18.html
    1. Genomic Disorders Research Centre. The Human Variome Project meeting − International collection of human gene variation. 2006. [Cited 20 June 2006.] Available from URL: http://www.humanvariomeproject.org/
    1. Olivier M, Eeles R, Hollstein M, Khan MA, Harris CC, Hainaut P. The IARC TP53 Database: new online mutation analysis and recommendations to users. Hum Mutat 2002; 19: 607–14. - PubMed
    1. Beroud C, Collod‐Beroud G, Boileau C, Soussi T, Junien C. UMD (universal mutation database): a generic software to build and analyze locus‐specific databases. Hum Mutat 2000; 15: 86–94. - PubMed
    1. Beroud C, Soussi T. The UMD‐p53 database: new mutations and analysis tools. Hum Mutat 2003; 21: 176–81. - PubMed