statitistical question: how can I say if there is a difference in the gene that fall inside/outside an especific region?

Question

[Lila M]

Hi community, I have an statistical question to ask you. I have a data set, for a specific time point I have 3 groups: -transcribed genes direction 1 (n =x) -transcribed genes direction 2 (n=y) -transcribed genes direction 3 (n=z)

and I have a list with specific nt of interest (n = 5k)

I've calculate the distances from those nt to the genes and I would like to know if there is any difference in those that are inside or outside the gene, lets say:

• for transcribed direction 1: 50/x are inside and 600 are at 1kb distance
• for transcribed genes direction 2 : 500/y are inside and 700 are at 1kb distance -for transcribed genes direction 3: 300/z are inside and 500 are at 1kb distance

what is the best way to show if they are different or not? any statistical test to show it?

Thank you

[Jean-Karim Heriche]

This looks like a contingency table so you could use a Chi-squared test.

[Lila M]

but they are not independent samples, so I'm not sure if chi2 is the best way