Introduction to CellMiner

Augustin Luna
26 January, 2016

Research Fellow
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute

Topics to be Covered

  • Introduction to CellMiner
  • Introduction to rcellminer

What is CellMiner?

  • Website:
  • Retrieval and integration for NCI-60 datasets: molecular and pharmacological
  • NCI-60
    • 60 human cancer cell lines from 9 tissues of origin: breast, central nervous system, colon, leukemia, melanoma, non-small cell lung, ovarian, prostate, and renal
    • Used by the Developmental Therapeutics Program of the National Cancer Institute to screen over 100,000 chemical compounds and natural products
  • A subset of ~21,000 drugs is provided by CellMiner
  • Drug activity levels expressed as 50% growth-inhibitory levels (GI50) were determined at 48 hours using the sulforhodamine B (SRB) assay
    • Determines cell density based on the measurement of total cellular protein content

What is rcellminer?

Pattern Comparison using rcellminer

library(rcellminer)

# Get drug and expression data
drugAct <- exprs(getAct(rcellminerData::drugData))
expData <- getAllFeatureData(rcellminerData::molData)[["exp"]]

# Create pattern of interest
patternOfInterest <- expData["SLFN11", ]

# Run pattern comparison to get correlated drugs and other gene expressions
r1 <- patternComparison(patternOfInterest, drugAct)
r2 <- patternComparison(patternOfInterest, expData)

head(r1, 3)
             COR         PVAL
639174 0.8343842 1.227589e-16
681636 0.7967239 1.243962e-13
34462  0.7950691 3.302182e-14
head(r2, 3)
              COR         PVAL
SLFN11  1.0000000 0.000000e+00
BCAT1   0.5847423 9.298535e-07
CCDC181 0.5766713 1.419268e-06

Embedded Shiny Applications

  • Simplified web applications to do common data exploration tasks
    • Compare any two molecular and drug profiles
    • Find related structures
    • View information on repeat screening for drug compounds

Getting Help

  • CellMiner
  • rcellminer
    • Augustin Luna: aluna [AT] jimmy [DOT] harvard [DOT] edu
    • Vinodh Rajapakse: vinodh [DOT] rajapakse [AT] nih [DOT] gov