genes not mapping to ENTREZID

Question

[adR]

Hi Dear Scientists

I want to ask a simple question but important to me. My question is, I have a list of DEG between the two conditions. While converting gene Symbole to their biological IDs(ENTREZID) few genes failed to map. Since they don't have ENTREZID, they aren't related to any KEGG pathways. Therefore, can I consider this unmapped list of genes as candidates to study their novel functions related to my conditions?

Thank you for sharing your knowledge!

[noodle]

How did you come up with your gene list? Do you expect the genes to be coding/novel? Try BLASTing the sequences that aren't found, or if you only care about KEGG annotations, you can enter a (protein) sequence in Pfam and look at the domain annotations which you can then relate to a KEGG pathway.

[adR]

Thanks, Joe for your answer! Actually, I did not design the study originally but they aim to answer both. Could please direct me on how to do BLASTing?. Where to access it!

[noodle]

So "BLASTing" a sequence will help to identify the source (organism, engineered, etc) and comes in 2 main varieties - by DNA sequence and by protein sequence. BLAST will return a list of proteins/DNA with similarity to your sequence. https://blast.ncbi.nlm.nih.gov/Blast.cgi

Alternatively/additionally, Pfam has a "sequence search" option which allows you to identify domains within a protein sequence, which can help you identify what type of protein you have if there are no similar proteins found by BLAST. http://pfam.xfam.org/

Answer 1

[Kevin Blighe]

They may be non-coding RNAs or just predicted genes, or something else. Can you paste a few IDs? It is expected that some genes will be recorded in one database but not another. Each database has different 'rules' about what should be included | excluded

[adR]

Hi Kevin, Thanks for answering my question. Here are three genes that I did not find their KEGG IDs or their ENTREZID. ADCK3, AES, AF09010

[Kevin Blighe]

The problem seems to be that these are aliases of what is the official gene symbol. For example:

• ADCK3 --> https://www.ncbi.nlm.nih.gov/gene/56997
• AES --> https://www.ncbi.nlm.nih.gov/gene/166
• AF09010 --> ¯ \ _(ツ)_ / ¯

You can try to avail of limma's alias2Symbol(), if you want: https://rdrr.io/bioc/limma/man/alias2Symbol.html

Otherwise, try to get the source annotation that was used, which may still have the Entrez mappings.