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4.10 MutationView

4.10.1 What is MutationView

MutationView is a database for mutations in human disease genes, which has been created at Department of Molecular Biology, Keio University School of Medicine (http://mutview.dmb.med.keio.ac.jp). The views of MutationView displayed in H-Inv DB are generated from a version with limited function.

4.10.2 Limitation of platforms, OS and browser versions

The platforms, OS and browser versions which can be display views from MutationView are limited as seen in Fig. 4.10.1.

Fig. 4.10.1 Suitable environment for MutationView

4.10.3 Main window of MutationView

By a click of MutationView in the Disease Information Table of H-inv DB, a main window of MutationView is displayed (Fig. 4.10.2). In this window, the structure of the gene is shown in the X-axis. Genome (exon/intron) structure in default can be changed to cDNA view or coding-region view (Fig. 4.10.3) with a pull down menu [View Type]. In the cDNA and coding-region view, protein functional domains are also shown if any. Scale of X-axis can be zoomed-in using [control]+click or [Zoom-in] button in the view, and can be zoomed-out using [shift]+click or [Zoom-out] button (Fig. 4.10.4 and Fig. 4.10.5). In the maximum zoomed-in condition, nucleotide sequence (and deduced amino acid sequence in coding region) is shown.

Fig. 4.10.2 Main window of MutationView
Fig. 4.10.3 Changing X-axis modes
Fig. 4.10.4 Zooming-in and zooming-out of the X-axis

Mutations are displayed with various symbols such as solid circle and cube, which can be seen in a symbol table displayed from a pull down menu [Help]. The histogram with mutation symbols represents case number of each mutation appeared in literatures.

The left part of main window is for various information and operation (Fig. 4.10.5). The data number is displayed in (ii) including total number of case (Case #), number of each different mutation (Mutation), number of polymorphism (Polymorphism) and total of mutation and polymorphism (Total).

Fig. 4.10.5 Various information of the gene and operation buttons

4.10.4 Mutation Details window

By a click of mutation symbol, the Mutation Details window is displayed (Fig. 4.10.6).
Fig. 4.10.6 A Mutation Details window

In this window, change of nucleotide, deduced amino acid and recognition sites of restriction enzyme are shown. Those information of normal allele is displayed in field (i) and (ii), while that of mutation allele is in field (iii) and (iv). Changed parts are shown in red color. For the mutation with gross change of transcription such as splicing and large deletion, schema of mutation is shown in this window (Fig. 4.10.7 left).

Fig. 4.10.7 Mutation Detail window for mutation in splicing site

In case of splicing mutation, nucleotide change display can be also shown by clicking [Detail] button (Fig. 4.10.7 right), and the display mode can be changed to cDNA or Coding Region (Fig. 4.10.8).

Fig. 4.10.8 Changing display mode in Mutation Detail window

4.10.5 Display of probe information

Probe display field is created above the mutation histogram with a pull down menu [View Type] - [Probe] (Fig. 4.10.9). Probe information such as PCR primer, ASO and DNA Clone are displayed. Clicking of each probe generates another window for Probe Details information, in which various information is available such as primer sequence, reaction condition and reference.

Fig. 4.10.9 Probe field and Probe Details window

4.10.6 Classify window

From a pull down menu [Classify], Classify window is displayed. In this window, various information with mutation data is classified according to each classification item such as ethnic origin, disease name and onset age.

Fig. 4.10.10 Classify window

4.10.7 Gene/Disease Details window

Clicking of [About This Gene] button in the main window creates the Gene/Disease Details window (Fig. 4.10.11). In this window, various information including gene/disease name, GDB symbol, OMIM symbol, OMIM number are displayed with link buttons to each database site.

Fig. 4.10.11 Gene/Disease Details window
Revised: March 30, 2007