Best UPDATED tool for enrichment anlysis
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6.5 years ago
ncl.lazzarini ▴ 120

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 (C: David enrichment analysis inconsistency). What could be the best update tool to perform and enrichment analysis?

enrichment analysis tool gene set • 6.4k views
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6.5 years ago
Manvendra Singh ★ 2.1k

Yes, David is not updated.

I would suggest

Gorilla for enrichment analysis

http://cbl-gorilla.cs.technion.ac.il/

and Panther for functionally annotating gene lists

http://www.pantherdb.org/

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2.2 years ago
jvwong • 0

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!

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4 months ago

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

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