- 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)
- ● Difference between the average of cell lines with a specific mutation/lineage and the median of all cell lines.
- ● Fold change based on z-score for chemicals and log2(fold change) based on log2(gene expression) for genes, respectively:
- and , where is the average of the cell lines with a specific mutation or lineage and is the median of all cell lines.
- 2.5 Enrichment Score
- ● Odds ratio between the observed odds and the expected odds:
- , where FC for Δz-score for chemicals/log2(fold change) for genes, and p for a significance value.
- 2.6 2D-based similarity for chemicals
- ● Calculation 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):
- , 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.
- Last update: July 2014