Bacteria/ non standard organisms in GeneMania
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23 months ago
Megan • 0

Hey all, I'm trying to analyse bacterial gene lists/ create a network in Cytoscape.

I've looked at both the online Genemania, and the app in cytoscape and have come accross a problem; I'm trying to import a new organism - which I think means importing in a text file with the gene names on each new file for each specific organism. But it is not recognising it neither online, nor in cytoscape.

I have the feeling as a newbie I am missing something out, must there be something else in the text file?

How should the data be laid out in the text file to import a non-standard organism?

Many thanks, Megan

Genemania cytoscape • 639 views
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can you give an example of the data that you mentioned you were trying to import into Cytoscape for us to get an idea of what it looks like?

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Well, in Genemania within cytoscape, it says: if you want to use a network that isn't in the standard set, upload a file containing all the IDs for the organism in question.

By IDs I think it means geneIDs so I uploaded a list of gene names, one per line...

gyrA gyrB ....etc

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Hi Megan. According to the documentation, you can upload a new organism into the GeneMANIA Cytoscape app by running the ID Importer (http://genemania.org/plugin/tools.html). Did you give that a try? From my reading, it looks like it you have the format correct, one line per gene, but you can also included aliases on the same line. Remember that they use Ensembl by default for Gene identifiers. Also note that once you've done that, the GeneMANIA reference networks, used to calculate the guilt-by-association may not have any information for that organisms, so you might also have to upload a series of networks for GeneMANIA to use that contains interactions for your organism.

-- scooter

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