Glossary of gene expression terms

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Top · 0–9 · A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

[edit] A

Activator - protein that binds to an enhancer (or activator binding region) and activates transcription from nearby promoter.

A-DNA - a form of DNA found at low relative humidity, with 11 bp per helical turn. This form assumed in solution by RNA-DNA hybrid.

[edit] 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.

[edit] C

Constitutive gene or constitutive expression - a gene that is transcribed continually compared to a facultative gene which is only transcribed as needed.

Candidate genes: see signature. Do not confuse with the genetics definition of Candidate gene

[edit] D

Distance measures - used to measure the dissimilarity between the expressions of different genes".^[1]

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).

[edit] E

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.

[edit] F

Facultative gene - a gene which is only transcribed as needed compared to a constitutive gene.
A feature - see probe or reporter

[edit] G

[edit] H

A 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 resepct to a gene expression assay, hybridization is a step in the experimental paradigm, while in molecular biology or genetics, hybridization is the chemical process.

[edit] I

Inducible gene is a gene whose expression is either responsive to environmental change or dependent on the position of the cell cycle.

[edit] J

[edit] K

[edit] L

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

[edit] M

MAGE - MicroArray and Gene Expression, a group that "aims to provide a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems".^[2]

MIAMI - a commercial standard developed at MGED based on MAGE to facilitate storage and sharing of gene expression data It stands for Minimum information about a microarray experiment.^[3].

MGED - the Microarray Gene Expression Data Society, which "aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments".^[4]

[edit] N

[edit] 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-dimmensional array, see oligonucleotide array or microarray.

[edit] 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.
Promotion is increasing the rate of gene expression.

[edit] Q

[edit] R

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".^[3] 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.

[edit] S

Signature - a vague term which 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.
Suppression - decreasing the rate of gene expression. See Down-regulation

[edit] T

[edit] 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).