Question: gene expression database for quary a gene
1
gravatar for rob.costa1234
3.0 years ago by
rob.costa1234280
United States
rob.costa1234280 wrote:

Is there a gene expression (RNAseq or array) database that can be be queried for expression level of a particular gene in specific cancer?

Thanks

rna-seq • 782 views
ADD COMMENTlink modified 3.0 years ago by Rahul Sharma620 • written 3.0 years ago by rob.costa1234280

In addition to HPRD and cBioPortal, there is CCLE as well which is cell line specific

Though cBioPortal has added advantage of being able to visualize effect of mut. vs. WT on the gene which you have queried.

ADD REPLYlink written 3.0 years ago by Amitm2.1k

Gemma

https://gemma.msl.ubc.ca/home.html;jsessionid=01A0E50596D27ED255B38B6052CA2D40

ADD REPLYlink written 3.0 years ago by A3.9k
1
gravatar for Michael Dondrup
3.0 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

How about the Human protein Atlas (sample query). If you are looking for a few genes only, the web-interface provides you with the context to interpret the data properly. Data can be downloaded from there as well. In addition, there is an estimate of the protein expression level and information on the prognostic performance of the gene.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Michael Dondrup48k
0
gravatar for GenoMax
3.0 years ago by
GenoMax96k
United States
GenoMax96k wrote:

cBioPortal and LinkedOmics.

ADD COMMENTlink written 3.0 years ago by GenoMax96k
0
gravatar for Rahul Sharma
3.0 years ago by
Rahul Sharma620
Germany
Rahul Sharma620 wrote:

Although that is very tricky to get gene signatures that could match to your query signatures, as many factor influence the expression profiles e.g cell type used, controls, number of replicates and way of generating expression profiles. Here are few on-line resources that I use for my analyses:

http://www.lincsproject.org/LINCS/tools/workflows/query-a-gene-expression-signature-against-the-lincs-11000-data http://www.expression.cs.cmu.edu/index.html

I hope this would be helpful

Best, Rahul

ADD COMMENTlink written 3.0 years ago by Rahul Sharma620
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