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Dear Alfons,<br>
<br>
Thanks for your reply. Could you please indicate what the fungal
species is? That might help to answer your questions.<br>
<br>
Thanks and regards,<br>
Paola<br>
<br>
On 6/27/12 1:27 PM, Alfons Weig wrote:
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<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);">Dear Paola, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US">the data are probably not yet included
in public databases, although the genome data and the
annotations are already available from the DOE JGI. Let’s
wait and hear what the west coast will suggest! <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US">I have also tried to use the Blast tool
at AMIGO. If I understood it correctly, it could be used to
blast protein sequences against annotated proteins and the
associated GO terms of the blast hits could be used to
subsequently look for GO term enrichments. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US">I think the Aspergillus background could
be used as a background, but I was not able to combine more
than one blast results in subsequent analyses. Would this
approach be an alternative?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US">Best regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US">Alfons<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" lang="EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Dr. Alfons Weig<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">DNA-Analytik & Ökoinformatik
- Univ. Bayreuth<o:p></o:p></span></p>
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font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">95447 Bayreuth - Germany<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Tel. +49 (0)921-552457<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);"><a class="moz-txt-link-abbreviated" href="http://www.daneco.uni-bayreuth.de">www.daneco.uni-bayreuth.de</a><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family:
"Tahoma","sans-serif"; color:
windowtext;">Von:</span></b><span style="font-size:
10pt; font-family:
"Tahoma","sans-serif"; color:
windowtext;"> Paola Roncaglia [<a class="moz-txt-link-freetext" href="mailto:paola@ebi.ac.uk">mailto:paola@ebi.ac.uk</a>]
<br>
<b>Gesendet:</b> Mittwoch, 27. Juni 2012 14:15<br>
<b>An:</b> Alfons Weig<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:go-helpdesk@mailman.stanford.edu">go-helpdesk@mailman.stanford.edu</a>;
<a class="moz-txt-link-abbreviated" href="mailto:go-software@mailman.stanford.edu">go-software@mailman.stanford.edu</a><br>
<b>Betreff:</b> Re: AW: AW: Enrichment GO Help query<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear Alfons,<br>
<br>
The error message shown below suggests that the AmiGO
enrichment tool may not be able to process unrecognized IDs
even if you provide a background set containing GO
annotations for all those IDs. Before suggesting other
solutions, I'd wait to hear back from the GO Software group
if they have any comments, as AmiGO is maintained by them.
They're located on the West Coast of the US, so it may be a
few hours before they're able to get back to you.<br>
<br>
As for the GAF file format, you may find details here:<br>
<a moz-do-not-send="true"
href="http://www.geneontology.org/GO.format.gaf-2_0.shtml">http://www.geneontology.org/GO.format.gaf-2_0.shtml</a><br>
Since it seems that the data you have have not been
submitted and included in any public database, if this is
the case you wouldn't be able to create a properly formatted
GAF file, as column 1 would have to indicate the database. I
was hoping that a simple tab-delimited text file, containing
the information you do have, would be sufficient for the
tool, but this may not be the case if AmiGO can't relate
your IDs to any database.<br>
In your example below, if you did have a database that you
could indicate, that would have to be column 1 (not "GO" )
if you wanted to make a GAF file. And yes, the gene product
IDs should go in column 2.<br>
<br>
I'm sorry I don't have any more suggestions at this time but
please bear with us while we wait to hear from the GO
Software group. <br>
Thank you and best regards,<br>
<br>
Paola Roncaglia, for GO help.<br>
<br>
On 6/27/12 11:48 AM, Alfons Weig wrote: <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";">Hello
Paola, </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">I have tried to follow your instructions but
was not able to overcome the error shown below. I am not
sure, in which colum of a GAF file the id should sho up,
but I assume it is column 2. </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"><img
id="Bild_x0020_7"
src="cid:part1.09060306.02010406@ebi.ac.uk" border="0"
height="164" width="1664"></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">I prepared two files </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Ex. 1, without col 1 filled in: </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0006468
0 ND biological_process
protein amino acid phosphorylation protein
taxon:41413 20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0018110
0 ND molecular_function
histone arginine kinase activity
protein taxon:41413 20120627 GO
0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0004871
0 ND molecular_function
signal transducer activity protein
taxon:41413 20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0018106
0 ND biological_process
peptidyl-histidine phosphorylation protein
taxon:41413 20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0004673
0 ND molecular_function
