how to compare the Ka/Ks ratio for chromosomes

Question

[upendrakumar.devisetty]

I am interested in comparing the Ka/Ks values for each of the chromosomes in my species of interest. I have already generated Ka/Ks values for all the genes on each of the chromosome and i am now wondering how i compare the KaKs values across the chromosomes. Basically my idea is to check to see what chromosome has significant positive selection based on Ka/Ks ratios. Am i thinking correct?

Thanks
Upendra

[Zev.Kronenberg]

What organism?

[upendrakumar.devisetty]

Its a plant species......Brassica rapa

Answer 1

[Sukhi Singh]

To make it more significant, you can subset on the type of genes, rather than all genes.

So, for a different subset of genes (e.g. genes involved in metabolism etc), then generate a table where each column is a subset of genes and rows are the chromosomes which would output a plot something like this

Or you can actually, plot all chromosomes on x axis (each bar is a chromosome) and bar is divided into different gene subsets, so you can compare it among all chromosomes. For significance, you can apply student t-test on that.