Cosmic Help

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Tissue View Display Page

  • Welcome to the tissue view display page. This page displays all the information for the tissues, histologies and genes selected.
Main Image

The main display image summarises all the selected results into a navigable histogram.

On top of the image there are six tabs:

  • Export: This tab will take the user to the export options page, from which they can select the export format and export the data contained within the main image.
     
  • Zoom Out: The zoom out tab is used to return the main image to the original zoom level, displaying the entire protein.
     
  • Switch View: Clicking on this tab will switch the view between tissue view and gene view. Altering the level of detail that is shown for the tissues.
     
  • References: This tab will take the user to the references page, from which they can view all references associated with the gene.
     
  • Summary: Click here to view a summary report. Each report displays an overview image, sample stats, reference information and links to other databases.
     
  • Tissue View: This tab has no click-able function and is only present to indicate what type of view is being presented. In this case the view is tissue based and so all information about the tissues is fully expanded.
     

The Main image is divided into seven main sections.

  • Title: The name of the gene that is being displayed.
     
  • AA/bp Subst.: The vertical scale bar on this diagram represents a variable scale, with an indication of the maximum number of mutations that occur in the currently viewed region of the gene (in your selected samples). Each vertical increment in the histogram (displayed as a coloured block when zoomed in) represents a mutation. The height of the column indicates the frequency of mutations at that point. Clicking on the mutation bars will present a pop-up menu.
    • Pop-up Title: This title indicates the amino acid or nucleotide that has resulted from the mutation at this point. The number indicates the number of samples in which this change has been observed .
       
    • Zoom In: The first three links in this menu are for zooming in on the mutation that is associated with the pop-up menu. The links display the mutation with 5, 10 or 20 residues either side.
       
    • References: This link will take the user to the references page and display all the references associated with the mutations at this point.
       
    • Mutation Details:The final link in this dropdown menu will take the user to a detailed mutation overview page, for the selected mutation.
       
  • Amino Acid/bp: The amino acid or nucleotide sequence of the gene being displayed. When there are less than 30 amino acids or nucleotides on the screen, each residues' single letter code will be drawn and coloured in. Clicking on any point in this track will bring up a pop-up menu.
    • Pop-up Title: This displays the name of the gene in the current main image.
       
    • Full Sequence: Provides a link to the fasta sequence, served by the Sanger Institute pfetch server.
       
    • Pfam Entry: Links directly to the gene entry in the Pfam database hosted at the Sanger Institute.
       
    • Ensembl Geneview: This links directly to the Ensembl gene report page.
       
    • Swissprot Entry: Links directly to the Swissprot entry for the gene, hosted on the Sanger Institute's SRS server.
       
  • Complex Muts. Any mutations that involve multiple bp or AA substitutions can be found here. Each mutation is rendered as a block of coloured residues, indicating the alteration to the sequence.

    • Pop-up Title: This title indicates the sequence that has resulted from the mutation at this point. The number indicates the number of samples in which this change has been observed .
       
    • Position: The start and end positions spanning the mutation.
       
    • Wildtype Allele: The allele normally associated with the sequence position.
       
    • References: Clicking this link will take the user to the references page and display all references associated with this mutation.
       
    • Zoom in: This link is for zooming in on the mutation that is associated with the pop-up menu. The link displays the mutation with 10 residues either side.
       
    • Mutation Details:The final link in this dropdown menu will take the user to a detailed mutation overview page, for the selected mutation.
       
  • Indels: All the insertion or deletion mutations can be found here. Insertions are represented by upward pointing red triangles which indicate the start of the insertion. Deletions are represented by downward pointing blue triangles which indicate the start of the deletion.
    • Pop-up Title: Displays the type of mutation, either insertion or deletion.
       
    • Between: The coordinates that the mutation occurs between
       
    • Inserted/Deleted: The sequence that was inserted or deleted, which resulted in the mutation.
       
    • Mutation Count: The number of times the mutation has been observed.
       
    • References: This link takes the user to the references page and displays all references associated with the mutation.
       
    • Mutation Details:The final link in this dropdown menu will take the user to a detailed mutation overview page, for the selected mutation.
       
  • Domains: This track represents all the protein domains (from interpro) that are associated with this gene. The domains are coloured according to their source. Clicking on any of the domains will present a pop-up menu.
    • Domain name: The first entry in this table displays the name that is associated with the domain.
       
    • Entry link: This links to the gene entry in the named database.
       
    • Start: The coordinates of the residue at which this domain begins.
       
    • End: The coordinates of the residue at which this domain ends.
       
  • Scale (AA/bp): This horizontal scale-bar shows the position of the amino acids or nucleotides in the sequence. Clicking on one of the black or white blocks will zoom the image so that only the area within the block clicked is visible.
     
  • Note: The references track has been removed. All references can now be found by clicking on the references tab at the top of the main image. References associated with a particular mutation are found by following the links in pop-up menu attached to each mutation.
Navigation

Provides a means to alter what information is displayed on the page, based on position and identity of the protein.

  • Gene : A drop down menu is used to display all the possible genes within the database. The currently visible name will be that of the gene in the image directly above the navigation tool-bar. Altering this value will change the gene that is displayed in the image above it, to the selected gene.
     
