Can I Filter Unknown Genes Before Go/Kegg Analysis?

Question

[woewow]

Hi Biostars,

I found some differential expressed genes. When I dropped them to DAVID for GO/KEGG analysis, I found a large number of genes enriched in a term with unknown functions or pseudogenes. Is it feasible that I filter out those genes and do the analysis again?

Many thanks in advance.

[Sudeep]

" I found a large number of genes enriched in a term with unknown functions or pseudogenes" Interesting, could you post a few of these genes with results from DAVID ?

[woewow]

These genes are enriched in the KEGG term "ribosome". Many of the genes are predicted genes with unknown functions or pseudogenes.

RPL18, RPL17, RPL36A, GM2000, GM13680, GM10159, GM10119, GM9385, GM14166, GM11703, GM15710, RPL22L1, RPS3A, RPLP0, GM10155, GM10259, RPL10, GM10294, GM10443, RPS27A, GM15500, GM3362, GM10240, GM10184, GM8420, RPS4X, GM8841, RPS18, GM6136, RPS19, RPL41, RPS12, RPS13, GM4167, RPS11, GM10288, KPNA2, GM14648, GM15148, RPS15A, GM15427, RPL39, GM11361, GM4963, RPS25, GM11425, RPS26, GM10036, RPS28, RPL32, RPL7, RPL3, GM10335, GM15772, RPL4, RPL10A, GM10132, RPS20, RPS23, GM5428, GM7536, RPSA, GM5621, GM9396, RPS9, RPL27, RPS6, RPS5, RPS7, GM13654, GM13653, RPL23, GM10020, GM5879, GM15887, GM10269

Answer 1

[Asaf]

It should be OK if you remove the pseudogenes and genes with unknown function from the background. This way your question will be: Among genes with at least one known function, is my group enriched with term X? Removing the "problematic" genes without doing so in the background would generate a bias.

[woewow]

Thank you very much for the reply. I was afraid of introducing bias after removing the genes.

[Asaf]

Actually, genes without known function shouldn't be in GO, maybe by trying other GO layers available in DAVID you'll get better results.