Question: Gene Ontology Enrichment Of Non-Model Bacterial Genome
gravatar for tkarasov
8.6 years ago by
tkarasov30 wrote:

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?


ontology • 5.8k views
ADD COMMENTlink modified 6.0 years ago by dago2.6k • written 8.6 years ago by tkarasov30

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

ADD REPLYlink written 6.0 years ago by dago2.6k
gravatar for dago
6.0 years ago by
dago2.6k wrote:

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:

ADD COMMENTlink modified 15 months ago by _r_am32k • written 6.0 years ago by dago2.6k
gravatar for huanglb0805
6.1 years ago by
huanglb08050 wrote:

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?

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by huanglb08050
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