Note: the 'Inferred breakpoint' section is the breakpoint position we have determined using the rule above, and the 'Observed mRNAs' are the expressed products actually reported as the result of experimental procedures. A single inferred breakpoint can allow the expression of a number of gene fusion mRNA variants, as above. However, additionally, a single observed mRNA can, between samples, be derived from a number of different breakpoints.
Fusion Overview - Fusions
List of fusions involving the specified pair of genes.
Inferred Breakpoint Table
- Mutation Id - links to the fusion summary page for more details of the inferred breakpoint.
- Gene Name - 5' partner gene involved in the fusion.
- Last Observed Exon - The last exon observed before the fusion breakpoint. In the 5' gene it can be ‘UTR’ or have ‘?’ if the breakpoint is unknown.
- Inferred breakpoint - mRNA breakpoint position in the 5'gene. A '+' followed by a number denotes a breakpoint downstream of the mRNA position given (in an intron or UTR). If the number is in parentheses the position is approximate.
- Gene Name - The 3' partner gene involved in the fusion.
- First Observed Exon - The first exon observed after the fusion breakpoint in the 3' gene. It can be ‘UTR’ or have ‘?’ if the breakpoint is unknown.
- Inferred breakpoint - mRNA breakpoint position in the 3'gene. A '?' indicates that the precise breakpoint is unknown. A '-' followed by a number denotes a breakpoint upstream of the mRNA position given (in an intron or UTR). If the number is in parentheses the position is approximate.
- Mutations - Number of unique samples found with this mutation.
- Mutation Frequency - Frequency (as a percentage) of mutated samples / total number of samples with this mutation.
Fusion Overview - Tissues
Tissue specific breakdown of the mutation frequency in inferred and observed breakpoints for the selected fusion gene pair in all the curated literature. This table also provides the ability to search, sort and export the table in csv or tsv format.
- Primary tissue - Tissues analysed for this gene pair, linking to the Cancer Browser (tissue overview) for further details. Moving the cursor over the tissue name also provides a tooltip listing 5 options to link to the more detailed 'Fusion export table' - which can be searched, sorted and exported in csv or tsv format.
- Positive (Inferred Breakpoints) - Lists all inferred breakpoints detailing all the samples analysed with fusion mutations.
- Positive (Including mRNA) - Lists all inferred breakpoints and observed mRNA transcripts detailing all the samples analysed with fusion mutations
- Positive and Negative (Inferred Breakpoints) - Lists all inferred breakpoints detailing all the samples with fusion mutations and samples analysed without mutations.
- Positive and Negative (Including mRNA) - Lists all inferred breakpoints and observed mRNA transcripts detailing all the samples analysed with fusion mutations and samples without mutations.
- Negative – lists the details of all the samples analysed without mutations.
- Mutated Samples - No. of unique mutated samples with the inferred breakpoint fusions.
- All Samples - Total no. of unique samples analysed for the fusion mutation.
- % Mutated - Frequency in percentage of mutated samples with total number of samples analysed with this fusion mutation.
Fusion Overview - References
This table lists all curated publications reporting this fusion. More details of the paper can be found by following the ‘COSMIC link’ or ‘Pubmed Link’. This table also provides the ability to search and export the table in csv and tsv format.
- Reference Title - The title of the article, mouse over the title to see the full article title name.
- Author – First author (s) of the publication, to see all authors of the publication please click the COSMIC or Pubmed link.
- Year - The publication year of the journal from which the article was taken.
- Journal - The abbreviated title of the journal from which the article was sourced, followed by the volume and page number.
- Status – There are currently three statuses:
- Curated : The reference has been fully curated in to COSMIC.
- Listed : The reference has been read, but the data was of insufficient quality for inclusion in to COSMIC.
- Reviews : These references are reviews of mutation data from other references. They are not entered into COSMIC as the data has generally been entered via the original papers.
- COSMIC – Links to a more detailed page for the reference. The page displays details of the selected publication including the samples and genes analysed.
- Pubmed - Links to Pubmed for more details about the publication.
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