How to count gene copy number in mammals?

Question

[skgmsnb]

I would like to count gene copy numbers of my gene list (more than 100 genes) in mammals (human, mouse, cow, etc.). For example, I want to know evolutional copy number changes of TP53, but I don't come up with an efficient solution.

Do you have any idea to count gene copy numbers systematically?

Thanks

[Titus]

Hi , Maybe you can get the fasta list corresponding to your genes of interest and blast it against mammals in NCBI.

Best

[skgmsnb]

I’ve always use NCBI using specific organism names. Thank you for your valuable comment.

Answer 1

[GenoMax]

NCBI Homologene has the alignment information available for Euteleostomi for TP53: https://www.ncbi.nlm.nih.gov/homologene/460

Ensembl has a number of comparative genomic analyses available (scroll down to the bottom of page): http://useast.ensembl.org/Homo_sapiens/Gene/Compara?db=core;g=ENSG00000141510;r=17:7661779-7687550

A table with orthologs from multiple species can be found here (scroll down the page) : http://useast.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000141510;r=17:7661779-7687550

[skgmsnb]

Thank you for the valuable links. All approaches seem to be good, and I'm checking three links to serve my purpose.

Again, thank you for your comments.

Answer 2

[h.mon]

Use the most efficient solution of all: use the work done by someone else. For example, look at the OrthoDB report for TP53 at mammalian level of clustering:

https://www.orthodb.org/?level=&species=&query=125711at40674

If you scroll down to Orthologs by organism and click-select the Show all available species, you can see which species have duplications of the gene in question. You can also download the information as a tab-delimited file, which is then easily parsed to get the information you want:

pub_og_id   og_name level_taxid organism_taxid  organism_name   int_prot_id pub_gene_id description
125711at40674   Cellular tumor antigen p53  40674   9305_0  Sarcophilus harrisii    9305_0:003593   TP53    Cellular tumor antigen p53
125711at40674   Cellular tumor antigen p53  40674   9361_0  Dasypus novemcinctus    9361_0:00312e   TP53    cellular tumor antigen p53
125711at40674   Cellular tumor antigen p53  40674   9365_0  Erinaceus europaeus 9365_0:0002dd   TP53    Cellular tumor antigen p53
125711at40674   Cellular tumor antigen p53  40674   9371_0  Echinops telfairi   9371_0:000064   LOC101647784    LOW QUALITY PROTEIN: cellular tumor antigen p53-like
125711at40674   Cellular tumor antigen p53  40674   9371_0  Echinops telfairi   9371_0:00380f   TP53    cellular tumor antigen p53

Finally, OrthoDB provides an API which can be used with curl or wget, this allows automation for the case of several genes. I never used it, though, so I can't provide guidance here.

Another source could be OMA.

[skgmsnb]

"Use the work done by someone else." I was impressed by your philosophy.

Also, your approach is appropriate for my purpose. I'm trying it using my genes.

Thank you for your valuable comment.