Hi there
I would like to know and to get your feedback about you favourite Gene-enrichment analysis software based in a graphical environment, preferably on-line.
Please give me your feedback about what you like most !... Thanks
All the best
Paco
Dear Francisco,
- For quick GO enrichment in multiple gene lists at once, I use g:Cocoa from g:Profiler: https://biit.cs.ut.ee/gprofiler/gcocoa.cgi
G:Cocoa also allows other enrichment analyses such as KEGG pathways. Its main problem is that usually the analysis goes too deep into the GO annotation and the results might be hard to "digest".
- This is why I mostly use DAVID, which also provide similar "Meta" analyses across different databases (KEGG, GO and so on), but it has the advantage of aggregating all these informations in functional clusters. It is also a solid GO enrichment tool: https://david.ncifcrf.gov/summary.jsp
- Another way to aggregate GO terms (coming from DAVID GO or any other tool really), one can use REVIGO, which provides plotting options and different degree of terms aggregation based on the terms semantic: http://revigo.irb.hr/index.jsp?error=expired
Here are other tools that can be of help.
- For broad functions enrichment I use GOTermMapper: https://go.princeton.edu/cgi-bin/GOTermMapper
- Under R, I use TopGO: https://bioconductor.org/packages/release/bioc/html/topGO.html
- Another useful online tool for GO enrichment is Metascape: http://metascape.org/gp/index.html
- To analyse protein interactions / genes network from a list of genes I use Genemania: https://genemania.org/
Best,
Gautier
I generally use FunRich. Its a standalone gene ontology enrichment tool. User can change the backend database and make it suit your need well.
Following is the link:
http://www.funrich.org/
Thanks,
Krishna
Dear Francisco,
- For quick GO enrichment in multiple gene lists at once, I use g:Cocoa from g:Profiler: https://biit.cs.ut.ee/gprofiler/gcocoa.cgi
G:Cocoa also allows other enrichment analyses such as KEGG pathways. Its main problem is that usually the analysis goes too deep into the GO annotation and the results might be hard to "digest".
- This is why I mostly use DAVID, which also provide similar "Meta" analyses across different databases (KEGG, GO and so on), but it has the advantage of aggregating all these informations in functional clusters. It is also a solid GO enrichment tool: https://david.ncifcrf.gov/summary.jsp
- Another way to aggregate GO terms (coming from DAVID GO or any other tool really), one can use REVIGO, which provides plotting options and different degree of terms aggregation based on the terms semantic: http://revigo.irb.hr/index.jsp?error=expired
Here are other tools that can be of help.
- For broad functions enrichment I use GOTermMapper: https://go.princeton.edu/cgi-bin/GOTermMapper
- Under R, I use TopGO: https://bioconductor.org/packages/release/bioc/html/topGO.html
- Another useful online tool for GO enrichment is Metascape: http://metascape.org/gp/index.html
- To analyse protein interactions / genes network from a list of genes I use Genemania: https://genemania.org/
Best,
Gautier
Beware of your Background. If you preselect your genes like by using only miRNA targets from a certain database or even using a microarray chip then you are limiting the genes where you have information. Lots of previously mentioned tools do not have this option.
I prefer DAVID - https://david.ncifcrf.gov/tools.jsp It was relativity recently updated
My favourite is currently PANTHER http://pantherdb.org/ HHere you need to register.
And I also like GORILLA with its simplicity. http://cbl-gorilla.cs.technion.ac.il/
I agree with Dezső Módos concerning the background.
For non-model species for example, one can analyse the GO enrichment of the homologues found in the closest model species and use as a background all the homologues found between the two species (non-model and model).
For example in the pea aphid Acyrthosiphon pisum I used GOrilla successfully to perform GO enrichment of genes conserved in Drosophila melanogaster using the above-mentioned parameters.
(Additional File 5 of Article Dosage compensation and sex-specific epigenetic landscape of...
, the method for the GO enrichment is described in the main text).
Enrichr compile several databases of pathways for gene enrichment http://amp.pharm.mssm.edu/Enrichr/
You can try with the following tools
https://david.ncifcrf.gov/tools. jsp It was relativity recently updated
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