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Gene categories glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty MSLS  mchitty@healthtech.com
Last revised July 10, 2019

Biology term index: Gene Categories is a sub-category of Gene definitions

antibody genes: The large and diverse population of antibodies is generated by random combinations of a set of gene segments that encode different antigen binding sites (or paratopes), followed by random mutations in this area of the antibody gene, which create further diversity.^[7][8] Antibody genes also re-organize in a process called class switching that changes the base of the heavy chain to another, creating a different isotype of the antibody that retains the antigen specific variable region. Wikipedia Antibodies accessed Feb 14 2011 http://en.wikipedia.org/wiki/Antibody 

assembled genes: See under immunoglobulin genes

candidate genes: Candidate genes for genetic studies are selected on the basis of: their location in the genome (if linkage data are available); prior knowledge of similar (related) diseases; knowledge of disease pathogenesis; or knowledge of the gene and its function. Aside from linkage based candidates, all of these involve a degree of speculation. One means of increasing the chance of success is to consider findings from other similar diseases or syndromes.  P T Donaldson, Genetics of liver disease: immunogenetics and disease pathogenesis, Gut. 2004 April; 53(4): 599–608  doi: 10.1136/gut.2003.031732.

Focus on particular SNPs thought to have a functional effect.  Within family studies SNPs spanning several generations can show relationships between a disease and a candidate gene or a chromosomal region.  Focuses on particular coding regions of the genome.  Involves less sequencing overall and is more likely to uncover SNPs that, in addition to serving as markers, have functional implications and thus may shed light on biochemical mechanisms.

caretaker genes; See under tumor suppressor genes

chimeric gene: A semi-synthetic gene, consisting of the coding sequence from one organism, fused to promoter and other sequences derived from a different gene. Most genes used in transformation are chimeric. See carrier DNA; binary vector; plasmid; transformation; vector.  FAO http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm 

constitutive genes: The widely accepted view is that genes fall into one of two basic categories: those that express themselves at a steady rate, regardless of environmental conditions (i.e., constitutive genes), and those that are subject to regulation (i.e., inducible genes). Massoud Stephane, Genetic and Environmental Interactions in Psychiatric Illnesses [letter], J Neuropsychiatry Clin Neurosci 15:386-387, August 2003 http://neuro.psychiatryonline.org/cgi/content/full/15/3/386 Related term: housekeeping genes

developmental genes: Genes connected with developmental processes.

differentiated genes: Genes which exhibit differential patterns of gene expression, particularly in connection with disease and "normal" states.

DNA library:  When a complete genome is dissected and cloned in this way [see under template], a DNA library is created which contains a collection of clones representing the complete genome. A typical library may contain 10⁵ to 10⁸ clones.   Related/equivalent? term: gene library

DNA repair genes: Genes encoding proteins that correct errors in DNA sequencing. DOE

The disregulation of repair genes can be expected to be associated with significant, detrimental health effects, which can include an increased prevalence of birth defects, an enhancement of cancer risk, and an accelerated rate of aging. Although original insights into DNA repair and the genes responsible were largely derived from studies in bacteria and yeast, well over 125 genes directly involved in DNA repair have now been identified in humans, and their cDNA sequence established. These genes function in a diverse set of pathways that involve the recognition and removal of DNA lesions, tolerance to DNA damage, and protection from errors of incorporation made during DNA replication or DNA repair. Additional genes indirectly affect DNA repair, by regulating the cell cycle, ostensibly to provide an opportunity for repair or to direct the cell to apoptosis. For about 70 of the DNA repair genes listed in Table I, both the genomic DNA sequence and the cDNA sequence and chromosomal location have been elucidated. In 45 cases single-nucleotide polymorphisms have been identified and, in some cases, genetic variants have been associated with specific disorders. With the accelerating rate of gene discovery, the number of identified DNA repair genes and sequence variants is quickly rising. This report tabulates the current status of what is known about these genes. The report is limited to genes whose function is directly related to DNA repair. A. Ronen, BW Glickman "Human DNA repair genes" Environ Mol Mutagen 37 (3) : 241- 283, 2001  Related term: DNA glossary DNA repair

essential genes: Deletion of these genes is lethal to the organism.  Knockouts have to be replaced by knockdowns or conditional knockouts to provide functional genomics information.

extranuclear genes: Organelle, mitochondrial or chloroplast genes. Any others?

