• Select the target field for search from Gene/Disease/Domain, and enter keywords separated by spaces. By clicking the [Go] button, the entries corresponding to the keywords are shown as list.
• A gene registered in MutationView will link to mutation list of the gene.

In Graphical Menu, genes are shown on the chromosomal idiograms, the anatomy chart or the protein models. By clicking a gene or a disease in the figure, Gene Structure window is displayed. Also, it is necessary to install Java for using Graphical Menu. If following figure is not displayed, Java is not installed, or Java is not enabled in your browser. Please enable Java in your browser by reference to "Install and Enable Java".
*In Graphical Menu, operation of the right click of the mouse, you can be replaced by (left) clicking while pressing [Shift].

Chromosome Overview window displays all genes, which are registered in MutationView, on the chromosomal ideograms.

• Keyword search can be conducted by selecting the target field to utilize for search from HUGO Gene Symbol, OMIM Title, OMIM Symbol, or Organ, and entering your search terms. If you would like to specify more than one keyword, place a space among each word and choose from either AND search (search genes including all of the keywords) or OR search (search genes including at least one of the keywords). Click the [Search] button, and genes corresponding to the keywords are marked with red. In addition, the numbers of corresponding genes and diseases are shown.
  
  
  
  
  
• By clicking while the mouse cursor is over a gene, Gene Structure window displays graphical images of gene structure, sequences, variations, and symptoms of the selected gene. By right clicking or clicking while pressing [Shift], detailed information about the selected gene is displayed. By clicking the chromosomal number, Chromosome Details window is opened.
  
  
  
  
  
• The displayed name of the genes is switchable to gene OMIM Title, related disease OMIM Title or related disease OMIM Symbol from the menu [List].
  
  
  
  
  
• When pressing [Ctrl] and [S] while Chromosome Overview window is located at the foreground, the overall image of the displayed Chromosome Overview is created by the server, and can be saved from the browser.
  
  
  
  

Chromosome Details window shows monogenic disease-causing genes located on the chromosome. Genes that are registered in MutationView appears with blue labels.

• Select the target field to utilize for search from HUGO Gene Symbol, OMIM Title, OMIM Symbol or Organ, and enter your search terms. If you would like to specify more than one keyword, place a space between each word and choose AND search (search genes including all of the keywords) or OR search (search genes including at least one of the keywords). Click the [Search] button, and genes corresponding to the keywords appear with red labels. In addition, the numbers of the corresponding genes and diseases are shown at the upper right of the window.
  
  
  
  
  
• By clicking a gene, Gene Structure Window displays graphical images of its gene structure, sequences, variations, and symptoms. By right clicking or clicking while pressing [Shift], detailed information about the gene is displayed.
  
  
  
  
  
• The displayed name of the gene is switchable to gene OMIM Symbol, related disease OMIM Title or related disease OMIM Symbol from the menu [List].
  
  
  
  
  
• When pressing [Ctrl] and [S] while Chromosome Details window is located at the foreground, the overall image of the displayed Chromosome Details is created by the server, and can be saved from the browser.
  
  
  
  
  

In the Anatomy Menu window, buttons showing names of organs and tissues are placed along the anatomical figure. You can search for diseases and disease-causing genes by selecting the buttons of diseased sites.

• By clicking a button of a given organ or tissue, a list of diseases that develop at that site, along with genes that cause the diseases is shown. The numbers of relevant genes and diseases are also shown. Multiple buttons can be selected simultaneously by clicking the button while pressing [Ctrl], which narrows down the list to diseases that affect in those sites. When you would like to clear the search condition and to view the full list, click [All]. In addition, you can execute a search by selecting from HUGO Gene Symbol, OMIM Title, OMIM Symbol or Organs, then entering keywords into the search field. To specify more than one keyword, place a space between each word and choose either AND search (search diseases or genes including all of the keywords) or OR search (search diseases or genes including at least one of the keywords). After clicking the [Search] button, the list is narrowed down to genes and diseases corresponding to the keywords. The numbers of search results are always shown at the upper right of the window.
  
  
  
  
  
  
• By double-clicking the selected gene or clicking the [Gene Structure] button, Gene Structure Window displays graphical images of gene structures, sequences, variations, and symptoms of the selected gene/disease. By right clicking or clicking while pressing [Shift], detailed information about the gene is displayed.
  
  
  
  
  
• By selecting a target gene from the list of genes and clicking [↓] button, the list of diseases is narrowed down to the diseases related to the selected genes. By clicking [↑] button, the list of diseases is narrowed down to the genes related to the disease-causing genes.
  
  

Protein Model window shows genes registered in Mutation View above the figure of the model of the protein.

• You can select a model from the list of models on the upper left. You are able to click a gene symbol with blue labels to display the Gene Structure window of the selected gene. By right clicking or clicking while pressing [Shift], detailed information about the gene is displayed.
  
