Glossary

ADAF

acronym for All Drug All Feature mode

CLI

A Command Line Interface (CLI) is an interface where the user types a command (text) and presses the return key to execute that command.

COSMIC

COSMIC is a global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. See the COSMIC website or pubmed reference for more details

CSV

acronym for Comma Separated Values, a file format. Extension must be .csv.

EC50

The EC50 is the half maximal Effective Concentration and refers to the concentration of a drug, antibody or toxicant which induces a response halfway between the baseline and maximum after a specified amount of time. It is used as a measure of drug’s potency

FDR

In genome research, it is common to examine a large number of features. When testing multiple hypotheses, one must guard against an abundance of false positive results. A criterion for error control is the false discovery rate (FDR), which is the expected proportion of falsely rejected hypotheses. This error rate is equal to FWER when all null hypotheses are true but is smaller otherwise. Benjamini and Hochberg, proposed a step-down procedure to control FDR for independent test statistics. This method is currently recommended in GDSCTools and is the default method gor multiple testing correction. See e.g., article

IC50

The IC50 is the half maximal Inhibitory Concentration that is a measure of effectiveness of a drug or substance in inhibiting a specific biological or biochemical function.

Sometimes, IC50 values are converted to the pIC50 scale that is .

pIC50 is usually given in terms of molar concentration (mol/L or M). Therefore to obtain pIC50, an IC50 should be specified in units of M. When IC50 is expressed in microM or nanoM, it will need to be converted to M before conversion to pIC50.

IPython

Python comes with a dedicated shell, which can be started in a terminal by typing python. However, an improved shell is provided with the IPython environment, which should be installed independently. Note that conda distribution usually comes with ipython already installed.

MEDIA

A factor used in the regression analysis. Stands for Growth MEDIA. MEDIA_FACTOR ir one of the possible column filled in Genomic Feature.

MoBEM

Data structure used in GDSC to store genomic information. This is a CSV file with specific header: (SAMPLE, TISSUE, TYPE, GENE)

MSI

Microsatellite Instability (MSI) are markers indicating the presence or absence of a MSI shift, allele homozygosity/heterozygosity, and loss of heterozygosity (LOH) observed in the tumor sample for each participant

ODAF

acronym for One Drug All Feature mode

ODOF

acronym for One Drug One Feature mode

OLS

An ordinary least squares (OLS) or linear least squares is a method for estimating the unknown parameters in a linear regression model, with the goal of minimizing the differences between the observed responses in some arbitrary dataset and the responses predicted by the linear approximation of the data

PANCAN

alias for set of cancer tissues (unlike cancer-specific tissue).

shell

A shell is a program that provides the traditional, text-only user interface for Linux and other Unix-like operating systems. It is a specialised CLI that is a command-line shell (e.g., bash) where users can execute programs.

TCGA

The Cancer Genome Atlas (TCGA) is a project to catalogue genetic mutations responsible for cancer, using genome sequencing and bioinformatics. See TCGA homepage

Terminal

Under Unix-like operating systems, a terminal is a program that run a shell. A unix terminal (Linux or Mac) starts with a specialised shell (e.g. bash shell). Under Windows, the “command prompt” available in All Programs -> Accessories is an entry point to a terminal for typing computer commands

TSV

acronym for Tabular Separated Values, a file format. Extension must be .tsv.