gatekeeper genes; See under tumor suppressor genes

gene components: The parts of the gene sequence that carry out the different functions of the GENES. MeSH 2003

gene library: A large collection of cloned DNA fragments from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences. MeSH, 1990

genomic library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns). MeSH, 1990 Related terms DNA library, gene library

housekeeping genes: In molecular biology, housekeeping genes are typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions.[1][2][3] Although some housekeeping genes are expressed at relatively constant rates in most non-pathological situations, the expression of other housekeeping genes may vary depending on experimental conditions.[4] The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA.[5] For experimental purposes, the expression of one or multiple housekeeping genes is used as a reference point for the analysis of expression levels of other genes. The key criterion for the use of a housekeeping gene in this manner is that the chosen housekeeping gene is uniformly expressed with low variance under both control and experimental conditions. Validation of housekeeping genes should be performed before their use in gene expression experiments such as RT-PCR. Wikipedia accessed 2018 Oct 26 https://en.wikipedia.org/wiki/Housekeeping_gene 

In theory, expressed in all genes.  Contrast with luxury genes.  Genes that encode housekeeping  proteins. Specific housekeeping genes can be used to normalize gene expression data.

hypothetical genes: Cannot be related to any previously characterized genes. Related term: ORFans

immediate-early genes: Genes that show rapid and transient expression in the absence of de novo protein synthesis. The term was originally used exclusively for viral genes where immediate- early referred to transcription immediately following virus integration into the host cell. It is also used to describe cellular genes which are expressed immediately after resting cells are stimulated by extracellular signals such as growth factors and neurotransmitters. MeSH, 1994

immunoglobulin genes Ig: Genes encoding the light and heavy chain segments of  immunoglobulins. Light chain gene segments are symbolized L-V (variable), J (joining) and C (constant); Ig heavy chain segments have, in addition, a diversity (D) gene. Each segment codes for certain amino acids, and each has a different nucleotide sequence; the genes are assembled by a remarkable shuffling of the segments during B lymphocyte maturation. MeSH, 1988

The immunoglobulin genes, which can be called assembled genes [107], do not fit any classical or neoclassical definition of the gene, since the genetic unit in the germ line and in the mature immune cell is completely different. Petter Portin in "The Origin, Development and Present Status of the Concept of the Gene: A Short Historical Account of the Discoveries" Current Genomics, 2000 https://pdfs.semanticscholar.org/a61a/4e1a2c28e517d6e4ca9a43fd63bbb65379e4.pdf 

inducible genes:  See under constitutive genes

interrupted genes: See split genes

jumping genes: See Sequences, DNA & beyond  transposons

lethal genes: Genes which result in the premature death of the organism; dominant lethal genes kill heterozygotes, whereas recessive lethal genes kill only homozygotes. MeSH, 1968   Related term: Functional genomics embryonic lethal

luxury genes: A gene that codes for specialized cell products and is expressed abundantly. Compare housekeeping genes.

marker genes: Biomarkers

mitochondrial genes: Useful for evolutionary research, population genetics, phylogenetics and conservation biology. https://www.biology-online.org/dictionary/Luxury_gene 
Wikipedia http://en.wikipedia.org/wiki/Mitochondrial_DNA#Genes   Related terms: Sequences, DNA & beyond mtDNA;   Cell biology mitochondria  

nested genes: Genes whose entire sequences are contained within other genes. MeSH 2003

A situation in which one gene resides within an intron of another gene, was first demonstrated in the Gart locus of Drosophila melanogaster by Steven Henikoff et al. [137]. In this particular case the nested genes were on opposite strands of DNA. Chun-nan Chen et al. [138] in turn demonstrated that in the large intron of the dunce locus of D. melanogaster there were actually two other genes residing, of which one was the known Sgs-4 gene. In this case the nested genes were on the same strand of DNA. Barbara Levinson et al. [139] were the first to demonstrate nested genes in man. The 22nd intron of the factor VIII gene included another gene in its opposite strand. The large intron of human neurofibromatosis gene includes a total of three other transcription units in two opposed orientation [140]. The existence of nested genes is in contradiction to the central hypothesis adopted by both the classical and neoclassical gene concept, that genes are located in linear order on the chromosome.  Petter Portin in "The Origin, Development and Present Status of the Concept of the Gene: A Short Historical Account of the Discoveries" Univ. of Turku, Finland, Current Genomics, 2000 https://pdfs.semanticscholar.org/a61a/4e1a2c28e517d6e4ca9a43fd63bbb65379e4.pdf 

non-nuclear genes: See extranuclear genes

non-protein coding gene: See RNA micro- RNA

non-structural genes: Don't code for proteins?  Compare structural genes

nuclear genes: Are these the vast majority of genes, all those except the ones found outside the nucleus?

