lnkRNA gene names not recognized by DAVID

Question

[chemcehn]

Hello,

I am trying to analyze lnkRNA results from RNA-seq. Uploading lnkRNA gene names into DAVID, but it does not recognize most of them. The gene names look like this: AC000068.5; AP001625.4.

Any suggestions how to sort out the problem with DAVID, and also what else one can do with this type of data?

Thanks!

[Christian]

The DAVID knowledge base has not been updated for years, so I suppose newer gene annotations will not be in there. See also Is the DAVID knowledgebase not updated any more?.

Answer 1

[EagleEye]

Current functional annotations only cover protein_coding genes. Only consider protein_coding genes when you do functional analysis (Gene Ontology or KEGG).

First RNA you mentioned is Antisense:

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000185065;r=22:19447893-19450105;t=ENST00000431090

Second one: Novel Intronic

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000239930;r=21:42496539-42497443;t=ENST00000416179

If you need information about LncRNAs, you can have a look into these available databases: (Information about functional annotation for LncRNAs are limited for now)

• http://www.lncipedia.org/
• http://www.lncrnadb.org/
• http://bioinfo.life.hust.edu.cn/lncRNASNP/
• http://lncrna.big.ac.cn/index.php/Main_Page
• http://www.lncrna2target.org/

JFI: You can also use GeneSCF tool which clusters all protein_coding genes based on functions (GeneOntology, KEGG and reactome) and gives detailed results for protein coding genes (Including statistics):

Gene Set Clustering based on Functional annotation (GeneSCF)

Update GeneSCF v1.1: Support for more organisms and for information please follow http://genescf.kandurilab.org/