GRCh38 · COSMIC v82

Overview

This section shows a general overview of information for the selected study (COSU identifier) or publication (COSP identifier). Studies may have been performed by the WTSI Cancer Genome Project, or imported from the ICGC/TCGA. You can see more information on the help pages.

Study
Pilot: DNA methylation and histone deacetylation
Study ID
COSU73
Description
CpG islands present in the 5' regulatory regions of many genes modulate transcription of the gene depending on their methylation status. If the CpG island is unmethylated the gene can become transcriptionally active but if it is methylated, gene expression is silenced. Methylation of DNA may physically impede transcription factor binding but more importantly, Methyl-CpG-binding domain proteins (MBDs) bind to the methylated DNA and then recruit histone deacetylases and other chromatin remodelling proteins. Chromatin remodelling then results in gene silencing. Hypermethylation of tumour suppressor genes has been associated with cancer. This gene set is comprised of DNA methyl transferases, which are responsible for methylation, MBDs, histone deacetylases and other proteins involved in methylation and chromatin remodelling.

Sequencing of any given sample through the gene sets should be considered work in progress. Lack of reported mutations in any given gene for a particular sample does not necessarily imply the sample is wildtype for the gene.
Genes Analysed
39
Mutated Samples
13
Total No. of Samples
40

Mutation Matrix

This section shows the correlation plot between the top 20 genes and samples. There is more information in our help pages.

Genes

This table shows genes with mutations in the selected study/paper [more details]
Genes Mutated Samples
This table shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)

Variants

This tab shows genes with mutations in the selected study/paper [more details]

Genes Samples CDS Mutation AA Mutation

This tab shows non coding variant in the selected study/paper [more details]

Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq FATHMM-MKL

This tab shows the gene expression and copy number variation data for this study [more details]

Table Information

Hide

The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

Sample Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

1. N/A represents cases where the average ploidy value is not available( mostly ICGC samples). For some TCGA samples where the minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

CNV

This table lists the samples in the selected study which have low/high methylation for each gene. [more details]

  Methylation (no. samples)
Tissue Gene Probe Position Low High Tested

This tab shows the fusion mutations observed in this sample [more details]

Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type

Samples

This table shows mutated samples in the selected study/paper.

Sample Name Mutation Count

This table shows samples without mutations in the selected study/paper.

Non-Mutant Samples Sample Id (COSS)