A

• Activator
  Activator (genetics)
  An activator is a DNA-binding protein that regulates one or more genes by increasing the rate of transcription. The activator may increase transcription by virtue of a connected domain which assists in the formation of the RNA polymerase holoenzyme, or may operate through a coactivator. A...
  
  - protein that binds to an enhancer (or activator binding region) and activates transcription from nearby promoter.

• A-DNA
  A-DNA
  A-DNA is one of the many possible double helical structures of DNA. A-DNA is thought to be one of three biologically active double helical structures along with B- and Z-DNA. It is a right-handed double helix fairly similar to the more common and well-known B-DNA form, but with a shorter more...
  
  - a form of DNA found at low relative humidity, with 11 bp per helical turn. This form assumed in solution by RNA-DNA hybrid.

• ArrayExpress - is a public repository for transcriptomics data, which is aimed at storing MIAME- and MINSEQE- compliant data in accordance with FGED Society recommendations.

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
  Genetics
  Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
  
   definition of Candidate gene
  Candidate gene
  A candidate gene is a gene, located in a chromosome region suspected of being involved in the expression of a trait such as a disease, whose protein product suggests that it could be the gene in question...
  
  .
• 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
  Cellular differentiation
  In developmental biology, cellular differentiation is the process by which a less specialized cell becomes a more specialized cell type. Differentiation occurs numerous times during the development of a multicellular organism as the organism changes from a simple zygote to a complex system of...
  
  . 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
  Cofactor (biochemistry)
  A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
  
   are required for the initiation of catalysis
  Catalysis
  Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
  
  .
• Conditional gene expression is 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 coregulator
  Transcription coregulator
  In molecular biology and genetics, transcription coregulators are proteins that interact with transcription factors to either activate or repress the transcription of specific genes. Transcription coregulators that activate gene transcription are referred to as coactivators while those that...
  
  s are proteins that work with transcription factor
  Transcription factor
  In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
  
  s to regulate gene expression.

D

• Distance measures - used to measure the dissimilarity between the expressions of different genes".

• DNA Microarray
  DNA microarray
  A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
  
  - 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 to determine relative abundance of nucleic acid sequences in the target. There are many types of microarrays.

• 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
  Emergenesis
  In psychology, a trait is called emergenic if it is the result of a specific combination of several interacting genes . Emergenic traits will not run in families, but identical twins will share them...
  
  - quality of genetic traits that result from a specific configuration of interacting genes, rather than simply their combination
• Epistasis
  Epistasis
  In genetics, epistasis is the phenomenon where the effects of one gene are modified by one or several other genes, which are sometimes called modifier genes. The gene whose phenotype is expressed is called epistatic, while the phenotype altered or suppressed is called hypostatic...
  
  - 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
  Gene expression
  Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
  
  - the transcription of DNA
  DNA
  Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
  
   into messenger RNA
  Messenger RNA
  Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
  
   by RNA polymerase
  RNA polymerase
  RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
  
  . The messenger RNA is then translated into protein
  Protein
  Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
  
   by the ribosome
  Ribosome
  A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
  
  . In gene expression analysis, expression level refers to the amount of mRNA detected in a sample.

F

• 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
  National Center for Biotechnology Information
  The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
  
   database for gene expression
• Gene knockout
  Gene knockout
  A gene knockout is a genetic technique in which one of an organism's genes is made inoperative . Also known as knockout organisms or simply knockouts, they are used in learning about a gene that has been sequenced, but which has an unknown or incompletely known function...
  
  - 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
  Gene knockdown
  Gene knockdown refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification 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...
  
  - 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
  Graph theory
  In mathematics and computer science, graph theory is the study of graphs, mathematical structures used to model pairwise relations between objects from a certain collection. A "graph" in this context refers to a collection of vertices or 'nodes' and a collection of edges that connect pairs of...
  
   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
  Housekeeping gene
  A housekeeping gene is typically a constitutive gene that is required for the maintenance of basic cellular function, and are found in all cells of an organism. Although some housekeeping genes are expressed at relatively constant levels , other housekeeping genes may vary depending on...
  
  - typically a constitutive gene that is transcribed
  Gene expression
  Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
  
   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
  Actin
  Actin is a globular, roughly 42-kDa moonlighting protein found in all eukaryotic cells where it may be present at concentrations of over 100 μM. It is also one of the most highly-conserved proteins, differing by no more than 20% in species as diverse as algae and humans...
  
