iLINCS- two group Proteo-transcriptomic analysis
Mahdavian, Elahe
Dear iLINCS Technical Support,
I am interested in using iLINCS platform to perform a two-group Proteo-transcriptomic analysis across two cancer cell lines. This task requires the selection of an appropriate dataset, create signature and the integrative analytic workflow similar to the use case #3 reported in the article below:
“Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS”
https://www.biorxiv.org/content/10.1101/826271v1
Using the available GDS datasets and iLINCS analytic tools, I am able to perform the 2-group comparison analysis for treatment/baseline set across CCLs, with the baseline option limited to other cancer cell lines. I do not find an option to select the matched normal cell line as the baseline.
I have additional questions regarding the analytic workflow. Would you be able to schedule a virtual meeting for me to discuss this with you?
Thank you!
Elahe
Elahe Mahdavian, M.Sc., Ph.D.
Professor of Biochemistry
Louisiana State University in Shreveport
One University Place
Shreveport, Louisiana 71115
Office: (318) 797-5227 Fax: (318) 797-5090
Email: emah...@lsus.edu
http://www.lsus.edu/elahe-mahdavian
Medvedovic, Mario (medvedm)
Dear Elahe,
Unfortunately the CCLE dataset, to the best of my knowledge, does not contain “normal cell lines”, only cancer derived ones. So, this will not be possible. It is the limitation (or the design) of the Cancer Cell Line Encyclopedia dataset.
Best,
Mario
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