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I have a list of genes (about 2000) from lines of drosophila subobscura, in the following format:

  • LOC117900589
  • LOC11788959
  • LOC11790331

I'm trying to represent this set of genes in a useful way.

So, I was recommended to represent the ontology function of these genes in a graphical way. I was recommended this tool: http://cbl-gorilla.cs.technion.ac.il/

One inputs a list of genes and it outputs this kind of graph: GOrilla example output

The problem is that, this tool, GOrilla only accepts genes from drosophila melanogaster.

I have to either:

  • a) convert the genes id to a homologous gene in melanogaster
  • b) find an alternative tool

A solution to either a) or b) would be helpful. Or an alternative solution.

For a) I tried:

  • Ncbi's homologene: which doesn't seem to be working for a the genes ID I tried so far (I didn't try them all)
  • Blasting the gene sequence on melanogaster's genome and looking through the list manually to find an homologous gene.

So far these methods have been impractical for the number of genes I have.

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1 Answer 1

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Have you tried DAVID for functional annotation (Gene Ontology and KEGG terms)?

I usually use DAVID to extract GO and KEGG terms and plot the results using R.

If you also want to plot a protein-protein interaction (PPI) network for your gene list you can use STRING database to extract interactions and network and use Cytoscape for visualizing this result.

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  • $\begingroup$ I tried putting a bunch of entrez id genes and I got nothing useful it seems? imgur.com/tZc6Vk8.png $\endgroup$ Sep 23 at 8:17
  • $\begingroup$ Can you mail me your gene list? So that I can tell you a better solution. My mail id is niteshkumar20sept@gmail.com $\endgroup$ 2 days ago

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