Gene Ontology Enrichment Of Non-Model Bacterial Genome

Question

[tkarasov]

I am a newbie to gene ontology enrichment analyses and would really appreciate any help. I recently annotated several bacterial genomes using RAST. RAST outputs a number of annotation files including a GFF3 file and a gtf file, but I do not know how to map the annotations from these files to gene ontology classifications. For instance, within the last column of the gtf file, some of the genes are labelled with an EC number, some genes with a TC number and the majority of genes have some putative annotated function, but no associated mapping number. Is there a standard way to map the output from the gtf file to GO terms?

Thanks!

[dago]

Are you interested in annotating your proteins using GO or to perform a gene-set enrichment analysis?

Answer 1

[dago]

For annotation using GO you can look:

• blast2GO
• here

For gene-set enrichment analysis you can use either R/Bioconductor:

• topGO
• GOstats
• Clusterprofiler

or you could use Cytoscape plug-in:

• Bingo
• ClueGO

Answer 2

[huanglb0805]

Hi,tkarasov,I have the same problem as you.I extracted the DGEs' AA sequences and made a fasta file,then I used iprscan5 to get their annotations,and used wego to make GO analysis，but I don't know how to make GO enrichment,is it practicable to get the annotations of bacterial genome as background and make hpergeometric test?