Question: What does this heatmap represent?
gravatar for banerjeeshayantan
3.7 years ago by
banerjeeshayantan190 wrote:

This figure is derived from the paper here. I had an issue with page 981 and the heatmap given at 982. Here is an extract defining the purpose of the heatmap.

"There was substantial variation between the cancers in the numbers and relative contributions of each of the six classes of base substitution (C>A, C>G, C>T, T>A, T>C, and T>G) (Fig- ure 1A). To provide greater depth of insight into the operative mutational processes, we incorporated the sequence context in which mutations occurred, by considering the bases immedi- ately 5 0 and 3 0 to each mutated base. Because there are six classes of base substitution and 16 possible sequence contexts for each mutated base there are 96 possible mutated trinucleo- tides. We have represented the fraction of mutations at each of the 96 mutated trinucleotides as a heat map for each cancer and normalized it according to the prevalence of each trinucleo- tide in the genome. The display therefore highlights mutational signatures generated by processes that favor particular classes of mutation and/or particular sequence contexts in which muta- tions occur (Figure 1C)"

This is the figure. see here

Here is my explanation: Each of the cells in the heatmap represents a trinucleotide. So for each sample there are 96. Now the shades in each of the cell represents the mutation rate by considering the relative abundance of the trinucleotides in the entire genome. more the abundance, more is the mutation rate, redder it is!
Am I correct in saying this?

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ADD COMMENTlink modified 3.7 years ago by christophersugai0 • written 3.7 years ago by banerjeeshayantan190
gravatar for christophersugai
3.7 years ago by
christophersugai0 wrote:

This is generally correct, although I would state it as prevalence rather than mutation rate. Mutation rate seems, to me at least, a different context than the paper.

ADD COMMENTlink written 3.7 years ago by christophersugai0
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