Question: How to check whether mutation in a gene activating or inactivating other genes?
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6 weeks ago by
newbie80
newbie80 wrote:

I have mutational data and created an oncoplot that shows the number of mutations and the type of mutation of genes in each sample.

Showing here an example plot:

enter image description here

How can I look whether DNMT3A gene mutation activating or inactivating other genes?

ADD COMMENTlink modified 6 weeks ago by JC11k • written 6 weeks ago by newbie80
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gravatar for JC
6 weeks ago by
JC11k
Mexico
JC11k wrote:

short answer: you can't

long answer: all your mutations seem to be deleterious, so you can expect the protein is not being active, to understand the effect of this you will need to generate a cell-line with that gene knocked-down, then do RNA-seq or other gene/protein expression technique to identify which genes are being affected. But this is cancer, so each cell-line is a particular mixture for a particular tumor, so any finding could be not directly applicable in any other study or real data. Alternatively, to extrapolate this, you could use TCGA or other large collection of data, select your cancer type and verify if the gene is being expressed in that cancer, if you're lucky, you can split your set into 2 categories, one for samples with DNMT3A mutations and other for no-mutations in the gene, then compare gene expression in both sets and detect DEGs.

ADD COMMENTlink written 6 weeks ago by JC11k
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