Question: Get Protein expression matrix
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gravatar for emanismail.92
10 months ago by
emanismail.920 wrote:

Hello, I have a huge list of uniprot proteins and need to get expression for all of them as matrix of genes and samples How can I get it from GEO or human protein atlas or any other resources I am new in that, Any one could help ? Thanks in advance

gene • 363 views
ADD COMMENTlink modified 10 months ago by Kevin Blighe42k • written 10 months ago by emanismail.920
0
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe42k
Guy's Hospital, London
Kevin Blighe42k wrote:

There are too many 'unknowns', from our perspective, in relation to your question - that's why nobody has yet responded.

You have a list of proteins. You want to get the gene expression of the genes relating to these proteins. In which tissues are you interested?; in which diseases are you interested?; have you considered that issue that gene and protein names can be entirely different?

A useful resource to look up the expression of genes in different tissues is: Genotype-Tissue Expression (GTEx). You can download data from GTEx via the Datasets tab

Apart from that, there are tens of thousands of GEO datasets, so, you an start searching Here to find out which datasets would be of most interest to you.

Kevin

ADD COMMENTlink written 10 months ago by Kevin Blighe42k

Thanks for your reply. I try to study relation between genes and diseases so I need gene expression to use it as features (as I suppose) I have a list of genes and I am searching for service/api that can use to get expression of each gene I found that GEO and human protein atlas have my question but I don't know how to use it

Thanks in advance,Sir

ADD REPLYlink written 10 months ago by emanismail.920

Cool. For Human Protein Atlas, there is information here: Downloadable data

For GTEx, there is information here: GTEx Datasets (you will have to create an account and log in).

Programmatic / API access may not always be implemented, in which case you cold just download the data to your local disk.

ADD REPLYlink modified 10 months ago • written 10 months ago by Kevin Blighe42k

Sir, I am trying to use GEOquery to retrieve exression of each gene using its name or symbol .. Could you help me with that ? Any recommendation will be appreciated Thanks in advance.

ADD REPLYlink written 10 months ago by emanismail.920
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