After differential expression analysis if we use gene symbols for further analysis we lose some DEGs. Is it ok?

Question

[Sib]

I performed a differential expression analysis by R. Now, I have a list of DEG GENE-SYMBOLs. My problem is that not all the DEGs had gene symbols. I am worried to lose some of the data by using gene symbols. But I see many articles used gene symbols. Is it a routine thing and we can not do something to avoid it? ( The same problem exists about using other gene IDs like Ensemble gene-ID, GB-ACC, and other identifiers.)

Answer 1

[Kevin Blighe]

The 'DEG symbols' to which you refer for which there are no official gene symbols may be related to hypothetical proteins or in silico predicted mRNAs - it is difficult to know from our perspective when you have not provided any examples of these.

Please do your own investigating on a few of these ['DEG symbols'] so that you may begin to understand what is happening.

Generally, for gene annotation, make a decision at the start of the study about the annotation to use (HGNC, Ensembl, Vega, etc.) and set strict rules about filtering in/out these.

Kevin

[Sib]

thank you for answering. Sorry, I think I explained badly. My meaning of DEG symbols was GEN_SYMBOLs of DEGs. In other words I have a list of DEGs in GENE_SYMBOl format.

[Kevin Blighe]

What is "GENE_SYMBOl" format?

[Sib]

It is an identifier. I think its complete name is HGNC-GENE-SYMBOl.