Hello, I've just performed a GO Enrichment analysis on my DEGs lists of interest.
My output looks like this:
GO Annotation Ont N Up Down P.Up P.Down
GO:0006629 lipid metabolic process BP 138 1 16 0.984250122 1.72E-06
GO:0003830 beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity MF 4.00E+00 0 3 1 8.64E-05
GO:0003677 DNA binding MF 993 28 48 0.627852839 0.000183477
GO:0004672 protein kinase activity MF 1.22E+03 54 56 0.001872221 0.000195863
GO:0004842 ubiquitin-protein transferase activity MF 105 2 10 0.820501102 0.000747032
GO:0003700 DNA-binding transcription factor activity MF 3.02E+02 13 18 0.113312829 0.002336883
GO:0030001 metal ion transport BP 6.90E+01 7 7 0.004184454 0.003187786
GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups MF 1.08E+02 5 9 0.214818268 0.00340728
GO:0005509 calcium ion binding MF 1.73E+02 5 12 0.581978935 0.003649999
GO:0004420 hydroxymethylglutaryl-CoA reductase (NADPH) activity MF 4 0 2 1 0.00455364
GO:0046983 protein dimerization activity MF 157 7 11 0.183217444 0.00489018
GO:0004722 protein serine/threonine phosphatase activity MF 3.10E+01 3 4 0.062507687 0.010628888
GO:0009269 response to desiccation BP 6 0 2 1 0.010965541
GO:0003979 UDP-glucose 6-dehydrogenase activity MF 6.00E+00 0 2 1 0.010965541
GO:0007034 vacuolar transport BP 1.70E+01 0 3 1 0.011183613
I'd like to create a nice Gene Ontology enrichment plot, providing a more impactful view of the terms found.
Here are some examples...
I particularly like the ones where terms are represented as cicles, whose size is proportional to the relevance. However, I'm a bit perplexed. Most of the scripts/codes I've found require parameters that don't seem to appear in goana output... FDR and Fold Enrichment (and z-score?). An adjusted p-value is often mentioned, which I assume is the P.Up / P.Down for up and down-represented GO terms in my output, respectively.
Do I have to calculate them myself? Did I have to set anything particular in goana arguments?
In general, any suggestions about how to plot goana output?
The classic bar plot diagram (like this one) is also an option, but I was wondering about how to obtain other types...
Thanks in advance for your help!
