Question: How to visualize a large number of GO terms in directed acyclic graphs
0
gravatar for oussumenten
5.1 years ago by
oussumenten40
United States
oussumenten40 wrote:

Hi,

I have a list of about 500 GO terms that I want to visualize in directed acyclic graphs so as to figure out their relationships.

Is there a tool that would let me input my list of GO terms and gives me directed acyclic graphs of the GO terms as output?

I tried EBI QuickGO tool, but it does not work with a lot of GO terms.

I am open to alternative strategies/suggestions.

Let me know if you have any questions.

Thanks.

 

ADD COMMENTlink modified 5.1 years ago by andrew.j.skelton735.7k • written 5.1 years ago by oussumenten40
0
gravatar for Pierre Lindenbaum
5.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

I wrote a XSLT stylesheet transforming GO to XML+GEXF . See https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/go/go2gexf.xsl

The resulting graph can then be visualized using http://gephi.org

 

 $ curl  "http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz" |\
gunzip -c |\
xsltproc --novalid go2gexf.xsl -

output:

<?xml version="1.0"?>
<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:g="http://www.gexf.net/1.2draft" xmlns:go="http://w
ww.geneontology.org/dtds/go.dtd#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:viz=
"http://www.gexf.net/1.1draft/viz" version="1.2">
  <meta>
    <creator>Pierre Lindenbaum</creator>
    <description>Gene Ontology</description>
  </meta>
  <attributes class="node">
    <attribute id="0" title="definition" type="string"/>
  </attributes>
  <graph mode="static" defaultedgetype="directed">
    <nodes>
      <node id="GO:0000001" label="mitochondrion inheritance">
        <attvalues>
          <attvalue for="0" value="The distribution of mitochondria, including the mitochondrial gen
ome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and
 the cytoskeleton."/>
        </attvalues>
      </node>
      <node id="GO:0000002" label="mitochondrial genome maintenance">

(...)

 

ADD COMMENTlink written 5.1 years ago by Pierre Lindenbaum120k

Hi Pierre,

Thanks for your help. So how do I input GO terms of interest? Can you clarify this code:

$ curl  "http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz" |\
gunzip -c |\
xsltproc --novalid go2gexf.xsl -
ADD REPLYlink written 5.1 years ago by oussumenten40
0
gravatar for andrew.j.skelton73
5.1 years ago by
London
andrew.j.skelton735.7k wrote:

Try out the RamiGO package in Bioconductor - http://www.bioconductor.org/packages/release/bioc/vignettes/RamiGO/inst/doc/RamiGO.pdf

It allows you to produce Amigo Trees which shows the relationship between GO terms

 

ADD COMMENTlink written 5.1 years ago by andrew.j.skelton735.7k

I have looked at RamiGO but it does not support a large number of GO terms. Thanks though.

ADD REPLYlink written 5.1 years ago by oussumenten40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1110 users visited in the last hour