Visualizing Genomic Position For Many Genes Graphically.

Question

[Ryan D]

I only put a table on a poster reluctantly. Here I am hoping to show each of 64 genes we investigated as part of a pathway analysis. I'd like to show where each sits in the genome and possibly next to each the number of SNPs investigated and number significant. A Manhattan is not correct this isn't part of a GWAS. Genome-graphs is similar to what I'm thinking, but doesn't list gene name. What do you all suggest?

Answer 1

[Sean Davis]

Sounds like circos might be useful?

[Ryan D]

Ahhh... I'll have to look at this site. I've seen spirographs in Nature Genetics before and wondered how they were made.

Answer 2

[Damian Kao]

If this is for a poster, maybe it will be better to pick a handful of interesting genes you want to focus on and graphically display those individually instead of all 64 genes.

Unless you are trying to show some kind of analysis/pattern related to their genomic positions, I don't think plotting all 64 will add to the poster.

[Ryan D]

I understand this. I think you are right. Perhaps it's just better to show the relationships between those significant associations than genomic positions and SNP number. The only reason I like to see number of SNPs in a given gene or LD patterns is to decide if I believe the result is significant. Here we have the results of a meta-analysis from 9 studies. So we're pretty sure our result is real; but showing each gene may add little value as you say.

Answer 3

[Philippe]

Hi,

I think this answer in Biostar (and the others for this question) can be of interest for you. To me it seems it adresses quite well your request.