  • AA/bp: This is composed of two text boxes. The first box is the start position. The second box is the end position. These positions determine what area of the gene's peptide sequence the image will cover. By altering these numbers the region of the protein displayed can be altered. This can be used to zoom in or out to a specific position within the sequence.
     
  • Sequence Type: There are two radio buttons used to determine the type of sequence that is used as the base of the scale system. Selecting 'cDNA' will cause the scale to be based on nucleotide sequence. Selecting 'Amino Acid' will base the scale on the amino acid sequence.
     
  • Selecting Display will enter the chosen selection and alter the display page accordingly.

Filters

The main image of filters summarises all the options in the list.It is a collapsible list with 4 options:

  • Mutation Type : Selecting any option in Mutation type will filter the data for this gene on the basis of mutation type selected
     
    • Deletion : This options will search for all the deletion mutations in this gene including Frameshift and Inframe.
       
      • Frameshift : This option particularly looks for Frameshift deletion in this gene.
         
      • Inframe : This option particularly looks for Inframe deletion in this gene.
         
    • Insertion : This options will search for all the Insertion mutations in this gene including Frameshift and Inframe.
       
      • Frameshift : This option particularly looks for Frameshift insertions in this gene.
         
      • Inframe : This option particularly looks for Inframe insertions in this gene.
         
    • Substitution : This options will search for all the Substitution mutations in this gene including Nonsense, Missense, Synonymous.
       
      • Nonsense : This option particularly looks for Nonsense Substitution in this gene.
         
      • Missense : This option particularly looks for Missense Substitution in this gene.
         
      • Synonymous :This option particularly looks for Synonymous Substitution in this gene.
         
      • Complex : This option selects any mutations that involve multiple bp or AA substitutions.
         
  • Sample Source : Selecting any option in Sample Source will filter the data for this gene on the basis of sample source selected
     
    • Cultured Sample: This options will only look for cultured samples that includes cell line samples.
       
    • Tumour Sample: This options will only look for tumour samples that includes primary tumour samples.
       
  • Somatic Status : Selecting any option in Somatic Status will filter the data for this gene on the basis of Somatic Status of the samples reported
     
    • Confirmed Somatic: This options selects all the samples that are confirmed somatic.
       
    • Previously Reported: This options selects all the samples that are Previously Reported.
       
    • Variant of unknown origin : This options selects all the samples that are Variant of unknown origin.
       
  • Systematic Screen : Selecting Systematic Screen option will filter the data for this gene on the basis of samples that are systematic screen analysed.
     
  • Button options :
     
    • Apply: Selecting Apply will enter the chosen selection and alter the display page with data and Image accordingly.
       
    • Previously Reported: Selecting Reset will clear all the selections made and resets it to the original page..
       


    Distribution

    This tab provides the image of Mutation Type chart and Sample Source chart.That shows all mutations and sample source for the currently selected sample set (by position) and Filter options.They can be located by clicking on the Distributions button.

    Here is a description for each pie chart and table:



    • Mutation Type chart: This pie chart and table displays distribution of all the mutations for the currently selected sample set or filter options for this gene.
       


    • Sample Source chart: This pie chart and table dispalys distribution of all the sample source for the currently selected sample set or filter options for this gene.
       


    Mutations

    The mutations tables show all mutations for the currently selected sample set (by position), that can be seen inside the main image. They can be located by clicking on the Mutations button.

    Here is a description for each column of the tables:

    • Position: This column contains the position of the mutation within the protein.
       
    • Mutation(n): This column contains all the mutant alleles, in HGVS notation, at the positon in the first column of the table. The number in brackets following each mutation is the number of times that mutation has been observed in the data set. Clicking on the allele will take the user to the detailed mutation overview page, for the selected allele.
       
    Details

    The details table provides a more detailed description of all the tissues and samples that are found in the selected gene and can be located by clicking on the Details button.

    Here is a description for each column of the table:

    • Primary Tissue: A list of all the tissues that have data available for the selected gene.
       
    • Sub Tissue: A break down of the sub tissue classifications that can be found within the primary tissue groups
       
    • Histology: The histological classifications associated with the tissue types
       
    • Sub Histology: This is a more detailed breakdown of the the histological classification of the samples
       
    • Mutated(% of All Samples): Each row shows the number of mutated tumour samples (and the percentage of the total number of samples analysed) that have been identified for the associated tissue type.
       
    • All Samples: The total number of samples that have been reported in the curated references.
       
    • Mutation Data: Each entry in this column is a link to a pop-up menu containing four entries.
      • These mutations on... : This will redraw the display to show only the information on the selected row.
         
      • View on other genes : This link will move the user to a selection form showing all the genes that have mutation data available for the selected tissue.
         
      • Sample Data :
         
        • Positive : Clicking on this link will display a table of the mutations associated with the current row's tissue type and provide more details about these mutations.
        • Positive and Negative : Clicking on this link will display a table of all the samples associated with the current row's tissue type and provide more details about them.
        • Negative : Clicking on this link will display a table of all the negative samples associated with the current row's tissue type and provide more details about them.

    Note: The values in the details table are not constant and will change based on the area of the gene displayed in the main image.

    Any More Questions?