I have a large set of data for which I already got the DEGs and also have them clustered. I need to get the functions enriched for each of the clustered genes. I was able to use the DAVID tool for just few of the clusters but DAVID is complaining that genes in other clusters are more than 3000 and could not get any result. Which other tool(s) can help. Note that I am dealing with human data.
Hi, you can use a big set of tools for Functional Enrihment analysis.
EnrichR : web tool with a lot data bases (GO, KEGG.. etc)
GeneCodis: web tool
Gorila
You can also perform an enrichment analysis using programs as GSEA (in java, with graphical interface). Easy to use and flexible, this program not apply the convectional statistic methods to perform enrichment ( as fisher, hypergeometric test..) and you can get interesting results.
You can also use R programming language, with packages as TopGO, GOstats.. among others..
I hope help you.
best regards
Hi, you can use a big set of tools for Functional Enrihment analysis.
EnrichR : web tool with a lot data bases (GO, KEGG.. etc)
GeneCodis: web tool
Gorila
You can also perform an enrichment analysis using programs as GSEA (in java, with graphical interface). Easy to use and flexible, this program not apply the convectional statistic methods to perform enrichment ( as fisher, hypergeometric test..) and you can get interesting results.
You can also use R programming language, with packages as TopGO, GOstats.. among others..
I hope help you.
best regards
The DAVID tool is widely used:
https://david.ncifcrf.gov/
It queries many databases and can be used for many species. In the beginning it looks a bit complex but there are tutorials.
Yes, that is true Alexander. I actually used DAVID tool. it analyzed some clusters that have few numbers of genes and complained about clusters that have genes more than 3000.
I am sorry, I forgot to read your text! I had only problems with DAVID when the gene list was too short or when I used strange identifier which DAVID did not know (although they exist, probably an issue of the human genome versions).
As an alternative you could directly query the GO website where the Panther Tool is available: http://www.geneontology.org/page/go-enrichment-analysis
Alex
Hi Jumoke,
You are on advantage while working on human gene expression data since it is highly annotated and several databases/tools are available for enrichment analysis. As mentioned in the previous answers there are several online tools available.
I would suggest you to try EnrichR webtool: http://amp.pharm.mssm.edu/Enrichr/
Besides for better visualization of your data and results you can use several cytoscape plug-ins viz. BinGO, ClueGO etc.
All the best.
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