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Old 09-04-2012, 04:05 PM   #1
Quat
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Default Gene Ontology Graphs

Hello,

I'm working on a transcriptome project. I generated a list of GO terms and numbers by aligning illumina reads against a reference transcriptome to get an ID, then retrieved the GO terms and numbers associated with that ID.

What I'd like to do is take my list of GO terms or numbers and create a graph of the level 2 or 3 biological functions to compare two sets of data.

The problem is that the numbers and terms I have are from the bottom level.

Is there a program which I can just load the terms I have into in order to generate this sort of graph, or some sort of perl framework that would let me look up the level 2 or 3 term of a GO term or number? The programs I have tried want to take a sequence, blast it, and then assign it a GO term, but this would take a significant amount of time with the hardware I have.

I have access to OBO files with the ontology.

Thank you
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Old 09-05-2012, 06:24 AM   #2
SES
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Ontologizer will do exactly what you want. Though, I've never used it with a single list, it's more for calculating enrichment between a study and population set. As far as Perl packages, there is GO::TermFinder, GO::Perl, GO, and presumably others (BioPerl also has some methods for annotating GO terms).
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Old 09-06-2012, 07:24 AM   #3
Quat
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Thank you, working with ontologizer now
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Old 09-06-2012, 07:35 AM   #4
SES
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Quote:
Originally Posted by Quat View Post
Thank you, working with ontologizer now
Okay, good luck. For just creating the graphs you might want to use the GO::View module (from GO::TermFinder) directly. I should have stated that before. Ontologizer can be a bit tricky to work around because you need several ontology and annotation files in a specific format. Since my last post, I also remembered a Python package called goatools that may do what you want, though I have never used it.
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