select genes (ecocyc IDS) on the basis of specific gene ontology terms / inspect gene ontology tree

[aless...@gmail.com]

Hello Everyone

I am quite unfamiliar with gene ontology 

I have a list of genes of interest of E. coli (about 1800 genes) in a  Matlab file

I have the needing to select those genes belonging to specific biological functions, like nutrient transport, stress defense etc..

I know the biological function but I don't exactly know how my broad definitions map into the gene ontology tree.

My idea was to use a program like OBO-edit to understand a bit more the parent to child structure of gene ontology, related to E. coli

in order to select the broadest GO term for each biological functions and then use matlab to identify corresponding genes belonging to each category.

I have however some doubts:

1) I downloaded the GO in the OBO format from http://go.princeton.edu/GOTermMapper/goSlimFiles/gene_ontology.obo

but i don't know how to select those terms that are present only in E.coli. E.g. motocondria related terms should be excluded

I also have the gene associacion file for E.coli in Ecocyc format. Is there an easy way to make such cross-correlation between ontologies and e coli genes with OBO-edit?

Is there a better and or easier program that can fullfill my needings?

Despite my struggling I am really interested in understanding more about the gene ontology structure and I am having some fun, but some help from you would be REALLY appreciated

Thank you in advance for the suggestions you will give and you patience!

Alessandro

[Yongqun He]

You can get the whole set of E. coli genes from OGG:
http://www.ontobee.org/browser/rdf.php?o=OGG&iri=http://purl.obolibrary.org/obo/OGG_2000511145

for each E. coli gene, OGG provides a GO association, for example,

for the E. coli gene accG:
http://purl.obolibrary.org/obo/OGG_3000947758

it has an annotation:
has GO association: GO_0042966

You can identify all GO associations for all E. coli genes. Then you can use the information for different applications.

Please see if you have any questions.

Oliver He

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[Asiyah Yu Lin]

Hi Alessandro,

I extracted the E.coli genes from the OGG owl file using OntoFox (http://ontofox.hegroup.org/). Please check the attached file. (unzip and you will see an owl file)

The gene is a class in OGG, and its GO association terms are annotated by following tag:

<obo:OGG_0000000029></obo:OGG_0000000029>

It should be relatively straight forward to extract the information that you would need for Matlab input.

Best,

Asiyah

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