Gene Ontology enrichment analysis of biological processes for up- and down-regulated genes?

Question

[WUSCHEL]

Is there any FREE interactive online tool for Gene Ontology enrichment analysis of biological processes for summarizing up- and down-regulated Arabidopsis thaliana genes?

For example, figures look like below;

If not, how can I do this in "R"? Could someone provide Stepwise guidance user-friendly vignette if possible.

I have output DEG .csv file for summarized data with columns;

Gene ID
adj.pval_Mutant1.WT
adj.pval_Mutant2.WT
adj.pval_Mutant3.WT
log2FC_Mutant1.WT
log2FC_Mutant2.WT
log2FC_Mutant3.WT
up.down_Mutant1.WT
up.down_Mutant2.WT
up.down_Mutant3.WT

Your help would be greatly appreciated.

Answer 1

[lessismore]

Basically everything you've posted can be done with ggplot2 (https://ggplot2.tidyverse.org/). For enrichment analyses in plants (with Arabidopsis in your case) i recommend to use AgriGO (http://bioinfo.cau.edu.cn/agriGO/) which has several features and it's quite friendly. The output can be then used for your summary plots in R.

[Antonio R. Franco]

Another posibility is to use Tools : GO enrichment feature included into the PlantRegMet web page, but this does not require the use of R. It gives you some graphics, but you don't have the control of them

Answer 2

[Antonio R. Franco]

To be honest, stepwise guidance is obtained from the R vignettes included in each of the packages. By searching into Bioconductor, you can get many different packages dealing with GO (topGo, and the like....)

Most cases you only need to adjust the code included into the vignettes with the names of your own files.

Should you require some instructions on how to learn about R, I recommend to run R with the swirl package, that teach you how to run R using R. This, combined with a short and handy manual, is all you need to start using R

[cpad0112]

I would recommend clusterprofiler package as a starting point

Answer 3

[grant.hovhannisyan]

Check ClusterProfiler, some plots that you have posted were generated by it.