Shulou(Shulou.com)06/01 Report--

In this issue, the editor will bring you GO notes on how to obtain all the genes of species. The article is rich in content and analyzes and narrates it from a professional point of view. I hope you can get something after reading this article.

Gene Ontology is one of the important databases to study the function of genes. In the enrichment analysis of GO, it is necessary to provide the GO annotation information of all genes. Here are several ways to obtain this information.

1. Download from the GO official website

The official website provides GO annotation information for several common species. The file format is GAF, and the download link is

Http://www.geneontology.org/page/download-go-annotations

The corresponding files for human are as follows

What is provided in this file is the GO information corresponding to the protein in the uniprot database. The uniprot database number corresponding to the protein, the gene symbol corresponding to the protein, and the GO annotation are given. The example is as follows

UniProtKB A0A024R161 DNAJC25-GNG10 GO:0003924

There are many columns in the original file. I only chose the first four columns, the first column represents the name of the database, the second column represents the number in the database, the third column is gene symbol, and the fourth column is the corresponding GO comment.

two。 Download from the GOA project

EBI analyzed the proteins in the uniprot database with GO annotations. The project is called gene ontology annotation, or GOA for short. The annotated information for species is also provided in FTP, as shown in the following diagram.

Take human as an example, the FTP address is as follows

Ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/

The content and format of the files here are the same as those on the GO official website, but there is a slight difference in quantity.

3. Download from NCBI Gene database

When you retrieve a gene in NCBI, you will see a lot of annotated information corresponding to the gene on the results page, including GO comments, which are available for download on FTP. The link is as follows

Ftp://ftp.ncbi.nih.gov/gene/DATA/

Examples of several major files are as follows

Gene2go is the GO annotation file corresponding to the gene. This file contains the GO information of all species, and the designated species can be extracted according to their corresponding tax id.

Each gene is identified by Entrez Id in NCBI, and the corresponding GO information of Entrez ID, Ensemble Id and Gene Symbol can be obtained through several other files.

4. Get from Bioconductor

For common species, the corresponding annotation packages are also available on Bioconductor, as shown below

Take org.Hs.eg.db as an example. This R packet stores a lot of information corresponding to human genes. The corresponding GO annotation information of genes can be obtained through keys and select functions. The code is as follows

> k select (org.Hs.eg.db, keys = k, columns = c ("GO", "ONTOLOGY"), keytype= "ENTREZID") 'select ()' returned 1:many mapping between keys and columns ENTREZID GO EVIDENCE ONTOLOGY1 1 GO:0002576 TAS BP2 1 GO:0003674 ND MF3 1 GO:0005576 IDA CC

The code here only gets GO comments based on Entrez ID. In fact, this R package also contains gene symbol, ensembl id and many other gene ID.

Many packages for enrichment analysis read GO annotations from the db packages corresponding to the species.

The above is the GO comments shared by the editor on how to obtain all the genes of the species. If you happen to have similar doubts, please refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.

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