Question: List of Genes According to Ontologies
0
gravatar for fusion.slope
12 months ago by
fusion.slope200
fusion.slope200 wrote:

Hello,

I was wondering if there is a website in which I can retrieve the list of genes for each ontology.

For example for the biological process "Regulation of Gene Expression," I would like to have all the list that belong to this ontology etc..

Thanks in advance

gene genome • 415 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum121k • written 12 months ago by fusion.slope200
2
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

I recently wrote a small tool to fetch all the children of a given term in GO: http://lindenb.github.io/jvarkit/GoUtils.html

there is an example to fetch all the associated genes:

Use GO annotation to retrieve genes associated to GO:0005216 ‘ion channel activity’

join -t $'\t' -1 1 -2 2 \
    <(java -jar dist/goutils.jar -A 'GO:0005216' | cut -f 1 | sort | uniq) \
    <(wget -q -O - "http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.goa_human.gz?rev=HEAD" | gunzip -c | grep -v '^!' | cut -f3,5 | uniq | LC_ALL=C sort -t $'\t' -k2,2) |\
sort -t $'\t' -k2,2 |\
grep SCN5A -A 10 -B 10

(...)
GO:0086006  SCN2B
GO:0005244  SCN3A
GO:0005248  SCN3A
GO:0005248  SCN3A
GO:0005248  SCN3B
GO:0086006  SCN3B
GO:0005248  SCN4A
GO:0005248  SCN4A
GO:0005248  SCN4B
GO:0086006  SCN4B
GO:0005244  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0005248  SCN5A
GO:0086006  SCN5A
GO:0086060  SCN5A
GO:0086061  SCN5A
GO:0086062  SCN5A
GO:0086063  SCN5A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN7A
GO:0005248  SCN8A
GO:0005248  SCN8A
GO:0005248  SCN9A
GO:0005248  SCN9A
GO:0005248  SCN9A
GO:0005272  SCNN1A
(...)
ADD COMMENTlink written 12 months ago by Pierre Lindenbaum121k
2
gravatar for EagleEye
12 months ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

With 'prepare_database' module in GeneSCF. you can download organism/species specific genes for corresponding process as a simple text in table format. Example:

Process1    gene1,gene2,gene3
Process2    gene4,gene6,gene2

Discussion on Biostar with example usage.

ADD COMMENTlink modified 12 months ago • written 12 months ago by EagleEye6.4k
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: 1046 users visited in the last hour