Cosmic Help

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Gene Summary Page

  • Welcome to the gene summary page. This page provides an overview of all the information, stored in COSMIC, associated with the selected gene.
     
  • This page is divided into five main sections:
     
Gene Name
  • This section provides the name of the gene and the date which information about the gene was last added or updated and any comments on its current status within the database.
     
Mutation Summary

  • The majority of this section is an image detailing all the mutations found in the gene (as above). The image is divided into five different tracks. Each track displays a different mutation type and the position of those mutations on the amino acid sequence.
     
  • The 'Mutations' track is coloured according to mutation density. The red areas have the highest concentration of mutations and the green ones the lowest.
     
  • Each track is interactive and clicking on any of the mutation blocks will produce a dropdown menu.
    • [number] mutations: The first item in the dropdown menu indicates the number of mutations that occur at this point in the transcript.
       
    • More details for ...: This link will display the full histogram of the gene, zoomed in to 5 amino acids either side of the mutation.
       
    • Whole gene details: The final item in the dropdown menu will provide the full histogram, zoomed out to cover the full transcript.
       
  • Click the button, as shown below, to view the histogram page and more details about the mutations found in this gene.
     
Rearrangement Mutation Summary (Fusions)

If the selected gene is involved in fusions with another gene, and if it has been curated by the COSMIC team, this section lists the gene names of the fused genes, with links to the Translocation Overview page for that gene pair. The number of mutations found, and the number of samples analyed are displayed in brackets alongside the gene name.


Additional Info
  • Fasta Files: Clicking on the cDNA or Protein id will provide you with a text file containing the fasta sequence.
     
  • Transcript and Protein: The linked text file contains an alignment between the cDNA transcript and the translated protein sequence.
     
  • External Databases: This section contains a list of links to other sites that have additional information about the selected gene.
     
  • DAS: This section contains links to the Ensembl Human contig view, for the selected gene. It diagrammatically represents the cosmic mutations and cosmic transcript against the Ensembl transcripts.
     

    There are 2 links in this section, the second of which only needs to be clicked once to activate the COSMIC DAS sources. Once this has been done, one should always click the 'Ensembl Contig View' link.
     

    Selecting the second more then once, can lead to some errors in the diagram for the contig view. If any problems are experienced, it is likely too many features have been added, so please follow the procedure below:
     

    • In the 'Detailed View' section on the Ensembl contig view page, click on the 'DAS sources' drop down menu, and select 'Manage Sources' from the list. This will open a new window.
    • Scroll to the bottom of the list displayed. There should only be one copy/row of each of the 'cosmic_mutations' and 'cosmic_transcripts' DAS sources.
    • If there is more then one of either of these, click on the red x icon, and close the window.
    • Refresh the page, and all cosmic mutations for the selected gene should be displayed. If you are still experiencing problems, please see the ensembl help pages

     

    The mutations are marked/represented as single base pair mutations, due to limitations in the drawing code. For example, if a deletion of 10 bp occurs in a gene, it will be positioned on the diagram at the 1st base pair of the mutation, as it exists on the cds.
     
References
  • Total number of references: The total number of references that have been used to gather information for this gene.
     
  • COSMIC curated paper...: Listed here is the currated paper that was most recently added to COSMIC. Click on the 'More Details' link to read more about the samples that were examined in this paper.
     
  • Click the button, as shown below, to view the complete list of all publications that have entries in COSMIC for this gene.
     
Studies
  • This section details studies performed by the Cancer Genome Project that have involved this gene.
     
  • Click on the [More Details] link to see an overview of the study within COSMIC.
Samples
  • Total number of sample analyses: This is the total number of samples that have been analysed for mutations in the selected gene.
     
  • Number of samples with mutations: The number of analysed samples containing mutations.
     
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