.. index:: ic50, ec50
.. glossary::
:sorted:
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
:math:`-\log10 (IC50)`.
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.
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
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
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 <http://bioinformatics.oxfordjournals.org/content/21/6/781.full>`_
TCGA
The Cancer Genome Atlas (TCGA) is a project to catalogue
genetic mutations responsible for cancer, using genome sequencing and
bioinformatics. See `TCGA homepage <http://cancergenome.nih.gov/>`_
MEDIA
A factor used in the regression analysis. Stands for Growth MEDIA.
MEDIA_FACTOR ir one of the possible column filled in Genomic Feature.
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 <http://cancer.sanger.ac.uk/cosmic>`_ or
`pubmed reference <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705836/>`_ for more details
ODOF
acronym for One Drug One Feature mode
ODAF
acronym for One Drug All Feature mode
ADAF
acronym for All Drug All Feature mode
CSV
acronym for Comma Separated Values, a file format. Extension must
be `.csv`.
TSV
acronym for Tabular Separated Values, a file format. Extension must
be `.tsv`.
PANCAN
alias for set of cancer tissues (unlike cancer-specific tissue).
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
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.
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 :term:`CLI` that is a command-line shell (e.g.,
bash) where users can execute programs.
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
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.
