Glossary of gene expression terms

A

• Activator – protein that binds to an enhancer (or activator binding region) and enhances transcription from nearby promoter.

B

• Baseline – a measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. Baseline expression may also refer to the expected or historical measure of expression for a gene.

C

• Candidate genes – see signature. Do not confuse with the genetics definition of Candidate gene.
• Cellular reprogramming – conversion of a cell from one tissue-specific cell type to another. This involves a conversion to a pluripotent state, otherwise known as dedifferentiation. One example is the conversion of mouse somatic cells to an embryonic state, which relies on the transcription factors of Oct4, Sox2, Myc, and Klf4. Citation: Nishikawa, S. (2007). Reprogramming by the numbers. Nature Biotechnology, 25, 877–878.
• Cofactor – non-protein compound that is bound to an enzyme. Cofactors are required for the initiation of catalysis.
• Conditional gene expression – controlled inducible expression of transgene either in vitro or in vivo.
• Constitutive gene or constitutive expression – a gene that is transcribed continually compared to a facultative gene which is only transcribed as needed.
• Cis-dominant – mutations (e.g., of an operator) that alter the functioning of genes on that same piece of DNA. It arises because the operator represents a site on the DNA rather than a gene that encodes a product.
• Coregulator – Transcription coregulators are proteins that work with transcription factors to regulate gene expression.
• Corepressor – A protein that reduces (represses) the expression of genes by binding to and activating a repressor transcription factor.

D

• Distance measures – used to measure the dissimilarity between the expressions of different genes.
• DNA Microarray – A DNA microarray is a high-throughput technology used to measure expression levels of mRNA transcripts or to detect certain changes in the nucleotide sequence. It is an array of series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence. This can be a short section of a gene or other DNA element that are used as probes to hybridize a cDNA, cRNA or genomic DNA sample (called target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by fluorescence-based detection of fluorophore-labeled targets t.
• Down regulation – decreasing the rate of gene expression.
• Down-regulated – describes a gene which has been observed to have lower expression (lower mRNA levels) in one sample compared to another sample (usually a control).

E

• Emergenesis – quality of genetic traits that result from a specific configuration of interacting genes, rather than simply their combination.
• Enhancer – A region of DNA that can be bound by an Activator to increase gene expression.
• Epistasis – the collective action of multiple genes that interact during expression. A form of gene action, epistasis can either be additive or multiplicative in its effects on specific phenotypic traits.
• Gene expression – the transcription of DNA into messenger RNA by RNA polymerase. The messenger RNA is then translated into protein by the ribosome. In gene expression analysis, expression level refers to the amount of mRNA detected in a sample.

F

• FGED – Functional GEnomics Data (FGED) Society, an organization that works with others "to develop standards for biological research data quality, annotation and exchange," and software tools that facilitate their use.
• Facultative gene – a gene which is only transcribed as needed compared to a constitutive gene.
• A feature – see probe or reporter

G

• Gene expression omnibus or GEO – a National Center for Biotechnology Information database for gene expression
• Gene knockout – is a genetic technique in which an organism is engineered to carry genes that have been made inoperative (have been "knocked out" of the organism).
• Gene knockdown – refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification (a change in the DNA of one of the organism's chromosomes) or by treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene.
• Genetic regulatory network (GRN) – a graph that represents the regulatory complexity of gene expression. The vertices (nodes) are represented by various regulatory elements and gene products while the edges (links) are represented by their interactions. These network structures also represent functional relationships by approximating the rate at which genes are transcribed.

H

• Housekeeping gene – typically a constitutive gene that is transcribed at a relatively constant level across many or all known conditions. The housekeeping gene's products are typically needed for maintenance of the cell. It is generally assumed that their expression is unaffected by experimental conditions. Examples include actin, GAPDH, and ubiquitin.
• Hybridization – refers to the process by which the single-stranded DNA or RNA preparation is added to the array surface, in solution, and potentially anneals to the complementary probe. Note that with respect to a gene expression assay, hybridization is a step in the experimental paradigm, while in molecular biology or genetics, hybridization is the chemical process.
• Heterogeneous expression

I

• Inducible gene – a gene whose expression is either responsive to environmental change or dependent on the position of the cell cycle.
• Inducer – A protein that binds to repressors (to disable them) or to activators (to enable them).
• Insulator – a stretch of DNA that prevents a gene from being influenced by the activation or repression of nearby genes.

