Question: Time series expression data for cancer cell lines
1
gravatar for mehmet.tan
6.3 years ago by
mehmet.tan10
Turkey
mehmet.tan10 wrote:

Does anybody know where I can find time series gene expression datasets for cancer cell lines? There are available datasets in CCLE or GDSC but as far as I know they are not time series data. 

Thanks in advance,

ADD COMMENTlink written 6.3 years ago by mehmet.tan10

Usually you would go to http://www.ebi.ac.uk/arrayexpress/ or http://www.ncbi.nlm.nih.gov/geo/ if you are interested in public gene expression data sets. Have you tried searching for cancer AND time? I don't think they have a distinct tag for time-series, but you would be able to pick up something.

ADD REPLYlink written 6.3 years ago by David Westergaard1.4k

I did actually, but could not come up with something useful as mostly either the data is small or it is not time-series. Thanks,

ADD REPLYlink written 6.3 years ago by mehmet.tan10

I am curious why you want that. You are looking at cancer cell lines. These have been selected to be stable growing cells, right? In other words a time series, without any intervention, should ideally not show any effect at all. 

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Chris Evelo10k

I was thinking that a time-series data allows me to infer protein networks, as it will show the change of gene expression over time for all genes. Therefore I will be able able to compute the correlations between genes, infer a gene network for each cell line, then see the differences between cell lines in terms of their protein/gene networks.

ADD REPLYlink written 6.3 years ago by mehmet.tan10

Ahh right. That should work only if the cell growth has been synchronised somehow, which can be done. See for instance: http://www.cancerci.com/content/13/1/77 

ADD REPLYlink written 6.3 years ago by Chris Evelo10k

hello. i have the same issue. Did you find your answer eventually? If so it would be a great help!

thanks

ADD REPLYlink written 5.1 years ago by Andrea40

Hello! I also have the same exact issue - if you or Andrea found good data sources please let me know! Many thanks!

ADD REPLYlink written 4.1 years ago by DEN0
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