protein histidine kinase activity
protein taxon:41413 20120627 GO
0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0016772
0 ND molecular_function
transferase activity, transferring phosphorus-containing
groups protein taxon:41413
20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Ex. 2, with col 1 filled in (I am not sure
whether ‘GO’ is correct)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">GO 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0006468
0 ND P protein amino
acid phosphorylation protein taxon:41413
20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">GO 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0018110
0 ND F histone
arginine kinase activity protein
taxon:41413 20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">GO 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0004871
0 ND F signal
transducer activity protein taxon:41413
20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">GO 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0018106
0 ND P
peptidyl-histidine phosphorylation protein
taxon:41413 20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">GO 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0004673
0 ND F protein
histidine kinase activity protein
taxon:41413 20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">GO 100258
jgi|Eurhe1|100258|CE89580_18773 0 GO:0016772
0 ND F transferase
activity, transferring phosphorus-containing
groups protein taxon:41413
20120627 GO 0 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Does this information help?</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Best regards</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Alfons</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><b><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Dr. Alfons Weig</span></b><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">DNA-Analytik &
Ökoinformatik - Univ. Bayreuth</span><o:p></o:p></p>
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font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Universitätsstrasse 30</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">95447 Bayreuth - Germany</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Tel. +49 (0)921-552457</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family:
"Tahoma","sans-serif"; color:
windowtext;">Von:</span></b><span
style="font-size: 10pt; font-family:
"Tahoma","sans-serif"; color:
windowtext;"> Paola Roncaglia [<a
moz-do-not-send="true"
href="mailto:paola@ebi.ac.uk">mailto:paola@ebi.ac.uk</a>]
<br>
<b>Gesendet:</b> Mittwoch, 27. Juni 2012 11:48<br>
<b>An:</b> Alfons Weig<br>
<b>Cc:</b> <a moz-do-not-send="true"
href="mailto:go-helpdesk@mailman.stanford.edu">go-helpdesk@mailman.stanford.edu</a>;
<a moz-do-not-send="true"
href="mailto:go-software@mailman.stanford.edu">go-software@mailman.stanford.edu</a><br>
<b>Betreff:</b> Re: AW: Enrichment GO Help query</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Dear Alfons,<br>
<br>
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.<br>
<br>
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:<br>
<br>
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. <br>
<br>
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. <br>
<br>
In the field labeled "Select the database filter", click
on "No selection".<br>
<br>
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:<br>
<a moz-do-not-send="true"
href="http://wiki.geneontology.org/index.php/AmiGO_Manual:_Term_Enrichment">http://wiki.geneontology.org/index.php/AmiGO_Manual:_Term_Enrichment</a><br>
<br>
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.<br>
<br>
As for your AmiGO BLAST questions:<br>
A manual page for the tool is available here: <a
moz-do-not-send="true"
href="http://wiki.geneontology.org/index.php/AmiGO_Manual:_BLAST">http://wiki.geneontology.org/index.php/AmiGO_Manual:_BLAST</a><br>
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.<br>
<br>
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.<br>
<br>
With best regards,<br>
<br>
Paola Roncaglia, for GO help.<br>
<br>
On 6/26/12 3:08 PM, Alfons Weig wrote: <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";">Dear
Paola, </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">thank you for your fast reply. </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">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. </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">#proteinId gotermId
goName gotermType goAcc</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">12647 815 rhodopsin-like receptor
activity molecular_function GO:0001584</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">12647 5270 G-protein coupled receptor
protein signaling pathway
biological_process GO:0007186</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">12647 9321 integral to membrane
cellular_component GO:0016021</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">13104 162 nucleotide binding
molecular_function GO:0000166</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">etc.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">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.. </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"><img
id="Bild_x0020_1"
src="cid:part2.07060508.06080703@ebi.ac.uk" border="0"
height="216" width="515"></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">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.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">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?</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Thanks for your help!</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Best regards</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US">Alfons</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><b><span style="font-size: 11pt;
