<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
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 class="moz-txt-link-freetext" 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 class="moz-txt-link-freetext" 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:
<blockquote
cite="mid:003f01cd53a5$291d7cc0$7b587640$@weig@uni-bayreuth.de"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]-->
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Vorformatiert Zchn";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Sprechblasentext Zchn";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";
color:black;}
span.HTMLVorformatiertZchn
{mso-style-name:"HTML Vorformatiert Zchn";
mso-style-priority:99;
mso-style-link:"HTML Vorformatiert";
font-family:Consolas;
color:black;}
span.E-MailFormatvorlage19
{mso-style-type:personal-reply;
font-family:"Arial","sans-serif";
color:#1F497D;}
span.SprechblasentextZchn
{mso-style-name:"Sprechblasentext Zchn";
mso-style-priority:99;
mso-style-link:Sprechblasentext;
font-family:"Tahoma","sans-serif";
color:black;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="2050" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<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">thank you for your fast reply. <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">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. <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">#proteinId gotermId
goName gotermType goAcc<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">12647 815 rhodopsin-like receptor
activity molecular_function GO:0001584<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">12647 5270 G-protein coupled
receptor protein signaling pathway
biological_process GO:0007186<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">12647 9321 integral to membrane
cellular_component GO:0016021<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">13104 162 nucleotide binding
molecular_function GO:0000166<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">etc.<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 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.. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);"><img id="Bild_x0020_1"
src="cid:part1.06000703.01000708@ebi.ac.uk" height="216"
width="515"></span><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>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);" 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.<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 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?<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">Thanks for your help!<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>
<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>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Arial","sans-serif";
color: rgb(31, 73, 125);">Universitätsstrasse 30<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
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>
</div>
<p class="MsoNormal"><span style="font-size: 11pt; font-family:
"Arial","sans-serif"; color: rgb(31, 73,
125);"><o:p> </o:p></span></p>
<div style="border-width: medium medium medium 1.5pt;
border-style: none none none solid; border-color:
-moz-use-text-color -moz-use-text-color -moz-use-text-color
blue; padding: 0cm 0cm 0cm 4pt;">
<div>
<div style="border-right: medium none; border-width: 1pt
medium medium; border-style: solid none none;
border-color: rgb(181, 196, 223) -moz-use-text-color
-moz-use-text-color; padding: 3pt 0cm 0cm;">
<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> Dienstag, 26. Juni 2012 15:46<br>
<b>An:</b> <a class="moz-txt-link-abbreviated" href="mailto:a.weig@uni-bayreuth.de">a.weig@uni-bayreuth.de</a><br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:go-helpdesk@mailman.stanford.edu">go-helpdesk@mailman.stanford.edu</a><br>
<b>Betreff:</b> Re: 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>
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>
<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"><span style="display: none;"><o:p> </o:p></span></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>
<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>
</body>
</html>