Try RefExA (Reference database for gene expression analysis). It is maintained by the Laboratory for Systems Biology and Medicine at the University of Tokyo. This database provides gene expression profiles from various human organs and cells. You can access the database here: http://157.82.78.238/refexa/main_search.jsp

I just recognized that the link doesn't work directly within ResearchGate. You have to copy the URL until the end ("...jsp") and paste it in the address field of your browser.

Hello Danielle,

the other way round: http://www.proteinatlas.org and then you can type in the searchfield for example CD44 and then you see cell lines where this is expressed.

You can also try gene atlas : http://www.ebi.ac.uk/gxa/.

There is also your BioGPS for tissue specific expression in mouse and human tissues.

http://biogps.org/#goto=welcome

you might wish to work with the 60 cell line panel data that you can find here:

http://www.bioinf.ucd.ie/people/aedin/R/pages/made4/html/NCI60.html or following the link given in the original article by Ross et al. (PMID: 10700174) or links in articles citing the original publication

and, if you are interested in breast cancer cell lines, you can find expression data in the suppl. info to the article of Neve et al. (http://www.cell.com/cancer-cell/abstract/S1535-6108(06)00314-X)

Thanks everyone, I managed to find what I needed using Genevestigator. A brilliant tool, highly recommended: https://www.genevestigator.com/gv/

Try also this:

http://medicalgenomics.org/celllinenavigator

and this one: http://xavierlab2.mgh.harvard.edu/EnrichmentProfiler/index.html

Also in https://www.oncomine.org/resource/login.html

Excellent links. Is there an equivalent for COS cells?

Dear Danielle Smith

I'm working on Muller cells. I was previously looking for cell lines to express positive markers. You can check GeneCards and especially ProteinAtlas Project. Both are very good. In Protein Atlas is much easier I guess.

Hi All,

Is there a good database that I can lookup to see all the genes expressed in GM24385 cell line?

Hello

Did you check in all previously mentioned websites?

yes, oncomine is good

TCGA, protein alas

Thomas, did you figure out if an expression dataset exists for COS cells?

hope this link is useful

amp.pharm.mssm.edu/.../CCLE+Cell+Line+Gene+Expression+Profile...

regards

Agree with Philip Zimmermann

Hope you good luck

regards

Do sombody know dbase where I could do ruther oposit things.

e.g. I have got gene set of the embryonic tissue using RNAseq analisis. Is there the dbase which suggests the cell contants in this tissue on base of gene profile (propobility/% of cell repertuar, cell signature e.c.t )?

Dear Danielle,

Maybe this page can help you, although it is exclusive to human cell to chemical and genetic perturbation.

https://clue.io/

This database is great:

https://www.ebi.ac.uk/gxa/experiments/E-MTAB-2770/Results

"RNA-seq of 934 human cancer cell lines from the Cancer Cell Line Encyclopedia"

I've been looking for something like this with an emphasis on RNA seq, and my PI and I have found these:

https://github.com/oscar-franzen/alona/

-Python seurat alternative that also predicts cell type via machine learning (manuscript not out yet, kind of a 'black box' so to speak)

https://panglaodb.se/

-A large database of RNAseq experiments identifying marker genes. Seems useful, although I can’t find on their site how they identify the cell types (by algorithm, from paper, or by a human deciding on their end?). Also shows tSNEs of experiments.

https://academic.oup.com/nar/article/47/D1/D721/5115823

-CellMarker seems somewhat similar to PanglaoDB, but they specify that the marker gene and cell population information is 'hand picked from publications. Very nice UI.