GO analysis of genes with SNPs and chromsomes

Question

[padmoo]

Hi everyone,

I'm trying to analysis some SNP data. I have a long list of genes with SNPs and would like to do a GO analysis to see which categories are overrepresented. I thought about doing goseq but this includes a length bias for each gene which I believe is not neccessary as I am not working with RNA-Seq data.

On top of this I would like to know which GO categories are overrepresented on each chromosome of my genome so I can compare this to the chrosomes with SNPs.

Does somebody know a good way of doing this analysis? Or do I have to worry about the lenght bias if I use goseq?

Thank you!

Regards, padmoo

Answer 1

[ivivek_ngs]

If you simply want to do GO analysis with your genes of a desired species then you can use PANTHER or GOrilla to find the GO terms for your gene list putting the desired species and since you have a huge number of genes as you are saying you can directly take the top significant GO terms and then them in ReviGO for over-represented terms.

You can also take a look at this thread Alternatively you can also take a look at MAGENTA

Hope these helps!