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Gene Ontology Enrichment Of Non-Model Bacterial Genome

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!

ontology
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updated by dago dago • written by tkarasov • tkarasov

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

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written by dago dago

3 answers

For annotation using GO you can look:

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

  • topGO
  • GOstats
  • Clusterprofiler

or you could use Cytoscape plug-in:

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updated by Ram Ram • written by dago dago

Hi,

What is GTF file?

Rama

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written by rama.gollapudi • rama.gollapudi

please don't post a new question as an answer

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written by Istvan Albert Istvan Albert

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?

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written by huanglb0805 • huanglb0805

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