How to do GO Annotation and enrichment Analysis in R language

How to do GO annotation and enrichment analysis in R language? aiming at this problem, this article introduces the corresponding analysis and solution in detail, hoping to help more partners who want to solve this problem to find a more simple and feasible method.

GO annotation and enrichment analysis

GO annotation and enrichment analysis are done using TBtools

The data used by the editor is sweet cherry chloroplast protein coding gene for GO annotation, and then select some genes for enrichment analysis, the selected gene is

RpoC1

RpoB

RpoA

RpoC2

AtpI

AtpF

AtpE

AtpH

AtpB

AtpA

AccD

RbcL

Rpl22

Rpl23

Rpl20

Rps8

Rps7

Rps16

Rps15

Rps14

Rps18

After enrichment analysis, the file GOenrichmentOutput.txt..GO.Enrichment.final.xls was obtained.

Pick out 5 columns based on the sample data of the GOplot package

Class GO_Name GO_ID GenesOfSelectedSetInGOterm corrected p-value (BH method)

As dataset 1

Dataset 2 includes

ID,logFC,AveExpr,t,P.Value,adj.P.Val,B

The column variables of dataset 2 should all be the results of transcriptome data analysis.

For example, logFC should be multiple change Fold change and then take log

AveExpr should be the average expression quantity, etc.

Then construct the dataset by imitating the example of the help document

Help (package= "GOplot")

Library (GOplot)

Data (EC)

File1