Question: Diagnosing topGo issue - single enriched gene per enriched GO term
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4 months ago by
s.bourne0
s.bourne0 wrote:

Hello,

When I run topGo on my geneset to find enriched genes, I get a high return of 1 term annotated, and 1 term significant (see below). I'm unsure how I have enriched terms with only one enriched gene, which seems counter-intuitive.

I'm running the default weight01 algorithm that should account for GO hierarchy.

Any ideas about what could be going on to see several enriched GO terms with only one enriched gene in?

    GO.ID                  Term Annotated Significant


1 GO:0003406 retinal pigment epithelium development 1 1 2 GO:0006002 fructose 6-phosphate metabolic process 1 1 3 GO:0006370 7-methylguanosine mRNA capping 1 1 4 GO:0018279 protein N-linked glycosylation via aspar... 1 1 5 GO:0021549 cerebellum development 1 1 6 GO:0030901 midbrain development 1 1 7 GO:0030917 midbrain-hindbrain boundary development 1 1 8 GO:0036265 RNA (guanine-N7)-methylation 1 1 9 GO:0043252 sodium-independent organic anion transpo... 1 1 10 GO:0045666 positive regulation of neuron differenti... 1 1 11 GO:0045721 negative regulation of gluconeogenesis 1 1 12 GO:0050482 arachidonic acid secretion 1 1 13 GO:0050665 hydrogen peroxide biosynthetic process 1 1

Thanks, Steve

written 4 months ago by s.bourne0

Welcome to the site. Could you please format your results better, I am not sure I understand the output. Also if you could share the function call and show some of your input data it would be easier to understand where the problem might be