data mining: find expression level of a specific gene in specific tisse
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:
- Can I search GEO based on chromosome location?
- Do you know of other databases that would allow me to do this?
- Should I download the raw reads and redo the analysis?
- other ideas?
As always, thanks for any help!
1 answer
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/
Log in to answer this question.
More posts like this
-
DESeq2 design formula considerations
written by nhaus •
-
Hierarchical clustering of a subset of genes from RNA seq expression data
written by imlia8989 •
-
Penalty for unexpressed genes
written by Sandhiya •
-
Microarray data do not have GEO2R option?
written by bio •
-
Find the genes that are commonly expression between 3 tissue
written by jihed.chouaref •
-
How to use GEO to assess presence/absence of a specific gene in specific tissue or cell line
written by WC103 •
-
nearby genes expression
written by ta_awwad
-
ChIp-seq RNA-seq overlap
written by Federico •
-
Identify sets of genes that distinguish cancer from normal cells
written by sidney.shc •
-
Using RNAseq to measure gene expression in a tissue when the gene is NOT differentially expressed
written by Rduncan
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.