Question: Gene Ontology without enrichment analysis
0
gravatar for biostart
4.6 years ago by
biostart350
Germany
biostart350 wrote:

Hello,

Here is a quick [s]stupid[/s] question:

I just want to classify my list of genes with respect to GO terms (how many genes fall into each GO term) without doing enrichment analysis. Is there a web tool that is doing this?

Thank you!

rna-seq chip-seq next-gen • 2.1k views
ADD COMMENTlink modified 10 months ago by yairgatt10 • written 4.6 years ago by biostart350
1
gravatar for Chirag Nepal
4.6 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

http://gostat.wehi.edu.au/cgi-bin/goStat.pl

ADD COMMENTlink written 4.6 years ago by Chirag Nepal2.2k

This one does not recognize all human genes:

Unique Genes: 114; Annotated Genes: 80; GOs: 619; Unique GOs: 325; All Unique Sub-GOs: 906; GO-DB: goa_human.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by biostart350
1

Not all genes are GO annotated.

ADD REPLYlink written 4.6 years ago by Benn8.0k

Just a suggestion. You many try blast2GO if you want to annotate GO for missing genes. Disclaimer: I have not used it before.

ADD REPLYlink written 4.6 years ago by Chirag Nepal2.2k
1
gravatar for ivivek_ngs
4.6 years ago by
ivivek_ngs5.0k
Seattle,WA, USA
ivivek_ngs5.0k wrote:

You can find the same with Gorilla, since it provides all the metrics for the genes that are enriched in each GO terms and also gives an enrichment score. Obviously the best way to analyze is to put two unranked list , one for you target genes and another the background you would like to chose. Like the genes that are all expressed for your data rather than putting all genes in Homo Sapiens.

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by ivivek_ngs5.0k
0
gravatar for onspotproductions
4.6 years ago by
United States
onspotproductions140 wrote:

You could try web Gestalt.

ADD COMMENTlink written 4.6 years ago by onspotproductions140
0
gravatar for dsull
10 months ago by
dsull1.6k
UCLA
dsull1.6k wrote:

You can use EnrichR for this.

https://amp.pharm.mssm.edu/Enrichr/

If you download the GO results, you'll see not only how many genes but also a list of every gene (from your gene list) that falls under a specific GO term.

(Edit: Sorry I didn't realize this was an old thread. It somehow was bumped up to the front page.)

ADD COMMENTlink modified 10 months ago • written 10 months ago by dsull1.6k
0
gravatar for padwalmk
10 months ago by
padwalmk100
padwalmk100 wrote:

Hi, you can try ENSEMBLE biomart. 1. Go to -> https://www.ensembl.org/biomart/martview/910b8e505dd410c87f1045df41b27ff0

  1. Select database human hg38

  2. Go to filter and click on gene and paster your gene list.

  3. Go to attribute and then feature and in feature select external, you will get gene ontology Menu, now you can select whatever information you require, and click ok Result.

  4. You will get all the ontology terms associated with your gene.

ADD COMMENTlink written 10 months ago by padwalmk100
0
gravatar for yairgatt
10 months ago by
yairgatt10
yairgatt10 wrote:

QuickGO is also an easy to use and useful tool

ADD COMMENTlink written 10 months ago by yairgatt10
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