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[go-friends] Searching with AND

Smith, Jennifer jrsmith at mcw.edu
Thu Jun 18 11:07:15 PDT 2020


RGD's OLGA (Online List Generator and Analyzer) tool also does this for eight mammalian species including human (e.g. see https://rgd.mcw.edu/rgdweb/generator/list.html?a=&mapKey=38 to access the tool for searches of human genes).  From the landing page, select "Ontology annotation" and then "GO: Molecular Function".  Begin typing the term "retinol dehydrogenase activity", select the term from the dropdown and click "Continue".  In the results page, select "Add Another Gene List" and repeat the sequence of actions for "NAD+ binding".  The tool will bring up a "preview" list of the human genes annotated to that term and give you selections for adding the lists together (Union), getting the overlap of the two (Intersection) or subtracting the second from the first (Subtract) to get a final result set of genes.

I took the liberty of trying the two terms that you mentioned and did not find any overlap in the resulting gene lists.  However, I was able to find three genes that overlapped in the intersection of retinol dehydrogenase activity and NAD binding (you can use the red X to the right of the first gene in a list in the WorkBench to remove that list from the results and redo the analysis with a different term).  Another possibility that might interest you is to query for overlap between the genes annotated to retinol dehydrogenase activity and those with gene-chemical interaction annotations (Ontology Annotation-->CHEBI) for NAD(+).  When I followed the same procedure in OLGA for that GO term and the ChEBI term NAD(+), the overlap was 9 genes.  In the final result page, "Analyze Result Set" will give you a number of options for analysis, including a link to download an Excel file of the list of genes in the final Result List.

I hope this is helpful!  If you need more information about this, please feel free to contact me directly.

Jennifer



Jennifer R. Smith
Project Manager
Rat Genome Database
Medical College of Wisconsin
8701 Watertown Plank Rd.
Milwaukee, WI 53226
Ph:  414-955-8871
Fax:  414-955-6595
jrsmith at mcw.edu
http://rgd.mcw.edu

-----Original Message-----
From: go-friends <go-friends-bounces at lists.stanford.edu> On Behalf Of Valerie Wood
Sent: Thursday, June 18, 2020 12:31 PM
To: go-friends at lists.stanford.edu
Subject: Re: [go-friends] Searching with AND

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________

Hi Ed,

Term Matrix tool will do this for you
https://urldefense.com/v3/__http://amigo.geneontology.org/matrix__;!!H8mHWRdzp34!qv9wQTLeiVoUMB9xbg7kOpvPTt0pEWZzHnCvnsjqFbaeAUkqtIjb27URGx27Kww$

Best,

Val



On 18/06/2020 17:55, Ed Siefker wrote:
> This seems like a very simple thing, but I haven't been able to figure 
> out how to do it.
>
> I want a list of gene products that match both GO:0070403 AND GO:0004745.
>
> I've tried QuickGO, and it gives me a list of gene products that match
> GO:0070403 OR GO:0004745.  I can't find any way to make it give me the 
> intersection of these sets.
>
> I've tried AmiGO, and each individual GO term gives me appropriate 
> gene products.  When I provide both GO terms, it gives me a list of
> gene products that match neither.   Why does it return Dopamine
> Receptors, when I'm searching for retinol dehydrogenase activity and
> NAD+ binding?
>
> This is pretty confusing, am I using the wrong tools?  Thanks -Ed 
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