Question: After differential expression analysis if we use gene symbols for further analysis we lose some DEGs. Is it ok?
1
gravatar for Sib
10 months ago by
Sib20
Sib20 wrote:

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.)

ADD COMMENTlink modified 10 months ago • written 10 months ago by Sib20
2
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

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

ADD COMMENTlink written 10 months ago by Kevin Blighe66k

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.

ADD REPLYlink written 10 months ago by Sib20

What is "GENE_SYMBOl" format?

ADD REPLYlink written 10 months ago by Kevin Blighe66k

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

ADD REPLYlink written 10 months ago by Sib20
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