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Question: How To Do An Go Enrichment Analysis In Galaxy?
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gravatar for Yan He
6.1 years ago by
Yan He • 240
Yan He • 240 wrote:
Hi everyone, I got a list of differentially expressed genes from my RNA-seq data. Is there a tool on Galaxy that I can do the GO enrichment analysis for the differentially expressed genes? Any help or suggestion is highly appreciated! Best regards, Yan
galaxy • 2.5k views
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modified 6.1 years ago by Björn Grüning • 350 • written 6.1 years ago by Yan He • 240
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gravatar for Björn Grüning
6.1 years ago by
Björn Grüning • 350
Björn Grüning • 350 wrote:
Hi Yan, have a look at the blast2GO wrapper in the toolshed. If you already have gene-ids you can download the GO in an appropriate format and intersect with your ids. Hope that works, Bjoern
ADD COMMENT • link written 6.1 years ago by Björn Grüning • 350
Hi Bjoern, Thank you very much for your reply! I am working on one species of oyster and the gene_ids are created from the transcriptome dataset, which is in our own defined format. I already have the gene_ids and GO annotation for each gene. I would like to do the GO enrichment to see which are highly represented in the data. Is there a tool in Galaxy to fulfill this? Thanks again, Yan 发件人: Björn Grüning [mailto:bjoern.gruening@pharmazie.uni- freiburg.de] 发送时间: Monday, October 08, 2012 2:06 PM 收件人: Yan He 抄送: galaxy-user@lists.bx.psu.edu 主题: Re: [galaxy-user] How to do an GO enrichment analysis in Galaxy? Hi Yan, have a look at the blast2GO wrapper in the toolshed. If you already have gene-ids you can download the GO in an appropriate format and intersect with your ids. Hope that works, Bjoern
ADD REPLY • link written 6.1 years ago by Yan He • 240
Hi Yan, If you already have the GO terms, then the summary, counting, and statistics tools for tab delimited are probably what you are looking for. Tool groups to look in are: Text Manipulation -> Cut, Compute Join, Subtract and Group -> Group Statistics There is also the tool "Phenotype Association -> g:Profiler" that may be interesting to explore. Good luck with your project, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD REPLY • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k
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