Question: data mining: find expression level of a specific gene in specific tisse
1
gravatar for Whetting
4.8 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

Hi,

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
1
gravatar for Adrian
4.8 years ago by
Adrian680
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: http://www.gtexportal.org/home/

ADD COMMENTlink written 4.8 years ago by Adrian680
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