Question: Gene Ontology without enrichment analysis
0
gravatar for biostart
3.7 years ago by
biostart310
Germany
biostart310 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 • 1.7k views
ADD COMMENTlink modified 3.7 years ago by ivivek_ngs4.8k • written 3.7 years ago by biostart310
1
gravatar for Chirag Nepal
3.7 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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

ADD COMMENTlink written 3.7 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 3.7 years ago • written 3.7 years ago by biostart310
1

Not all genes are GO annotated.

ADD REPLYlink written 3.7 years ago by Benn7.9k

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 3.7 years ago by Chirag Nepal2.2k
1
gravatar for ivivek_ngs
3.7 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k 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 3.7 years ago • written 3.7 years ago by ivivek_ngs4.8k
0
gravatar for onspotproductions
3.7 years ago by
United States
onspotproductions140 wrote:

You could try web Gestalt.

ADD COMMENTlink written 3.7 years ago by onspotproductions140
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