About Human Protein Coding Gene Copy Number Across Genome

Question

[Free Man]

I just want to obtain the information of human protein coding gene copy number. For each gene, whether it is a single copy gene or duplicated gene across chromosomes. What should I do? Is that such a database for all human protein coding gene? Thank you!

Answer 1

[VS]

Goto Ensembl Biomart ,

1. choose Human genes dataset
2. choose filter to be gene-->genetype-->protein_coding
3. choose attribute to be Homologs-->Paralogs--> Homology Type ++

So, what I mean by ++ above is that you can choose other paralogy attributes such as %identity etc. You can download these results and then polish up the results to remove redundancy (ex. paralogs X and Y will be reported twice : geneX-geneY, geneY-geneX) and filter further as per your needs.

[DG]

This is good if you want to know just about whether genes have paralogs in the genome or not. Which I am assuming the OP wants to address. Also adding info for copy-number variants would be more complicated.

Answer 2

[Free Man]

I just found that: http://dgd.genouest.org/ provides duplicated genes by groups. http://goods.ibms.sinica.edu.tw/DNVs/download.html identifies over 10% of human genes associated with duplicated gene loci (DGL).