Create a Gene Enrichment GO plot from goana output
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Raito92 ▴ 60
Last seen 11 months ago

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...

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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...

enter image description here

Thanks in advance for your help!

goana RNASeq edgeR RnaSeq GO • 1.8k views

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