Best UPDATED tool for enrichment anlysis

Question

[ncl.lazzarini]

I have several gene sets and I'd like to perform an enrichment analysis in order to get GO terms, KEGG pathways and, possibly, PubMed IDs statistically overrepresented. I performed some analysis using DAVID. Unfortunately I noticed that DAVID is not up to date, in fact the last update of its knowledge base was in 2009. As results some GO terms are associated with some genes even if the latest GO database version doesn't include this association (David enrichment analysis inconsistency). What could be the best update tool to perform and enrichment analysis?

Answer 1

[Renesh]

Also Try:

• BinGO
• topGO
• EasyGO

[avi.maayan]

Also try:

Enrichr

Answer 2

[Manvendra Singh]

Yes, David is not updated. I would suggest Gorilla for enrichment analysis and Panther for functionally annotating gene lists

Answer 3

[EagleEye]

Try real-time enrichment tool, Gene Set Clustering based on Functional annotation (GeneSCF)

A: Inconsistent numbers when using Kegg pathway analysis via DAVID?

How outdated information can influence your results for enrichment analysis?

Answer 4

[jvwong]

Hi folks - Shameless plug but we at Pathway Commons have a new search engine:

e.g. https://apps.pathwaycommons.org/search?gt=0<=250&q=pcna%20xrcc2%20xrcc3%20rad50%20rad51&type=Pathway

It will recognize genes you type in (HGNC, UniProt Accession) and allow you to launch an enrichment analysis for GO and Reactome pathways. The results are displayed as an Enrichment Map where nodes are pathway and edges show similarity. Give it go!

Answer 5

[farang.subson]

Another shameless plug: https://whatismygene.com . Massive underlying database, unique tools, simple interface. Insights are likely. ☺