Question: Enrichment analysis and Fisher's exact test
gravatar for h.stotz
2.2 years ago by
European Union
h.stotz10 wrote:

I have a gene list and a table file with GO terms.  How can I make the gene list be used in the enrichment analysis.  Apparently the program is set such that only tables can be compared, not gene lists.



galaxy • 900 views
ADD COMMENTlink written 2.2 years ago by h.stotz10

What exact tool are you using? Capture the full name including the wrapper version or better, use "Options > view in Tool Shed" and capture the link to the tool and share it back here.

Is this at or somewhere else?

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson24k

Linking in details and closing duplicated posts.

Rank Terms as part of Genome Diversity

Rank Terms Error message

These are older tools with specific input requirements. Would you please send in a bug report from the error dataset noted in the other posts? We can try to help with usage, but it can be difficult. Please make sure that all inputs are left undeleted in the submitted bug report.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson24k

I am sorry, but I did not understand the response to my question. Where can I find it?

Henrik Stotz, PhD School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire AL10 9AB United Kingdom Phone: +44 (0) 1707 284251 Email:

From: Jennifer Hillman Jackson on Galaxy Biostar [] Sent: 18 February 2016 17:34 To: Stotz, Henrik <> Subject: [galaxy-biostar] C: Enrichment analysis and Fisher's exact test

Activity on a post you are following on Galaxy Biostar<http:"">

User Jennifer Hillman Jackson<http:"" u="" 254=""/> wrote Comment: Enrichment analysis and Fisher's exact test<http:"" p="" 16055="" #16120="">:

Linking in details:

Rank Terms as part of Genome Diversity<https:"" p="" 16117=""/>

Rank Terms Error message<https:"" p="" 16118=""/>

ADD REPLYlink written 2.1 years ago by h.stotz10

Hello, This is the tool in use? 

Rank Terms : Assess the enrichment/depletion of a gene set for GO terms (Galaxy Version 1.1.0)

The input accepted is a list of Emsembl transcript identifiers. If you have other gene names/symbols in use, then these need to be converted. Find a data provider that can be used as source for a file that contains both values (try UCSC, Biomart, Emsembl, etc.). Once you identify and load a file with the mapping, this tool can be used to associate the common value (whatever gene name/symbol you are using) to link in the Ensembl transcript name. The result can be then used with the tool by selecting the Ensembl transcript name column on the form.

Join two Datasets side by side on a specified field

The exact input requirements are described in the tool form's help section (area below the upper input/submission section). This tool is unlikely to be modified to accept different inputs by the original authors, but if you wanted to create a modified version, it would be welcomed in the Tool Shed

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson24k
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