Question: Mutational landscape plot
1
gravatar for shivangi.agarwal800
5 months ago by
shivangi.agarwal80050 wrote:

Hi I am trying to make waterfall plot using GenVisR as shown here. I just put an example data like

sample           gene_name  amino.acid.change  trv_type
TCGA-BH-A0WA-01  BRCA1      X1559_splice       splice_site_del
TCGA-AN-A0XU-01  BRCA1      G1788V             missense
TCGA-A2-A25B-01  BRCA1      E720*              nonsense
TCGA-D8-A27M-01  BRCA1      P1614Qfs*19        frame_shift_del
TCGA-E9-A1NC-01  BRCA1      Q139*              nonsense
TCGA-C8-A12T-01  BRCA1      D1344H             missense
TCGA-A2-A4S0-01  BRCA1      K50T               missense
TCGA-LL-A5YP-01  BRCA1      D96H               missense
TCGA-PE-A5DE-01  BRCA1      E1419K             missense
TCGA-A1-A0SI-01  BRCA1      E9Q                missense
TCGA-AO-A1KR-01  BRCA1      C644del            in_frame_del
TCGA-E2-A1L9-01  BRCA1      S1027I             missense
TCGA-EW-A2FR-01  BRCA1      D366N              missense

and getting plot as shown here:

waterfall plot

But in that, I did not understand how it is plotting translational effect, because there is no information regarding synonymous or non-synonyms mutations.

plot mutation • 438 views
ADD COMMENTlink modified 4 months ago by RamRS20k • written 5 months ago by shivangi.agarwal80050

How to add images to a Biostars post

ADD REPLYlink written 5 months ago by WouterDeCoster37k

A missense or indel variant is non-synonymous, and that information is in your table.

ADD REPLYlink written 5 months ago by WouterDeCoster37k

But, in this case, its not like that, all missense mutations are not non-synonyms.

ADD REPLYlink written 5 months ago by shivangi.agarwal80050

all missense mutations are not non-synonyms

A missense variant is by definition non-synonymous.

ADD REPLYlink written 5 months ago by WouterDeCoster37k

Ok, I got it. That is fine. But, among non-synonyms, if we want to indicate the lethal mutation in the plot itself, how it can be done?

ADD REPLYlink written 5 months ago by shivangi.agarwal80050
1

What do you mean by "lethal" mutations? That's not a standard classification.

ADD REPLYlink written 5 months ago by Devon Ryan88k

It means that the mutations having deleterious functional impact. It is not a standard classification, but it can be predicted using different tools. I got the information from cbioportal. My concern is if we can show these mutations in the graph itself while giving its information in input file.

ADD REPLYlink written 5 months ago by shivangi.agarwal80050
1
gravatar for Devon Ryan
5 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

You need to annotated these using something like Ensembl's variant effect predictor (there are a number of alternatives to this).

ADD COMMENTlink written 5 months ago by Devon Ryan88k

That is fine, but I need to plot these in waterfall plot itself. Can it be done?

ADD REPLYlink written 5 months ago by shivangi.agarwal80050

You have to label them before you can plot them.

ADD REPLYlink written 5 months ago by Devon Ryan88k

Hi

I noticed one problem while plotting this plot. When I simply plotted data given in the link, I noticed that the gene which is having two same types of mutation with different variant in the same sample is being shown in the plot only once. example, the gene MAP3K1 is having two frame shift mutations, as p.H1058fs and p.I1218fs in sample 12, the plot shows only first one, and not showing second mutation. The plot is shown here:

    12  MAP3K1  frame_shift_ins p.H1058fs
    12  MAP3K1  frame_shift_ins p.I1218fs

Why it is so? Is there any other code to add to plot both one. Please suggest.
Thanks in advance.

ADD REPLYlink modified 4 months ago by RamRS20k • written 5 months ago by shivangi.agarwal80050

Ask Obi, it's his tool.

ADD REPLYlink written 5 months ago by Devon Ryan88k
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