font-family:
"Arial","sans-serif"; color:
rgb(31, 73, 125);">Dr. Alfons Weig</span></b><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">DNA-Analytik &
Ökoinformatik - Univ. Bayreuth</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Universitätsstrasse 30</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">95447 Bayreuth - Germany</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Tel. +49 (0)921-552457</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);"><a moz-do-not-send="true"
href="http://www.daneco.uni-bayreuth.de">www.daneco.uni-bayreuth.de</a></span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";"> </span><o:p></o:p></p>
<div style="border-width: medium medium medium 1.5pt;
border-style: none none none solid; padding: 0cm 0cm 0cm
4pt; border-color: -moz-use-text-color -moz-use-text-color
-moz-use-text-color blue;">
<div>
<div style="border-right: medium none; border-width: 1pt
medium medium; border-style: solid none none; padding:
3pt 0cm 0cm; border-color: -moz-use-text-color;">
<p class="MsoNormal"><b><span style="font-size: 10pt;
font-family:
"Tahoma","sans-serif";
color: windowtext;">Von:</span></b><span
style="font-size: 10pt; font-family:
"Tahoma","sans-serif"; color:
windowtext;"> Paola Roncaglia [<a
moz-do-not-send="true"
href="mailto:paola@ebi.ac.uk">mailto:paola@ebi.ac.uk</a>]
<br>
<b>Gesendet:</b> Dienstag, 26. Juni 2012 15:46<br>
<b>An:</b> <a moz-do-not-send="true"
href="mailto:a.weig@uni-bayreuth.de">a.weig@uni-bayreuth.de</a><br>
<b>Cc:</b> <a moz-do-not-send="true"
href="mailto:go-helpdesk@mailman.stanford.edu">go-helpdesk@mailman.stanford.edu</a><br>
<b>Betreff:</b> Re: Enrichment GO Help query</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Dear Alfons,<br>
<br>
Thank you for writing to GO.<br>
<br>
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?<br>
<br>
For your reference, a list of GO tools for enrichment
analysis is available here:<br>
<a moz-do-not-send="true"
href="http://www.geneontology.org/GO.tools_by_type.term_enrichment.shtml">http://www.geneontology.org/GO.tools_by_type.term_enrichment.shtml</a>
<br>
<br>
With best regards,<br>
<br>
Paola Roncaglia, for GO help.<br>
<br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
<table class="MsoNormalTable" style="width: 100%;"
border="0" cellpadding="0" cellspacing="0" width="100%">
<tbody>
<tr>
<td style="padding: 0cm;">
<div>
<p class="MsoNormal">Subject: <o:p></o:p></p>
</div>
<p class="MsoNormal">GO Help query (from website)<o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding: 0cm;">
<div>
<p class="MsoNormal">From: <o:p></o:p></p>
</div>
<p class="MsoNormal"><a moz-do-not-send="true"
href="mailto:a.weig@uni-bayreuth.de">a.weig@uni-bayreuth.de</a><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding: 0cm;">
<div>
<p class="MsoNormal">Date: <o:p></o:p></p>
</div>
<p class="MsoNormal">Tue, 26 Jun 2012 00:14:36
-0700<o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"> <o:p></o:p></p>
<table class="MsoNormalTable" style="width: 100%;"
border="0" cellpadding="0" cellspacing="0" width="100%">
<tbody>
<tr>
<td style="padding: 0cm;">
<div>
<p class="MsoNormal">To: <o:p></o:p></p>
</div>
<p class="MsoNormal"><a moz-do-not-send="true"
href="mailto:go-helpdesk@mailman.stanford.edu">go-helpdesk@mailman.stanford.edu</a><o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<pre>Email: <a moz-do-not-send="true" href="mailto:a.weig@uni-bayreuth.de">a.weig@uni-bayreuth.de</a><o:p></o:p></pre>
<pre>Name: Ontology (from Alfons Weig)<o:p></o:p></pre>
<pre>Text: Hello, <o:p></o:p></pre>
<pre>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. <o:p></o:p></pre>
<pre>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. <o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Is there any tool where I can analyse a subset of GO terms for enrichment/slim analyses. <o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Best regards<o:p></o:p></pre>
<pre>Alfons Weig<o:p></o:p></pre>
</div>
<p class="MsoNormal"><br>
<br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Dr Paola Roncaglia<o:p></o:p></pre>
<pre>GO Editorial Office<o:p></o:p></pre>
<pre>EMBL-EBI<o:p></o:p></pre>
<pre>Wellcome Trust Genome Campus<o:p></o:p></pre>
<pre>Hinxton<o:p></o:p></pre>
<pre>Cambridgeshire, UK<o:p></o:p></pre>
<pre>CB10 1SD <o:p></o:p></pre>
<pre>p: +44 1223 492600<o:p></o:p></pre>
<pre>f: +44 1223 494468 <o:p></o:p></pre>
</div>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Dr Paola Roncaglia<o:p></o:p></pre>
<pre>GO Editorial Office<o:p></o:p></pre>
<pre>EMBL-EBI<o:p></o:p></pre>
<pre>Wellcome Trust Genome Campus<o:p></o:p></pre>
<pre>Hinxton<o:p></o:p></pre>
<pre>Cambridgeshire, UK<o:p></o:p></pre>
<pre>CB10 1SD <o:p></o:p></pre>
<pre>p: +44 1223 492600<o:p></o:p></pre>
<pre>f: +44 1223 494468 <o:p></o:p></pre>
</div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Dr Paola Roncaglia<o:p></o:p></pre>
<pre>GO Editorial Office<o:p></o:p></pre>
<pre>EMBL-EBI<o:p></o:p></pre>
<pre>Wellcome Trust Genome Campus<o:p></o:p></pre>
<pre>Hinxton<o:p></o:p></pre>
<pre>Cambridgeshire, UK<o:p></o:p></pre>
<pre>CB10 1SD <o:p></o:p></pre>
<pre>p: +44 1223 492600<o:p></o:p></pre>
<pre>f: +44 1223 494468 <o:p></o:p></pre>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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 </pre>
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