broad的 CTRP Cancer Therapeutics Response Portal (CTRP)
- Cancer Therapeutics Response Portal (CTRP v1, 2013) dataset
- Cancer Therapeutics Response Portal (CTRP v2, 2015) dataset
broad的CCLE: Cancer Cell Line Encyclopedia (CCLE)
CCLE 目前有1,400多个cell line，涉及十几种肿瘤类型。
sanger的 GDSC : Genomics of Drug Sensitivity in Cancer
- 数据下载 : EGAS00001000610. ArrayExpress accession number E-MTAB-2706.
Typically it is IC50 value. It is the concentration of an inhibitor where the response (or binding) is reduced by half. The IC50 is obtained by plotting a measure of the cell death rate vs the concentration of the drug. IC50 is expressed as a concentration so the higher the concentration of drug needed to kill the cell line the more resistant that cell line is. If the IC50 is very low then the concentration (or amount) of drug needed to kill the cell line is also very low which means the cell line is more sensitive. Typically you get a S curve or sigmoidal curve. IC50 is the middle point of the sigmoidal curve. The threshold for calling a drug sensitive/resistant changes depending upon the IC50 value and you need to see how the sigmoidal curve.
However, recent publications from John Quackenbush's lab has shown that IC50 values are not a good measure of calling a drug resistant or sensitive. I am not an expert but these are good starting point to understand the problems and possible measures:
cd institute/drugs/ mkdir genetect gdsc ctrp ccle cd genetect # E-MTAB-2706 - RNA-seq of 675 commonly used human cancer cell lines nohup wget -c https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2706/E-MTAB-2706.additional.1.zip & nohup wget -c https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2706/E-MTAB-2706.additional.2.zip & nohup wget -c https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2706/E-MTAB-2706.idf.txt & nohup wget -c https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2706/E-MTAB-2706.sdrf.txt &