9 Reporting results

Once we have done an enrichment analysis - how to communicate the results? Like everything - it depends what you need to say. Some examples are below.

9.1 In text

If you just need to emphasise that the differential expression relates to a condition of interest, you don’t need much:

Genes differentially expressed after SH-SY5Y cell differentiation were enriched for GO term “regulation of neurogenesis”, adjusted pval < 0.01).

And in the methods:

Enrichment calculated for differentially expressed genes with the g:GOSt enrichment tool (Raudvere et al, 2019) using a background of tested genes.

9.2 As a table

For a more complete view, a table of the significant or top n terms can be useful. E.g In a supplementary figure

The top 10 enriched GO terms for the differentially expressed genes;

GO:BP Term	Term ID	Adjusted p-value	Term Size	Num DE Genes
system process	GO:0003008	2.90E-04	1243	45
nervous system development	GO:0007399	4.19E-04	1985	60
regulation of cell development	GO:0060284	1.98E-03	795	33
central nervous system development	GO:0007417	2.67E-03	805	33
regulation of neurogenesis	GO:0050767	5.59E-03	707	30
regulation of nervous system development	GO:0051960	5.78E-03	790	32
regulation of cell differentiation	GO:0045595	6.03E-03	1471	47
multicellular organismal process	GO:0032501	2.04E-02	5300	111
system development	GO:0048731	2.88E-02	3668	85
neurogenesis	GO:0022008	4.36E-02	1375	43

9.3 As a figure

Plots of -log p-value are a popular option for a figure. By taking the exponent of the p-value bigger bars indicate more significance.

For instance, this figure is taken from the (Pezzini et al. 2017) paper. Note that in this figure shows 2 specifics categories from the IPA (ingenuity) database using the IPA tool (not covered here), so the terms themselves differ.

You can also build on such a plot with number of genes and the like. For an example, see the ‘bubble’ chart produced by a package called pathfindR here: https://www.biostars.org/p/322415/

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There are also tools like cluego (a cytoscape plugin) that build enriched terms into a network : http://apps.cytoscape.org/apps/cluego