  , GAPDH and ubiquitin
  Ubiquitin
  Ubiquitin is a small regulatory protein that has been found in almost all tissues of eukaryotic organisms. Among other functions, it directs protein recycling.Ubiquitin can be attached to proteins and label them for destruction...
  
  .

• 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
  Complementarity (molecular biology)
  In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...
  
   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 is a gene
  Gene
  A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
  
   whose expression is either responsive to environmental change or dependent on the position of the cell cycle
  Cell cycle
  The cell cycle, or cell-division cycle, is the series of events that takes place in a cell leading to its division and duplication . In cells without a nucleus , the cell cycle occurs via a process termed binary fission...
  
  .
• Insulator - a stretch of DNA that prevents a gene from being influenced by the activation or repression of nearby genes.

L

• Library - a collection of DNA
  DNA
  Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
  
   or oligonucleotide probes, often stored in a microtiter plate
  Microtiter plate
  A Microtiter plate or microplate or microwell plate, is a flat plate with multiple "wells" used as small test tubes. The microplate has become a standard tool in analytical research and clinical diagnostic testing laboratories...
  
  , which are transferred to the array during fabrication.

M

• MAGE
  Magé
  Magé is a city and a municipality located in the Brazilian state of Rio de Janeiro.Magepe-Mirim was established in 1566 by Portuguese colonists...
  
  - MicroArray and Gene Expression, a group that "aims to provide a standard for the representation of DNA microarray
  DNA microarray
  A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
  
   gene expression
  Gene expression
  Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
  
   data that would facilitate the exchange of microarray information between different data systems".

• MIAME
  MIAME
  MIAME is a standard created by the FGED Society for reporting microarray experiments. It is intended to specify all the information necessary to interpret the results of the experiment unambiguously and to potentially reproduce the experiment...
  
  - 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, which "advocates for open access to genomic data sets... and develop[s] standards for biological research data quality, annotation and exchange".

O

• oligo - short for oligonucleotide
  Oligonucleotide
  An oligonucleotide is a short nucleic acid polymer, typically with fifty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized, in a sequence-specific manner, from individual nucleoside phosphoramidites...
  
  , a small chain of nucleic acid
  Nucleic acid
  Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
  
   residue
  Residue (chemistry)
  In chemistry, residue is the material remaining after a distillation or an evaporation, or to a portion of a larger molecule, such as a methyl group. It may also refer to the undesired byproducts of a reaction....
  
  s.
  • 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.
• Operon
  Operon
  In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create...
  
  - a genetic unit for coordinating expression of different genes.

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 facilitates the transcription of a particular gene.
• Promotion is 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

• Replication
  Replication (statistics)
  In engineering, science, and statistics, replication is the repetition of an experimental condition so that the variability associated with the phenomenon can be estimated. ASTM, in standard E1847, defines replication as "the repetition of the set of all the treatment combinations to be compared in...
  
  - a technique to estimate technical and biological variation in experiments for statistical analysis
  Multivariate analysis
  Multivariate analysis is based on the statistical principle of multivariate statistics, which involves observation and analysis of more than one statistical variable at a time...
  
   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
  Covalent bond
  A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding....
  
   attached to the array surface. See probe or probe-set.
• Repression - decreasing the rate of gene expression.
• Repressor
  Repressor
  In molecular genetics, a repressor is 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. This blocking of expression is called...
  
  - 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
  RNA splicing
  In molecular biology and genetics, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation...
  
  - 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 splicing
  Alternative splicing
  Alternative splicing is a process by which the exons of the RNA produced by transcription of a gene are reconnected in multiple ways during RNA splicing...
  
  s, which have various functional effects.

S

• Signal transduction pathway
  Signal transduction
  Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response...
  
  - 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
  Phosphorylation
  Phosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes....
  
   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.
• 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
  Transcriptional bursting
  Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of genes from bacteria to humans. Transcription of genes, the process which transforms the stable code written in DNA into the mobile RNA message can occur in "bursts" or "pulses"...
  
  - transcription (and also translation) occurs in "bursts" or "pulses", with periods of gene activity separated by irregular intervals.

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).