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[go-helpdesk] Enrichment GO Help query

Paola Roncaglia paola at ebi.ac.uk
Wed Jun 27 02:47:47 PDT 2012


Dear Alfons,

Thank you for your email. If I understand correctly, the identifiers in 
the column labeled "#proteinID" have been arbitrarily assigned by your 
sequencing lab? Are these identifiers already included in any public 
database? Because if so, I might point you to a way to convert your gene 
product IDs into something that the enrichment tool will recognize.

You might still be able to use the AmiGO enrichment tool as follows - 
I'm not entirely sure this will work as I've never used it with a newly 
sequenced species, but it's worth a try, and I'm cc-ing the GO Software 
group on this email in case they have any comments:

In the field labeled "Input your gene products", enter the list of 
identifiers for your induced/repressed genes. These identifiers should 
be in the same format as the ones in the column labeled "#proteinID" in 
your example (they should be a subset of those proteinIDs). You may 
simply write the IDs in the box (separated by a whitespace), or upload a 
text file with the IDs separated by a newline or a whitespace.

Then, in the field labeled "Input your background set", upload the full 
dataset you received from the genome sequencing project. You may not 
need a full GAF file; the information you have in your example might 
suffice. If this does not work, we might have to explore other solutions.

In the field labeled "Select the database filter", click on "No selection".

In the field labeled "IEA annotations", "use IEAs in calculation" - 
select "yes". Because your fungal species is newly sequenced, most of 
the annotations are likely to be IEAs (inferred from electronic 
annotation); please review the manual page for the AmiGO enrichment 
tool, if you haven't already done so:
http://wiki.geneontology.org/index.php/AmiGO_Manual:_Term_Enrichment

I presume your microarray is not a commercial one. If it were 
commercial, there may be other publicly available enrichment tools you 
could use - feel free to let us know in that case.

As for your AmiGO BLAST questions:
A manual page for the tool is available here: 
http://wiki.geneontology.org/index.php/AmiGO_Manual:_BLAST
In particular, see the section "Entering sequences". You may use more 
than one gene, but the format to use depends, again, on whether your 
gene products are included in any public database or not. If not, you 
may use FASTA sequences. Please refer to the manual for full details. 
You probably would not want to use BLAST results to do an enrichment 
analysis, as those results will be from species that may be quite 
different from your fungal one.

I hope this answers your queries. If the AmiGO term enrichment doesn't 
work, please let us know and we'll look into other solutions.

With best regards,

Paola Roncaglia, for GO help.

On 6/26/12 3:08 PM, Alfons Weig wrote:
>
> Dear Paola,
>
> thank you for your fast reply.
>
> Unfortunately, I do not have a full gene association file. I have 
> already looked at you GAF1.0 and GAF2.0 specifications, but there are 
> too much columns in there, which I cannot fill with my data. The only 
> dataset I received from the genome sequencing project have the 
> following content (4 lines as an example). It is probably to less to 
> create a valid GAF background file.
>
> #proteinId        gotermId         goName          gotermType    goAcc
>
> 12647  815      rhodopsin-like receptor activity         
> molecular_function    GO:0001584
>
> 12647  5270    G-protein coupled receptor protein signaling 
> pathway         biological_process      GO:0007186
>
> 12647  9321    integral to membrane cellular_component    GO:0016021
>
> 13104  162      nucleotide binding      molecular_function    GO:0000166
>
> etc.
>
> I have also tried to figure out what exactly a "list containing gene 
> products" as the background set would mean (see screenshot below taken 
> from the GO Term Enrichment page) , but I could not find any example 
> for that type of file..
>
> So, I was looking for a tool which would allow me to enter GO terms 
> directly (taken from induced/repressed genes) and to overlay it to a 
> GO graph.
>
> I have also seen the BLAST tool at AMIGO, but I could not figure out 
> how I can combine Blast results from more than one gene to initiate a 
> subsequent GO Term enrichment analysis; I can only use the results of 
> one single gene, right?
>
> Thanks for your help!
>
> Best regards
>
> Alfons
>
> *Dr. Alfons Weig*
>
> DNA-Analytik & Ökoinformatik - Univ. Bayreuth
>
> Universitätsstrasse 30
>
> 95447 Bayreuth - Germany
>
> Tel. +49 (0)921-552457
>
> www.daneco.uni-bayreuth.de
>
> *Von:*Paola Roncaglia [mailto:paola at ebi.ac.uk]
> *Gesendet:* Dienstag, 26. Juni 2012 15:46
> *An:* a.weig at uni-bayreuth.de
> *Cc:* go-helpdesk at mailman.stanford.edu
> *Betreff:* Re: Enrichment GO Help query
>
> Dear Alfons,
>
> Thank you for writing to GO.
>
> I have a few questions so I may provide you with better indications. 
> Do you have a gene association file for the fungal species you're 
> working on? That is, a file that includes both the full list of genes 
> in your fungus' genome (and/or the genes on the microarray) and the GO 
> terms associated to each gene. Is the microarray you're using a 
> commercial one?
>
> For your reference, a list of GO tools for enrichment analysis is 
> available here:
> http://www.geneontology.org/GO.tools_by_type.term_enrichment.shtml
>
> With best regards,
>
> Paola Roncaglia, for GO help.
>
>
>
> Subject:
>
> GO Help query (from website)
>
> From:
>
> a.weig at uni-bayreuth.de <mailto:a.weig at uni-bayreuth.de>
>
> Date:
>
> Tue, 26 Jun 2012 00:14:36 -0700
>
> To:
>
> go-helpdesk at mailman.stanford.edu <mailto:go-helpdesk at mailman.stanford.edu>
>
> Email:a.weig at uni-bayreuth.de  <mailto:a.weig at uni-bayreuth.de>
> Name: Ontology (from Alfons Weig)
> Text: Hello,
> I have identified induced/repressed genes by microarray analysis from a fully sequenced fungus. Most of these genes were already annotated with GO terms during the sequencing and annotation project. However, this organims is not included in the reference organisms in AMIGO's GO Term enrichment.
> I am looking for a tool where I can enter GO terms directly to see whether some term are enriched. My hope was to use GO Slimmer using the fungal or Aspergillus slims, but - again - genes are required for input.
>   
> Is there any tool where I can analyse a subset of GO terms for enrichment/slim analyses.
>   
> Best regards
> Alfons Weig
>
>
>
> -- 
> Dr Paola Roncaglia
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
> p: +44 1223 492600
> f: +44 1223 494468

-- 
Dr Paola Roncaglia
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492600
f: +44 1223 494468

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