Question: Map GO Terms to Protein/Gene of E.coli
0
gravatar for Benni
2.9 years ago by
Benni30
Benni30 wrote:

I have a list of Proteins/Genes and I want to find out, which GO Terms (especially Cellular Component) belong to every Protein. Is there maybe a simple .csv file available online? I looked at Gene Ontology, Uniprot and EcoCyc, but I couldnĀ“t find such a list. Alternatively there could be a online tool, that maps such a list?

Thanks

go e.coli • 1.5k views
ADD COMMENTlink modified 2.9 years ago by EagleEye6.4k • written 2.9 years ago by Benni30
2
gravatar for EagleEye
2.9 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Try GeneSCF to retrieve complete list of GO terms with corresponding Genes as simple text file.

./prepare_database -db=GO_all -org=ecocyc

The above command downloads complete GO db as simple text file in following location, 'geneSCF-tool/class/lib/db/ecocyc/' (This will have Biological Process, Molecular Function and Cellular Component as separate files)

Alternatively, you can provide the list of genes to the tool as input. It will cluster all the genes according to GO terms it belongs. Example for Cellular component,

./geneSCF -m=update -i=INPUTgene.list -t=gid -db=GO_CC -o=/ExistingOUTPUTfolder/ -org=ecocyc --plot=yes --background=#NumberOfBackgroundGenes

NumberOfBackgroundGenes=3836 (number derived from total genes from GeneOntology database for E.coli)

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by EagleEye6.4k

Instead of using the quote tool formatting you may want to switch to code tool (101010 button) for these code examples. It makes it easier to see the code.

ADD REPLYlink written 2.9 years ago by genomax70k

Thanks for the information :)

ADD REPLYlink written 2.9 years ago by EagleEye6.4k
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