David Gene Id

Question

[Kritika]

Hello all I have output of david functional annotation and gene conversion tool in functional annotation the gene column is giving david Id per row many ids how will i convert it to gene name which is reported in gene conversion tool. any help

[venu]

• If you've a list of Gene ids / symbols you can paste them in DAVID tool at Step 1: Enter Gene List and select the type you've entered at Step2 (Official genesymbol / Ensemble id ..etc). After functional annotation it must return the result with the same ids you've entered.
• If you don't know whether your input is of ids or symbols, select Not Sure at Step 2, it will direct you what to do.

You can also convert those DAVID ids to normal gene symbols from result which requires extra steps such as taking DAVID ids out-->converting them to gene symbols-->pasting them to original result

[Kritika]

oh thanks Girolamo I will try panther also... But draw back of panther is. they do not have all organism reported. And also what i found is panther and reactome will not analysed entire gene compare to DAVID. panther will unmapped gene but when you compare with DAVID they consider that gene too which panther could not do.

Answer 1

[Girolamo]

David is outdated. Do not to use it. Use Panther or other updated tools for doing functional analyses.

[WouterDeCoster]

I would like to add Webgestalt and Enrichr to your list: http://bioinfo.vanderbilt.edu/webgestalt/login.php http://amp.pharm.mssm.edu/Enrichr/

Answer 2

[EagleEye]

Please be critical in selecting functional enrichment or annotation tool. Here is the recent comparison with DAVID,

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

Importance of using up-to-date tool

A: Pathway Grouping with Genes

Try GeneSCF, specifically designed to handel all organisms form GeneOntology and KEGG (and human REACTOME) in real-time manner,

Gene Set Clustering based on Functional annotation (GeneSCF)