Help:What Is The Meaning Of The Activity Sd In Processing The Ccle Data?

Question

[zerohsy]

Hello,I am processing the CCLE data,but I do not understand the meaning of the Activity SD.When I browsed the publications,I do not find anything about it.Is there anyone who has processed the data and know the meaning of i?Thanks a lot!!!

[Michael]

Nobody will most likely be able to answer this question, your mistakes:

• useless use of acronyms, what's CCLE (not very common concept in bioinformatics)
• "the publications" which? Provide a link
• "processed the data" which? provide a link or an example

Answer 1

[Obi Griffith]

I completely agree with the above comment about this being a problematic question. It feels like you are perhaps fishing for answers to a homework assignment. But, in the hopes that I am wrong I will give you some pointers and try to clarify your question. The CCLE refers to the Cancer Cell Line Encyclopedia published in Nature: http://www.ncbi.nlm.nih.gov/pubmed/22460905. I believe "Activity" refers to the normalized measure of cellular proliferation as described in the supplementary materials here (pages 10-11): http://www.nature.com/nature/journal/v483/n7391/extref/nature11003-s2.pdf.

The cell–compound mixtures were incubated for 72 to 84 hours; afterwards, cell numbers were determined by measuring the amount of ATP per well using Cell Titer Glo (Promega). Luminescence/well was measured using a ViewLux plate reader (Perkin Elmer). Within a cell line plating day, compounds were tested in duplicate; occasionally, lines were assayed multiple times (weeks to months apart), yielding additional replicate values. On all plates, wells containing vehicle only or the positive control compound MG132 (a proteasome inhibitor toxic to most cell lines at 1 μM) were also included. Raw values were normalized on a plate-by-plate basis such that 0% was equivalent to the median of vehicle wells and -100% equivalent to the median of the MG132 positive control. The normalized data was further corrected using a surface pattern model to remove edge and region effects.

You are probably referencing supplementary Table S11 from here: http://www.nature.com/nature/journal/v483/n7391/extref/nature11003-s3.xls. As described above, at each dose, for each cell line and drug combination there are at least duplicate measurements, and sometimes more replicates. The "Activity SD" is likely the standard deviation of these replicate values for each of these Activity measurements. It is from these data that the IC50, EC50, Activity area, etc are being calculated and then used in machine learning approaches with genomic data.

You may want to read this paper as well for potential caveats with the CCLE drug assay data: http://www.ncbi.nlm.nih.gov/pubmed/24284626. They compared the results of CCLE drug response assays to a similar highthroughput effort published here: http://www.ncbi.nlm.nih.gov/pubmed/22460902

[Michael]

This is an excellent response to an insubstantial question.