Question: Gene Ontology enrichment analysis of biological processes for up- and down-regulated genes?
3
gravatar for Wox
10 months ago by
Wox370
HUJI
Wox370 wrote:

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;

GO-enrichment-and-KEGG-pathway-analysis-for-up-and-down-regulated-genes-in-PCa-a 21731-309033-1-PB 12864-2019-6181-Fig5-HTML 12864-2018-5318-Fig2-HTML

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.

rna-seq R • 363 views
ADD COMMENTlink modified 10 months ago by grant.hovhannisyan2.0k • written 10 months ago by Wox370
2
gravatar for lessismore
10 months ago by
lessismore930
Mexico
lessismore930 wrote:

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.

ADD COMMENTlink written 10 months ago by lessismore930
1

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

ADD REPLYlink modified 10 months ago • written 10 months ago by Antonio R. Franco4.5k
1
gravatar for Antonio R. Franco
10 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

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

ADD COMMENTlink modified 10 months ago • written 10 months ago by Antonio R. Franco4.5k

I would recommend clusterprofiler package as a starting point

ADD REPLYlink written 10 months ago by cpad011214k
1
gravatar for grant.hovhannisyan
10 months ago by
grant.hovhannisyan2.0k wrote:

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

ADD COMMENTlink written 10 months ago by grant.hovhannisyan2.0k
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