operator genes: Control the structural genes. Nobel Prize in Physiology or Medicine awarded in 1965 to Francois Jacob, Andre Lwoff and Jacques Monod for discoveries related to these.

orphan genes: (also called ORFans, especially in microbial literature) ^[1][2] are genes without detectable homologues in other lineages.^[2] Orphans are a subset of taxonomically-restricted genes (TRGs), which are unique to a specific taxonomic level (e.g. plant-specific).^[3] In contrast to non-orphan TRGs, orphans are usually considered unique to a very narrow taxon, generally a species. Wikipedia accessed 2018 March 20 https://en.wikipedia.org/wiki/Orphan_gene

overlapping genes: Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells. MeSH, 1991

The first observations of overlapping genes were made in the bacteriophages FX 174 [108] and G4 [109], and in the animal virus SV40 [110, 111]. In the bacteriophage FX 174 several genes overlapped, encoding different proteins read from the same DNA strand but in different reading frames. In G4 the situation was even more complicated. In that phage the same DNA strand encoded as many as three different proteins, the messenger RNA's of which were transcribed overlappingly in all three possible reading frames. In these phages, however, the genes overlapped for only a few codons. In the SV40 virus, on the other hand, the genes overlapped for as many as 122 nucleotides.

Since these early findings, overlapping genes have also been found in eukaryotic multicellular organisms such as Drosophila melanogaster [112], mouse [113], and rat [114]. Overlapping genes can be located on the same DNA strand or on opposite strands.   Petter Portin in "The Origin, Development and Present Status of the Concept of the Gene: A Short Historical Account of the Discoveries" Current Genomics, 2000 https://pdfs.semanticscholar.org/a61a/4e1a2c28e517d6e4ca9a43fd63bbb65379e4.pdf 

parasitism genes: Genes encoding members of the parasitome.  In plant- parasitic nematodes, parasitism genes are genes expressed in nematode esophageal gland cells that encode secretory proteins that are secreted by the nematode through its stylet into host tissue to direct the complex process of parasitism. EL Davis et. al,  Annual Review of Phytopathology 38: 365- 396, 2000  Related term: -Omes & -omics parasitome

plasmid genes: A plasmid is a small DNA molecule within a cell that is physically separated from a DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that may benefit the survival of the organism, for example antibiotic resistance. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful to the organism under certain situations or particular conditions. ...

pleiotropic gene: A gene affecting more than one (apparently unrelated) characteristic of the phenotype. IUPAC Biotech

polygene: Gene definitions polygenic: Genetic variations

predicted genes: See under orphan genes and  Drug discovery informatics "gene prediction"

processed genes: See under pseudogenes.

promoter genes: See promoter, promoter region Sequencing DNA & beyond

pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non- functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double- stranded DNA), they are called processed genes. MeSH, 1998

Pseudogenes are sequences that are generally untranscribed and untranslated and which have high homology to identified genes . However, it has recently been shown that in different organisms or tissues functional activation may occur. Therefore, the previous policy of assigning the gene symbol of the structural gene followed by "P" and a number will only be approved on a case by case basis. In future, pseudogenes will usually be assigned the next number in the relevant symbol series, suffixed by a "P" for pseudogene (or "PS" in the specific cases) if requested e.g. OR5B12P "olfactory receptor, family 5, subfamily B, member 12 pseudogene". However, the designation "pseudogene" will remain in the gene name. Hester M. Wain et. al, "Guidelines for Human Gene Nomenclature" Genomics 79(4): 464-470, 2002  http://www.genenames.org/guidelines.html  Related term: pseudogenomics : -Omes & -omics  

putative genes: Genes predicted from EST clusters or from genomic sequence with EST evidence, but showing no structural or functional homology, are regarded as putative These are designated by the chromosome of origin, the letters "orf" for open reading frame and a number in a series.  Human Genome Nomenclature Committee  Hester M. Wain et. al, "Guidelines for Human Gene Nomenclature" Genomics 79(4): 464-470, 2002   

Conjectural genes, predicted by gene or exon identification software.  Related term? transcript clusters

quantitative gene: See under Gene definitions polygene.

rRNA genes: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into ribosomes. Prokaryotic rRNA genes are usually found in operons dispersed throughout the genome, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.  MeSH, 1999  Related term: tRNA.

regulator genes:  A gene which codes for a protein (an activator or repressor) having the ability to induce or repress the transcription of other genes. IUPAC Biotech

Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for proteins (repressors or activators) which regulate the genetic transcription of the structural genes and/ or regulatory genes. MeSH, 1968

regulatory region: Wikipedia http://en.wikipedia.org/wiki/Regulatory_region 

Prediction of regulatory regions remains difficult.

reporter genes: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.  MeSH, 1994

repressors: See under regulator genes

silent genes:  Genes that scientist believe are turned off are actually functioning at a low level that has previously been undetected, a discovery that could help answer questions about chronic disease and aging. Of the about 25,000 human genes science has identified, half are believed to be silent at any particular time and activated only when needed. But Andre Ptitsyn, biomedical and computer expert in the Center for Bioinformatics at Colorado State University, has discovered that current tools cannot measure extraordinarily low levels of gene expression signals. "Genes that we have believed to be silent are actually whispering," said Ptitsyn, who applied a common physics principle to find oscillating patterns of gene expression in genes previously thought to be shut off. In most studies, genes that are believed to be silent are excluded from analysis in early stages of research. However, with Ptitsyn's research, genes expressed below the current measurements show the pattern of expression coordinated with other genes. Genes Previously Believed To Be Silent Are Actually Whispering Key Information Science News 2003 https://www.sciencedaily.com/releases/2008/03/080326193819.htm     Related to Functional genomics gene silencing?

split genes:  The first observations of interrupted (split) genes, i.e. genes in which there exist noncoding intron sequences between the coding exon sequences, were made in animal viruses in 1977 [74 - 76]. These observations were based on physical mapping of the inner structure of the genes by means of so- called Southern blotting ... Almost at the same time as the virus observations, split genes were also found in eukaryotic organisms [77 - 85]. Since then, split genes have been found in all eukaryotic organisms investigated and their viruses, and it can be said that interrupted genes are the rule rather than the exception in the organization of the genes of multicellular eukaryotic organisms. Petter Portin in "The Origin, Development and Present Status of the Concept of the Gene: A Short Historical Account of the Discoveries" Current Genomics, 2000 https://pdfs.semanticscholar.org/a61a/4e1a2c28e517d6e4ca9a43fd63bbb65379e4.pdf  Related terms: Sequences DNA & beyond introns

structural genes: Genes that have a suppressor allele or suppressor mutation (SUPPRESSION, GENETIC) which cancels the effect of a previous mutation, enabling the wild- type phenotype to be maintained or partially restored.  MeSH, 1968

Relationship (if any) to gene structure? Compare non-structural genes

suppressor genes:: Genes that inhibit expression of a previous mutation. They allow the wild- type phenotype to be wholly or partially restored. MeSH, 1991

A gene which helps to reverse the effects of damage to an individual’s genetic material, typically effects which might lead to uncontrolled cell growth. A suppressor gene may code for a protein which checks genes for misspellings, and/ or which triggers a cell’s self- destruction if too many genetic mutations have accumulated. PhRMA  Narrower term: Cancer tumor suppressor gene

susceptibility genes: Molecular Medicine

syntenic genes: See under Gene definitions: synteny

virulence genes: Viruses also have notable virulence factors. Experimental research, for example, often focuses on creating environments that isolate and identify the role of "niche-specific virulence genes". These are genes that perform specific tasks within specific tissues/places at specific times; the sum total of niche-specific genes is the virus' virulence. Genes characteristic of this concept are those that control latency in some viruses like herpes. Murine gamma herpesvirus 68 (γHV68) and human herpesviruses depend on a subset of genes that allow them to maintain a chronic infection by reactivating when specific environmental conditions are met. Even though they are not essential for lytic phases of the virus, these latency genes are important for promoting chronic infection and continued replication within infected individuals.[1] Wikipedia accessed 2018 Oct 26 https://en.wikipedia.org/wiki/Virulence_factor

wild-type: SNPs & other genetic variations

Genes resources
DDBJ/ ENA/ GenBank Feature Table, 2018  http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
FAO Glossary of Biotechnology for Food and Agriculture: Revised and augmented edition, Food and Agricultural Organization, 2001  http://www.fao.org/DOCREP/004/Y2775E/Y2775E00.HTM   Searchable database, 2,000 plus terms http://www.fao.org/biotech/index_glossary.asp  Not just for food or agriculture.
IUPAC  International Union of Pure and Applied Chemistry, Glossary for Chemists of terms used in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1): 143-168, 1992. 200 + definitions.
Lewin, Benjamin Genes https://books.google.com/books/about/Lewin_s_GENES_XI.html?id=yXFfPkLq4yEC  preview

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.