Entering edit mode
8.8 years ago
mehmet.tan ▴ 10
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
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.
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,
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.
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.
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
Hello. I have the same issue. Did you find your answer eventually? If so it would be a great help!
Hello! I also have the same exact issue - if you or Andrea found good data sources please let me know! Many thanks!