Hi guys,
Where can I find the gene expression level in multiple cell lines, such as I want to see the level of gene A in multiple gastric cancer cell lines? And this level could be either mRNA or protein.
Is there any bioinformatic website you guys know that can address this type of question?
Thank you in advance!
Dear Xingchen Dong ,
look the link, may be useful.
https://link.springer.com/article/10.1134/S0006350915060172
Regards, Shafagat
Hi Xingchen
take a look at the NCBI website, especially the GEOprofile tool (https://www.ncbi.nlm.nih.gov/geoprofiles/) where you'll find your favorite gene expression in many cell types.
fred
Dear Xingchen,
please refer the following link (Expression Atlas - EMBL-EBI) to search the answer of your question.
https://www.ebi.ac.uk/gxa/
when you exploring gene expression atlas, there are three options available on above mentioned link. 1. gene/gene properties 2. Organism 3. Biological conditions
In biological conditions option type cancer and select cancer cell lines, choose suitable cell lines as per your area of interest.
Hi Xingchen,
you could use the expression data from some large scale pharmacogenomics study like CCLE or GDSC. For GDSC using the following link you can download the gene expression (microarray) data for 1000 cell lines (including ~ 30 gastric cell line). The preprocessed expression data is the "RMA normalised expression data for cell lines". The columns are the COSMIC IDs for cell lines, while the rows are the ensembl gene IDs. Hope it helps,
Bence
http://www.cancerrxgene.org/downloads
hello
https://www.ncbi.nlm.nih.gov/pmc/articles
https://www.ncbi.nlm.nih.gov/pmc/articles
Guys thank you all so much and i will look into all these websites you guys mentioned.
Really appreciate it!
Hi,
a very well documented site exists: http://atlasgeneticsoncology.org/
sincerely
NCBI, GEO advance search (http://www.ncbi.nlm.nih.gov/gds/advanced) is my favorite. You can write them directly () for assistance. Regards.
cBioPortal is another good source (http://www.cbioportal.org/). They also have clinical data, which are much needed in many analyses.
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