  

In Protein Functional Domain window, you are able to search for genes from protein functional domains.

• Specify a retrieval domain 1:
  1. By clicking the [Add] button, Select Domains dialog is opened.
  2. Enter keywords and select a target field to utilize for searching from [Pfam ID & Description] or [InterPro Abstract].
  3. Click the [Search] button.
  4. Domains corresponding to the keywords will appear below.
  5. Select domains as a retrieval key to search for genes. (If more than one domain is selected, search result will show genes that include any of the domains.)
  6. Click the [OK] button to determine the domains.
  7. You can specify a retrieval key to search for genes by selecting domain in Selected Domains dialog.
  
  
  
  
  
• Specify a retrieval domain 2:
  By right clicking or clicking while pressing [Shift], some domains in Gene Structure Window, a pull-down menu is displayed. You can add the selected domain as a retrieval key in the search window by clicking the [Add Search Condition] button in the pull-down menu.
  
  
  
  
  
• Specify a retrieval domain 3:
  By clicking the [Add signal peptide]/ [Remove signal peptide] button, you can add or remove signal peptide as a retrieval key.
  By clicking the [Add transmembrane]/ [Remove transmembrane] button, you can add or remove transmembrane as a retrieval key.
  
  
  
  
  
• By clicking [Submit] button after retrieval keys are specified, genes corresponding to the keys are displayed. If multiple retrieval keys are specified, genes corresponding to all the retrieval keys are shown. By clicking the [Open] button, Gene Structure Window that displays graphical images of its gene structure, sequences, variations, and symptoms appears.
  

Gene Structure Window displays genetic variations with graphical images of gene structures, base sequences and symptoms.

• Structure of the graph
• The X-axis shows the structure of a gene, and the unit represents the number of base sequences. From the menu [View Type], you can also switch the unit of the axis to cDNA or Coding Region.
• The Y-axis represents a histogram of the number of cases of mutations in the nucleotide position on the X-axis.
• The unit of Y-axis can be changed to frequency from the menu [View Type].
• The symbol at the top of the histogram represents the type of mutation. By clicking the symbol, detail of the mutation is displayed.



• Chang the structure of X-axis
• You can switch the structure of X-axis to cDNA or Coding Region in menu [View Type].
• When X-axis is selected as [cDNA] or [Coding Region], domains are shown on the X-axis. If you select [DB domain] from the menu [View Type], domains predicted by the domain databases, such as Pfam, are shown.



• Zoom of X-axis
• By right clicking or clicking while pressing [Shift] on a graph, the X-axis is zoomed in. By clicking while pressing [Ctrl], X-axis is zoomed out. X-axis can also be zoomed from the buttons in the toolbar located at the left of the window.
  
  
  
• By right clicking or clicking while pressing [Shift] after selecting a region by dragging, a pull-down menu is displayed. By selecting [Zoom] from the menu, you can zoom in on the selected region into full width.
  
  
  
• The numbers of cases in the selected region are counted.
• Selecting a region: By right clicking a structure, such as exon, intron, domain, or dragged region, a pull-down menu is shown. By clicking [Add Region] in the pull-down menu, the selected region is shown in the [Selected Region] field.
  
  
  
  
  
• Execution of count: By clicking the [Set Region] button located at the left of the window, the numbers of cases in the selected region are re-counted and shown.
  
  
  
  
  
• Displaying domains in X-axis and searching genes from displayed domains
• By changing the structure of X-axis to cDNA or Coding Region from the menu [View Type], the domain is shown along with the structure.
• When you select [DB domain] from the menu [View Type], domains predicted by the domain databases, such as Pfam, are shown.
• By right clicking or clicking the domain while pressing [Shift], a pull-down menu is displayed. Click the [Add Search Condition] button in the menu, and the selected domain is added as a retrieval key in the search window.
  
  
• Sequence search: By clicking [Search Sequence] in menu [Tools], Search Sequence window is opened, which enables searching for the corresponding position of the sequences from the region displayed in the window.
  
  
  
  
• View sequence: By clicking [View Sequence] in the menu [Tools], View Sequence window is opened. View Sequence window shows base sequences of each structure, such as exon, intron, and cDNA.
  
  

By selecting the menu [Classify], Classify window is opened.

• Classify window shows (i) classifications of the variation additional information, and (ii) the number of cases with each value of the classifications. By clicking [Classify] button after a value is selected, mutations that include the selected values are shown in a graph.
  
  
  
  
  
• Grouping of values: By selecting values that belong to a classification, you can group the values. By clicking the [Classify] button, the created group is reflected on the graph.
  1. By right clicking or clicking while pressing [Shift], you can select values as a target for grouping.
  2. By clicking while pressing [Ctrl], grouping dialog is opened.
  3. You can execute Grouping by entering a name of the group and clicking the [Grouping] button.
  4. A grouping layer with the names of groups and selected values is shown.