Question: Best UPDATED tool for enrichment anlysis
2
gravatar for ncl.lazzarini
4.7 years ago by
United Kingdom
ncl.lazzarini90 wrote:

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?

tool analysis set enrichment gene • 4.8k views
ADD COMMENTlink modified 5 months ago by jvwong0 • written 4.7 years ago by ncl.lazzarini90
2
gravatar for Renesh
4.7 years ago by
Renesh1.6k
United States
Renesh1.6k wrote:

Also Try:

BinGO http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

topGO http://www.bioconductor.org/packages/release/bioc/html/topGO.html

EasyGO http://bioinformatics.cau.edu.cn/easygo/

ADD COMMENTlink written 4.7 years ago by Renesh1.6k
1
gravatar for Manvendra Singh
4.7 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

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/

ADD COMMENTlink modified 4.7 years ago by Istvan Albert ♦♦ 80k • written 4.7 years ago by Manvendra Singh2.1k
1
gravatar for EagleEye
2.7 years ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

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How outdated information can influence your results for enrichment analysis?

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by EagleEye6.4k
0
gravatar for jvwong
5 months ago by
jvwong0
jvwong0 wrote:

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!

ADD COMMENTlink written 5 months ago by jvwong0
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