# Determine if a gene is mitochondrial or not

I need to determine whether a gene is mitochondrial or not for C. Elegans automatically from its name by running a regular expression on a dozen of thousands of gene names. Currently I am having gene symbols like:

clec-190, clec-189, 21ur-8912, nduo-1, 21ur-6539, 21ur-13096, nduo-6, 21ur-14241, ndfl-4


I tried running grepl("^mt-", symbols) and it found nothing. I am sure that there are some mitochondrial genes just from their descriptions. I would assume that first I need to convert gene symbols to some other symbols to do that but I am not sure here.

Basically, I am trying to do it in a similar way to the tutorial of single cell RNAseq.

• Please edit your question and clarify what species and what sort of gene identifier you will be using. In any case, the chances of this being the type of problem you can solve with regular expressions are vanishingly small. Is this something you will need to do once or many times? It would be much simpler to query online databases for information on the gene rather than try to parse the names. Dec 14 '17 at 0:40
• Ok, I added the species and a bit of clarification Dec 14 '17 at 2:36
• I also have Worm Base identifiers for the genes if that can help Dec 14 '17 at 2:56
• I know that the gtf files provided by illumina for C elegans use Wormbase identifiers ("WBGene*"): jp.support.illumina.com/sequencing/sequencing_software/…. The gtf files contain the chromosome, so with tools like grep and awk, you can easily know wheter a given identifier is from the mitochondrial chromosome.
– bli
Dec 14 '17 at 13:23

From your list, only nduo-1, nduo-6, and ndfl-4 are mitochondrial.