K

Karyoptyping

L

• Library – a collection of DNA or oligonucleotide probes, often stored in a microtiter plate, which are transferred to the array during fabrication.

M

• MAGE – MicroArray and Gene Expression, a group that "aims to provide a standard for the representation of DNA microarray gene expression data that would facilitate the exchange of microarray information between different data systems".
• MIAME – a commercial standard developed by FGED based on MAGE to facilitate storage and sharing of gene expression data It stands for Minimum information about a microarray experiment.
• MINSEQE – commercial standard developed by FGED for storage and sharing of high-throughput sequencing data. It stands for Minimal Information about a high-throughput SEQuencing Experiment.
• MGED – former name of the FGED Society.

N

• NBF or Neutral Buffer Formalin – a common solution used in the fixation of cells or cellular tissue for marking and study.

O

• oligo – short for oligonucleotide, a small chain of nucleic acid residues.
  • When used to detect the presence of larger mRNA molecules, see probe or reporter.
  • When assembled into a two-dimensional array, see oligonucleotide array or microarray.
• Operon – a genetic unit for coordinating expression of different genes.
• Overexpression – an abnormally and excessively high level of gene expression which produces a pronounced gene-related phenotype.

P

• Probe – a term to describe a reagent used to make a single measurement in a gene expression experiment. See reporter, probe-set.
• Probe-set – a collection of two or more probes that are designed to measure a single molecular species. For example, several oligonucleotides designed to hybrize to various parts of the mRNA generated from a single gene.
• Promoter – a region of DNA that initiates the transcription of a particular gene.
• Promotion – increasing the rate of gene expression.
• Putative genes – a nucleotide sequence thought to be a gene based on the identification of its open reading frame (ORF). The gene is "putative" in the sense that no function has been assigned to its products.

R

• Regulation of gene expression – the cell's system for controlling the expression of genes.
• Replication – a technique to estimate technical and biological variation in experiments for statistical analysis of the microarray data. Replicates may be:
  • technical replicates, such as dye swaps or repeated array hybridizations, or
  • biological replicates, using biological samples from separate experiments that test the effects of the same treatments.
• Reporter – a MIAMI-compliant term to describe a reagent used to make a single measurement in a gene expression experiment. MIAMI defines it as "the nucleotide sequence present in a particular location on the array". A Reporter may be single-stranded DNA that is covalently attached to the array surface. See probe or probe-set.
• Repression – decreasing the rate of gene expression.
• Repressor – a DNA-binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes.
• RNA splicing – modification of an RNA strand where exons (the coding regions of a transcribed gene) are retained and the introns are removed. Sometimes the exons are recombined either in vivo or experimentally to form alternative splicings, which have various functional effects.

S

• Signal transduction pathway – a set of biochemical reactions and biomolecular interactions that convert a stimulus into a metabolic response. A signaling molecule initially binds to a receptor on the surface of the cell, which stimulates the activation of immediate early genes and second messenger molecules. This further activates enzymes that carry out larger-scale processes such as phosphorylation and gene expression. The process just described is known as a signaling cascade, during which the initial stimulus is amplified to have a far-reaching effect on the cellular environment.
• Silencer – A region of DNA that can be bound by Repressors.
• Signature – refers to the set of expression measurements which satisfy a certain arbitrary threshold criteria, such as 1.5 fold change with a significance p<0.01. Analysts may define a signature for a given experiment or compare gene signatures across many experiments.
• Spatially-restricted gene expression – genes that are expressed only in a specific anatomical region or tissue, often in response to a paracrine signal. The boundary between two spatially-restricted genes can set up a sharp gradient, often expressed phenotypically as striping patterns.
• Suppression – decreasing the rate of gene expression. See Down-regulation

T

• Tissue-specific expression – Gene function and expression which is restricted to a particular tissue or cell type. For example, the glycoprotein hormone alpha subunit is produced only in certain cell types of the anterior pituitary and placenta, not in lungs or skin; thus expression of the glycoprotein hormone alpha-chain gene is said to be tissue-specific. Tissue specific expression is usually the result of an enhancer which is activated only in the proper cell type.
• Transcriptional bursting – transcription (and also translation) occurs in "bursts" or "pulses", with periods of gene activity separated by irregular intervals.
• Transcription factor – a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA

U

• Up regulation – increasing the rate of gene expression.
• Up-regulated – describes a gene which has been observed to have higher expression (higher mRNA levels) in one sample compared to another (usually the control).

Z

Z form gene.