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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