Study Overview

This tab shows a general overview of information for the selected study performed by the Cancer Genome Project. If linked through a COSS study link, this will be a study involving a particular sample. If linked through a COSP paper link, information will be shown for the selected publication .

  1. Reference/Study - Title of the study or the paper.
  2. Id - A unique identifier used within COSMIC
  3. Authors - Lists all the authors of this paper ( only for publications ).
  4. Journal - This section describes the Journal name, year, volume and page number and pubmed link to see more details on this article ( only for publications ).
  5. Abstract/Description - A description of the study, or the full abstract of the article (only for publications).
  6. Paper 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 have not been entered into COSMIC for one of many reasons.
    • Reviews : These references are reviews of mutation data from other references. They are not entered into COSMIC as the data have generally been entered via the original papers.
  7. Genes Analysed - Number of unique genes screened in this study/publication with/without mutations.
  8. Mutated Samples - Number of unique samples found with mutation in this study/publication.

Study/Paper - Mutation Matrix

This tab shows a "Mutation Matrix" plot between genes and samples for the selected study/paper. The chart contains a maximum of 20 genes (rows) and 175 samples (columns) with each box representing a Gene-Sample combination.

Each box is colour coded with purple representing Point mutations, orange representing CNV gain and blue representing CNV Loss. For aberrant gene expression a red border indicates over expression or a green border under expression. When samples are positive for multiple categories colour codes will be combined eg for CNV gain and Over expression the box will be orange with a red border.

Gene ranking:

Genes are ranked based on the total count of samples having an aberration from the chosen category (highest at the top). Each category is explained below.

  1. All - All annotations ( Point mutations/ CNVs/ Gene expression )
  2. Point - Point mutations
  3. Gain - Copy number gain
  4. Loss - Copy number loss
  5. Over expression - Over expressed gene
  6. Under expression - Under expressed gene.

Sample ranking:

Samples are ranked based on the count of aberrations in the top 20 ranked genes. The more genes with aberrations the higher the rank (highest on the left). Multiple annotations in the same category are equally weighted e.g a gene having 10 point mutations, 1 CNV gain, and 1 Over expression will be counted as 1 in categories All, Point, CNV Gain and Over expression, but counted as 0 in categories CNV Loss and Under expression.

Study Overview - Mutations

This tab shows a table of genes and mutations from the selected study/publication. This table also provides the ability to search, sort and export the table in csv or tsv format.

  1. Gene Name - Gene name in which the mutation has been found. It links to the gene overview page for more details on that gene.
  2. Samples - Sample name in which the mutation has been found. It links to the sample overview page for more details on that sample.
  3. CDS mutation - Details of the change that has occurred in the nucleotide sequence. Formatting is based on the recommendations made by the Human Genome Variation Society. The mutation type is shown in brackets after the mutation string. The description of each type can be found by following the link to the Mutation Overview page.
  4. AA Mutation - Details of the change that has occurred in the peptide sequence.Formatting is identical to the method used for the nucleotide sequence.

Study Overview - Non-Mutant Genes

This tab shows a table of genes associated with the selected study/paper which were screened but no mutations were observed. This table also provides the ability to search, sort and export the table in csv or tsv format.

Study Overview - Non-Mutant Samples

This tab shows a table of samples associated with the selected study/paper which were screened but no mutations were observed. This table also provides the ability to search, sort and export the table in csv or tsv format.

Study Overview - Mutated Samples

This tab shows a table of samples associated with the selected study/paper which were screened and mutations were observed. This table also provides the ability to search, sort and export the table in csv or tsv format.

Study Overview - Non-Coding Mutations

This tab shows a table of non-coding mutations observed in samples associated with the selected study/paper. This table also provides the ability to search, sort and export the table in csv or tsv format.The last column in the table shows the FATHMM-MKL score, with values ≥ 0.7 indicating functional significance. Please see http://fathmm.biocompute.org.uk/downloads.html for more information about the FATHMM-MKL algorithm, and the 'Mutation Impact' section of Cancer Genome Annotation for help interpreting the scores.

Study Overview - CNV & Expression

This tab shows a table of aberrant gene expression and copy number variation (CNV) data for the study with links to the CNV, Sample overview page and (icons) ChromoView (to view all CNVs across the whole chromosome), the COSMIC Genome Browser and Ensembl. The table contains the following columns -

  1. Sample - Sample identifier which links to the sample page.
  2. Gene - Gene name which links to the gene analysis page
  3. Expression - classified as 'Under', 'Over', 'Normal' or '-' where there is no data.
  4. Expr Level - The Z-score value for gene expression. Normal range -2 to 2. Over > 2. Under < -2.
  5. CN Type - Type of CNV, either Loss or Gain.
  6. Minor Allele - Minor allele count for the specified CNV
  7. Copy Number - Total Copy Number for the specified CNV (major allele + minor allele counts)
  8. CN Segment Posn. - Genomic position of the CNV and icon links to the ChromoView page (to view CNVs across the whole chromosome), the COSMIC Genome Browser and Ensembl.
  9. Average Ploidy - average ploidy across the whole genome of the sample
  10. CNV - Unique CNV Identifier which links to CNV overview page.

Study Overview - Methylation

This tab contains a list of all the genes/probes where there is differential methylation for the selected study. The 'Low', High' and 'Tested' columns show the number of samples.This table also provides the ability to search, sort and export the data in csv and tsv format.

  1. Tissue - the primary tissue of the samples
  2. Gene - Lists the gene associated with the probe/target CpG or '-' if none (eg the probe maps to an intron, UTR or promoter).
  3. Probe - the unique identier of the probe.
  4. Position - the genomic location of the probe (with links to the COSMIC Cancer Genome Browser and Ensembl).
  5. Methylation Low - The number of samples where the beta-value is <0.2 and the methylation state is altered relative to the normal average.
  6. Methylation High - The number of samples where the beta-value is >0.8 and the methylation state is altered relative to the normal average.
  7. Methylation Tested - The total number of tumour samples tested.

For more details on counts please follow this link.

For more details on methylation data analysis and definitions used, please follow this link.

Study Overview -Fusions

This tab shows a table of fusions for all tumour samples in the study. The table contains the following Columns -

  1. Gene - Gene pair involved in the fusion (5' gene first). Links to Gene Overview page
  2. Sample Name - Name of the tumour sample
  3. Id Sample(COSS) - Unique identifier for the tumour sample
  4. CDS Mutation - CDS syntax for the fusion
  5. Somatic status - Can be confirmed somatic, previously reported or variant of unknown origin
  6. Zygosity - Homozygous, Heterozygous or unknown
  7. Validated - is the mutation somatic and is it detected repoducibly
  8. Type - Fusion

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