How to count gene copy number in mammals?
3
0
Entering edit mode
2.7 years ago
skgmsnb • 0

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

gene duplication • 735 views
ADD COMMENT
1
Entering edit mode

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

Best

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
2.7 years ago
GenoMax 110k

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

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
2.7 years ago
h.mon 33k

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.

ADD COMMENT
0
Entering edit mode

"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.

ADD REPLY

Login before adding your answer.

Traffic: 2744 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6