Question: data mining: find expression level of a specific gene in specific tisse
gravatar for Whetting
4.8 years ago by
Bethesda, MD
Whetting1.5k wrote:


I am trying to figure out whether my gene of interest is expressed differentially between two tissues. I have been looking at GEO, but I am not clear on how to actually find my gene. I have tried all possible names I can come up with, but GEO does not seem to know the gene.

I guess this leaves me with the following questions:

1) Can I search GEO based on chromosome location?

2) Do you know of other databases that would allow me to do this?

3) Should I download the raw reads and redo the analysis?

4) other ideas?


As always, thanks for any help!

rna-seq database geo • 1.3k views
ADD COMMENTlink modified 4.8 years ago by Adrian680 • written 4.8 years ago by Whetting1.5k

I always download .sra files and redo the analysis, in this way I know the quality, how reads are mapped and moreover, how the expression is estimated.

ADD REPLYlink written 4.8 years ago by Manvendra Singh2.1k
gravatar for Adrian
4.8 years ago by
Cambridge, MA
Adrian680 wrote:

Are you looking at a particular dataset in GEO?  More specific details would be helpful.

You might want to have a look at GTEX, which is a large systematic dataset of gene expression and eQTLs across many human tissues:

ADD COMMENTlink written 4.8 years ago by Adrian680
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