How to use enricher in clusterProfiler for enrichment Analysis

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1. problem

GO or kegg enrichment analysis of genes requires annotation information from the GO and KEGG databases of all genes in the genome. It is very simple for people who are model species to have ready-made annotation results, which can be used directly. For example, clusterProfiler can be directly used for gene set enrichment analysis. However, for the research objects of non-model animals and plants, there are often no ready-made annotation results, so it is impossible to carry out enrichment analysis directly.

Therefore, it is very important to learn the batch annotation of gene function; here is a method for GO and KEGG enrichment analysis of all non-model species.

two。 Batch annotation of gene

EggNOG is used to annotate the genome. in order to carry out enrichment analysis, we must first have GO annotation and KEGG annotation of the background data set, and eggNOG is selected for annotation here.

It is an online server, which can be annotated by uploading with a click of the mouse without complicated configuration. Although eggNOG is a web server, it can annotate up to 100000 sequences at a time, which should fully meet the requirements. Submit the corresponding cds sequence or protein sequence of your gene to this website for annotation.

Documents to be prepared for 3.GO enrichment analysis:

To study the corresponding GO files of all genes in the species genome:

Go2gene.tsv: collated from the eggNOG comment result file

GOGENE

CLASSGO:0000165Pg_S3686.2

Biological_processGO:0003674Pg_S3686.2

Molecular_function.

Function description file corresponding to go2name.tsv:GO term

First of all, you need to go to GO to download the obo file of GO. Here I use go-basic.obo, and then I write a script that parses the obo file into the following format:

Http://purl.obolibrary.org/obo/go/go-basic.obo

GODESCCLASSGO:0000001mitochondrion inheritancebiological_processGO:0000007low-affinity zinc ion transmembrane transporter activitymolecular_function

4. Documents needed for KEGG enrichment analysis

Ko2gene.tsv: collated from the eggNOG comment result file

KOGENEko00920Pg_S3686.2

Ko01100Pg_S33386.2

The name of the ko2name.tsv ko path

KODESCko00440Phosphonate and phosphinate metabolismko00450Selenocompound metabolismko00460Cyanoamino acid metabolismko00471D-Glutamine and D-glutamate metabolismko00472D-Arginine and D-ornithine metabolismko00473D-Alanine metabolismko00480Glutathione metabolismko00510N-Glycan biosynthesisko00513Various types of N-glycan biosynthesisko00512Mucin type O-glycan biosynthesis5. Enrichment analysis

Enrichment analysis is carried out by using the general function enricher in clusterProfiler:

Library (clusterProfiler) ko2name