Question: GO Enrichment Analysis representation
0
gravatar for int11ap1
3.8 years ago by
int11ap1310
Barcelona
int11ap1310 wrote:

Hello,

I have 10 organisms, with the corresponding information about the Gene Ontology Enrichment Analysis... I was wondering... could I graphically represent The species, the enriched GO terms, and their score.

Thanks.

go • 2.7k views
ADD COMMENTlink modified 3.7 years ago by A. Domingues1.5k • written 3.8 years ago by int11ap1310
3
gravatar for Guangchuang Yu
3.7 years ago by
Guangchuang Yu1.8k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.8k wrote:

you may interesting the figure in http://online.liebertpub.com/doi/full/10.1089/omi.2011.0118

ADD COMMENTlink written 3.7 years ago by Guangchuang Yu1.8k
0
gravatar for A. Domingues
3.7 years ago by
A. Domingues1.5k
Mainz, Germany
A. Domingues1.5k wrote:

similarly to the figure that suggests Yu, I also like to use heatmaps to visualize GO terms when I have multiple samples:

- rows are the GO terms

- columns the samples

- colour intensity represents significance of GO term (or enrichment)

One of the advantages is that, at least in R, one can also choose to cluster the samples by how similar they are in terms of GO term enrichment.

ADD COMMENTlink written 3.7 years ago by A. Domingues1.5k

How do you get the color intensity for each grid square? That implies you have a GO significance or enrichment per sample, and it's usually defined for groups of samples or differential expression between groups. 

ADD REPLYlink written 3.7 years ago by karl.stamm3.2k
1

I am working with DEG data of several conditions compared to the same control. I use the list of differentially expressed genes from each comparison an input for, let's say, David. So for each comparison (not sample as such) I have a value for GO significance or enrichment.

Then I choose the top5 GO terms per comparison and use those (along with the enrichment score/pvalue) for the plotting.

Does that make sense?

 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by A. Domingues1.5k

Yes, thanks. The key point being that your columns are not samples per se, but comparisons between a set and a common control. Then it makes sense to speak of GO Enrichments. I'm developing some new software to actually make GO scorings per sample, and am on the lookout for similar methods, because I think no one has done it before.

ADD REPLYlink written 3.7 years ago by karl.stamm3.2k
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