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1. System requirements
2. Data description 2.1 Raw data for chemicals
2.2 z-score
2.3 log2(gene expression)
2.4 Fold change and log2(fold change)
2.5 Enrichment Score
2.6 2D-based similarity for chemicals
2.7 3D shape similarity for chemicals
2.8 Profile based similarity
3. Software support
4. Troubleshooting 4.1 Java plugin error
  • 1. System requirements
    •    ● Internet Explorer 10 or later
    •    ● Java 1.7 or later
  • 2. Data description
  • 2.1 Raw data for chemicals
  •    ● Drug response data provided by NCI60, quantified by -logGI50 [M] value which is the concentration required to inhibit the growth of an exposed cell line culture to 50% relative to the untreated control.
  • 2.2 z-score
  •    ● Normalized -logGI50 data for chemicals as follows:

  •    , where x is -logGI50 for a chemical, is the average of all chemicals; is the standard deviation of all chemicals.
  • 2.3 log2(gene expression)
  •    ● Microarray gene expression data for NCI60 cell lines (GEOID: GSE32474), released in a log2 scale following RMA normalization.
  • 2.4 Fold change and log2(fold change)
  •    ● Both mean difference between the average of cell lines with a specific mutation/lineage and the median of all cell lines.
  •    ● Fold change (a.k.a. Δz-score ) for chemicals based on z-score and log2(fold change) for genes based on log2(gene expression), respectively.
  • 2.5 Enrichment Score
  •    ● Odds ratio between the observed odds and the expected odds:
  •    
  •    
  •    
  •    , where FC means Δz-score for chemicals and log2(fold change) for genes, respectively.
  • 2.6 2D-based similarity for chemicals
  •    ● Correlation between a query and the target structures in terms of structure description based on molecular fingerprints comprised of bit string (a sequence of 0 and 1).
  •    ● Three types of structural similarity (0≤range≤1):

  • TypeEquation
    Similarity
    Substructure
    Superstructure
  •    , where
       - NA: the number of 1 bits in the query structure A,
       - NB: the number of 1 bits in the target structure B, and
       - NA∩B: the number of 1 bits common to both structure A and B.
  • 2.7 3D shape similarity for chemicals
  •    ● Three-dimensional shape-based metrics (0≤TanimotoCombo≤2), implemented in the FastROCS package.
  • 2.8 Profile based similarity
  •    ● Pearson Correlation Coefficient of cell line-based profiles between chemicals, genes, a chemical and a gene.
  • 3. Software support
  •    ● MarvinSketch for structure editor and MarvinView for the 2D structures of chemicals developed by ChemAxon
  •    ● OpenBabel for generating 2D structure fingerprints
  •    ● Omega for generating 3D conformers and FastRocs for calculating 3D shape similarity developed by OpenEye
  • 4. Troubleshooting
  • 4.1 Java plugin error
  •    
  • - Check whether Java is installed in your computer. If not, install Java from here.
  • - Then, test whether JavaScript is enabled in your web browser here.
  • Last update: July 2019