RNA-SEQ Gene Enrichment Analysis Using DAVID

Question

[vrrani]

Steps followed under Upload tab in DAVID

1. GeneList -- Pasted the list of gene symbols
2. Select Identifier – Selected ‘Official_Gene_Symbol”
3. List Type – Opted Gene List radio button
4. Clicked on “Submit List”

The below warning message is displayed

"You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your chosen identifier type. Please use the Gene Conversion Tool to determine the identifier type."

After selecting Option “Continue to Submit the IDs That David Could Map”, Gene list manages (under List tab) provided Homo sapiens as 46 out of 107 gene symbols that I submitted.

Questions:

1. Why is the warning message (the gene list is from RNA.Sequencing). Am I going wrong with any of the options under ‘Upload tab’ (Select Identifier)?
2. Why is only 46 were identified as Homo sapiens where I have given 107 genes of homo sapiens?
3. Is this common with RNA.Seq data?
4. Do I have to check with any of the options from ‘Background’ tab?
5. If DAVID is not the preferred tool for analysis of RNA-SEQ data, do we have any other tools for analysis? I noticed few apps like MSigDB, GSEA, GO, KEGG, Ingenuity, Pathway Studio and GeneGo MetaCore, but not sure which of these is perfect for RNA-SEQ data.

Please clarify me, I am relatively new to this domain.

Answer 1

[lshepard]

It is a bit hard to answer this question without actually seeing the gene list, but a few possibilities to why this is happening could be (that I can think of):

1) Genes which may not have an official symbol yet (only Ensembl IDs etc...)

2) Too many non coding RNAs

With that said, to answer your questions:

1. If you are using DAVID version 6.8, this warning should normally not occur given that you list doesn't fall under the two categories above
2. In my experience with mRNA-seq, almost all genes were found in DAVID 6.8
3. Depends on the kind of RNA-seq (for mRNA, not normally).
4. Depends on the analysis you want to performs, but if you just want to compare against all genes for the species of interest, then no.
5. There is no perfect tool for GO/KEGG analysis. Each one has its own nuances, and at least one from your list is licensed (Ingenuity).

[vrrani]

Thanks a lot for the help. Yes, i am using DAVID 6.8 version and still experiencing the issue. I will start using ingenuity.

Answer 2

[janwillembruggeman]

https://www.reddit.com/r/bioinformatics/comments/7g49e2/is_david_broken_at_the_moment/