Created by: Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, John Turner, Stephan Schurer*
Contact: Stephan Schurer stephan dot schurer at gmail dot com
The role of a scientist who has designed an assay and requested it to be run at a screening center.
The role of a compound that is routinely run in the same manner as the test compounds in every run of the assay. This term does not refer to the plate controls used to define the maximum and minimum responses, and they may or may not be a “literature standard” or “reference” compound.
It is the role played by the solvent (e.g. DMSO) in which the perturbagen was dissolved. The negative control is used to determine the base-line to compare the effect of the test perturbagen.
The role of a chemical compound or reagent used in each plate of an assay to normalize the response of the test perturbagens (by plate). Compounds that can have a positive control role are known from previous experiments or is a previously established standard. It is usually highly active resulting in a strong response of the intended effect. In an inhibition assay the positive control would usually result in the complete inhibition, which is then used for normalization (i.e. set as 100%). In an activation assay it would be activator used to normalize activity. Using controls provides an external reference and reduces the number of false negatives and false positives.
The role played by a cell line in supporting the growth of another cell line (e.g., stem cell). The feeder cell, e.g., mouse embryonic fibroblasts (MEFs) provides an adhesive surface to which the stem cells can attach and also secrete factors required for their growth.
The role played by the substrate, which is titrated without inhibitor to reflect the maximum enzyme activity at each substrate concentration.
The role played by the substrate, which is titrated without enzyme and without inhibitor. The low controls should reflect the signal expected for no enzyme activity at each substrate concentration. Depending on the composition of the inhibitor stocks, DMSO might be needed in the control wells to assure consistency across all the experiments.
The role played by the reading obtained from wells to which the sample or one of the reagents was not added. This is subtracted from all the experimental readings prior to further analysis.
The role of an organization or individual to add an assay to a repository, such as PubChem.
The role of an individual or a company as a creator of an assay kit, compound library, or detection instrument.
The role played by a soluble molecule, such as a hormone, neurotransmitter, or small molecule that binds to a biomolecular entity, such as a receptor.
The role of a molecular entity of being the output of a biological reaction or process that is quantitated either directly (by the presence of a tag or probe) or indirectly in a coupled reaction.
The role played by a protein in modulating immune cell function via cell signaling, subsequent to binding to its cognate cell surface receptor.
The role played by a protein in initiating cell division via cell signaling, subsequent to binding to its cognate cell surface receptor.
The role played by a molecular entity as being the substrate for a coupled enzyme (see definition of coupled enzyme). For e.g., luciferin, which is generated by cytochrome P450 (from modified luciferin) in a coupled enzyme reaction is the coupled substrate for luciferase.
The supportive role of a protein in mediating attachment of cells to a cell culture dish, on which it is coated.
The role of a chemical entity to bind inside the pore of a specific type of ion channel and block the flow of ions through it, resulting in an alteration of the electrochemical gradient of the cell membrane.
The molecular entity that brings about the transformation of less specialized cells to more specialized cell types, which differ morphologically and /or functionally.
The role of a molecular entity to bring about an increase of a predefined stimulus in an assay.
The role of a small molecule to act as a standard in a particular assay type, e.g., 1,4-Dioxane (for NMR), Cediranib (for Kinomescan).
Role of a protein in the transport of ions, small molecules, or macromolecules across a semi-permeable membrane, such as plasma membrane.
The role played by an enzyme in reporting the activity of a different enzyme by being able to use the substrate or product of the latter in its own reaction (either as a substrate or cofactor). E.g., luciferase acts as a coupled enzyme for cytochrome P450, as the luciferin generated (from modified luciferin) by the latter acts as its substrate.
The role of a molecular entity (e.g., barium chloride, acetylcholine) to change a cell's membrane potential, making it more positive.
The role played by a molecular entity that is added as an ingredient to a broth that is used to culture cells.
The role of a molecular entity of mediating the introduction of a foreign nucleic acid into cells, e.g., Lipofectamine 2000, Fugene 6, etc.
The role of the peptide that is appended at the N- or C-terminal of a protein (e.g., GST, His, HA, Myc, etc) which allows for easy identification and/or separation of that protein.
The role of an organization or individual in the various stages of implementation of an assay, such as manufacturing an assay kit or depositing an assay in a repository.
The role of a company as a creator of an assay kit, compound library, or detection instrument.
The role of an individual, who works at an academic institution as a creator of a chemical compound.
The role of a company as a creator of reagents and assay kits.
The role of a company as a creator of a compound library.
The role of a company as a creator of detection instrumentation.
This categorizes the distinct roles played by antibodies in recognizing either the antigen or an antibody itself.
The role of an antibody to detect and bind a specific antigen in a sample (cell, tissue, protein blot).
The role of an antibody to detect and bind a primary antibody in a sample (cell, tissue, protein blot).
A gene that performs the role of encoding a reporter protein, which can easily be detected in an assay, e.g., luciferase gene that encodes the luciferase protein. DNA constructs that contain reporter genes are excellent tools to understand regulation of gene expression.
The role played by a molecular entity that is added as an ingredient to an assay.
The role of a molecular entity to initiate a biological process. E.g., interferon-gamma has an inducer role in STAT-1 mediated transcriptional activation of cells.
The role of a molecular entity (small molecule, siRNA/shRNA, etc.) in altering the activity of proteins that serve as targets in a bioassay.
The role of a molecular entity as a known activator of a target/pathway, added prior to screening the compounds for selective inhibitor indications (e.g., forskolin is a potentiator for Gi/o pathway of G-proteins).
The role of a protein to be easily detected in an assay by virtue of its innate properties (fluorescence) or catalyzing a reaction that result in easily measurable products, such as luminescence, colored product, etc. Examples include luciferase, GFP, beta-galactosidase, etc.
The role of a compound to increase or decrease the ability of a cell to respond to its signaling molecule.
The role of a molecular entity to serve as the input for an enzymatic reaction that generates a product, e.g. ATP has the role of a substrate for ATPase, which hydrolyzes it to produce ADP and Pi.
The role of a molecular entity (protein or nucleic acid) that is the presumed subject of an assay and whose activity is being regulated by an entity with a perturbagen role in that assay.
The role of a molecular entity of specifying the cell's status of being alive, e.g., ATP.
A chemical entity that has the role of depolarization, which is to make the cell's membrane potential more negative.
The role of a chemical entity to distinguish two populations of cells, e.g., ampicillin is added to culture medium to identify ampicillin resistant bacteria.