Get the GO terms associated to all genes contained in a list with Python

Question

[jopealfe]

Hi!

I'm wondering if theres is a simple way or package that I can use to retrieve all GO terms that are associated to all genes that I have in a .txt file in python. I'm currently aware of packages like mygene, etc. However, all of them does not contain any function that gives all the GO terms.

Thank you in advance!

[Matteo Schiavinato]

I know it's not python, but you can definitely do that in R (I am also a python programmer but I went for R in that particular aspect).

Have a look at GO.db: https://bioconductor.org/packages/release/data/annotation/html/GO.db.html

[jopealfe]

With a quick view I didnt found any method that can output the desired atributes. Is there any one that can make the conversion of gene2GOterm ? Anyway, I'll see the doc with more attention!

[Matteo Schiavinato]

Well, it strongly depends on the oganism you work with! 99.9% you don't have such luck that someone already annotated all of them. Perhaps you should try something like Blast2GO where you input sequences and you get GOTerms out.

[jopealfe]

I'll look upon that! Thanks!

[shoujun.gu]

If you can find the file with gene names and the terms you need. (maybe some file in http://www.geneontology.org/) Then it's just the dataframe processing job..

Answer 1

[EagleEye]

Try GeneSCF. It gives all the GO terms related to the list your give as input (irrespective of whether the term is significantly enriched or not). Also using 'prepare_database' (example) module from GeneSCF, you can download entire gene ontology terms with corresponding genes as a simple text file in table format.

[jopealfe]

Thanks! This is a very usefull tool! However, it only runs in linux? Or there is also a version for Windows?

[EagleEye]

You can use in windows 10 linux bash.