Gene Ontology visualization
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7.4 years ago
inadamj ▴ 60

Hello all

currently I am working on GO visualization (gene_association.aspgd.gz -- GO Annotations File from http://www.aspergillusgenome.org/download/go/)

and I have ZERO knowledge about it and from where to start.

is there any good JavaScript library can help OR any paper can explain GO visualization/ tool.

I read about GO slim but nothing makes it clear

visualization gene Gene-Ontology GO • 6.3k views
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Hi,

Following on the topic, how can I get a list of GO ids along with p-values from PANTHER Overrepresentation to use with REViGO? (Right now all I can get are the actual terms, but REViGO needs GO number...).

Thank you in advance,
M

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Post a new question please.

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7.4 years ago

Next time, provide more information about the file and what you wanna do exactly. This file is checked contains all GO annotations for Aspergillus nidulans genes (protein and RNA).

From the ref website,

The gene_association.aspgd.gz file uses the standard file format for gene_association files of the Gene Ontology (GO) Consortium. A more complete description of the file format is found here: ftp://ftp.geneontology.org/pub/pub/go/gene-associations/readme/aspgd.README

Here it summarises most of the gene ontology tools, depending on what you want to do, you can go for one.

http://neurolex.org/wiki/Category:Resource:Gene_Ontology_Tools

For most of my needs, DAVID, REVIGO, PANTHER suffice but it really depends what you want to do.

The above is a list of all GO annotations for Aspergillus nidulans, so just as an example, I picked first 2000 terms and submitted it to REVIGO to generate a visualisation for Biological Process branch.

grep -o 'GO:.*' gene_association.aspgd | cut -f1 | head -n 2000

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Sukhdeep Singh: thanks a lot and sorry for being not clear.

what I ant to do is showing the gene ontology for specific file EX: Aspergillus clavatus NRRL 1 file from http://www.aspergillusgenome.org/download/gff/A_clavatus_NRRL_1/

and since the data is large I was thinking of GO slim >> I am looking for a tool or JS library that I can include it to the webpage that I am creating

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I updated the link in my answer. That webpage summarises the comprehensive list of tools, and a few are java based as well (not sure about js).

Damian did something like this using D3, check http://blog.nextgenetics.net/?e=19

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