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You are here Biopharmaceutical/ Genomic glossary Homepage/Search > Biology> Gene definitions > Gene categories Gene categories
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Map 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 In 1989, we set out to map and sequence all the human antibody genes. Over a 10 year period, 16 scientists at the MRC Laboratory of Molecular Biology and the MRC Centre for Protein Engineering were involved in the work which resulted in the first publication of the complete maps of the human heavy chain and lambda light chain genes and the compilation of the V BASE database. Our results demonstrated that there are far fewer functional genes than originally anticipated ... by analysing the use of individual antibody genes and the extent of somatic mutation we went on to show that the pattern and extent of diversity introduced by somatic hypermutation is complementary to that created by combinatorial rearrangement. Finally, many of the germline genes cloned during the mapping and sequencing work were used as building blocks in the creation of a number of semi- synthetic phage- antibody libraries and, more recently, we have used the analysis of main- chain conformations and side- chain diversity in the human immune system to generate a range of new 'superantibody' libraries. Laboratory of Molecular Biology, Medical Research Council, UK "Human Antibody Genes" c2000 http://www2.mrc-lmb.cam.ac.uk/groups/arrays/genes.html 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. 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. DME Drug Metabolizing Enzyme genes Pharmacogenomics glossary 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 epigenetic genes: Genetic Manipulation & Disruption glossary epigenetic, epigenetics 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 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" Univ. of Turku, Finland, 2000 http://www.bentham.org/cg/sample/cg1-1/Portin.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:
Specialized genes with specific functions. Compare with housekeeping
genes. marker genes: Biomarkers mitochondrial genes: Human mitochondrial DNA (one of the smallest known) is only 16,569 base pairs in length … We now know the complete DNA sequence … It codes for ribosomal RNAs and transfer RNAs used in the mitochondrion, and contains only 13 recognizable genes that code for polypeptides … the mitochondrial genome, unlike the much larger nuclear genome, is directly transmitted through the maternal line, making it an ideal piece of DNA with which to trace family lineages. Kenneth Miller, Brown Univ. “The fire within: the unfolding story of human mitochondrial DNA, 1997 http://biocrs.biomed.brown.edu/Books/Chapters/Ch%207/Mitos/Mito-Genes.html Useful for evolutionary research, population genetics, phylogenetics and
conservation biology. Related terms: Sequences, DNA & beyond mtDNA; Cell biology glossary 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 http://www.bentham.org/cg/sample/cg1-1/Portin.pdf non-nuclear genes: See extranuclear genes non-protein coding gene: See RNA glossary 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? oncogene: Cancer glossary 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. organelle genes: After serendipitously detecting mitochondrial DNA (mtDNA) synthesis in the rotifers and the transfer of mtDNA from nurse cells to maturing oocytes, I turned to yeast (Saccharomyces cerevisiae) as a better experimental system for studying organelle genetics. I demonstrated that mitochondrial genes show intracellular selection and random drift of gene frequencies within single cells. Random drift was also demonstrated in chloroplast genes in Chlamydomonas. From these studies I developed the general concept that organelle genes differ from nuclear genes in replication and partitioning at cell division are relaxed, with genomes selected randomly for replication and partitioned randomly to daughter cells.... Banks and Birky (1985) did the first large-scale measurement of organelle gene diversity in a natural plant population. Later my students and I began to study molecular evolution in Polytoma C. William Birky "Research History" Univ. of Arizona http://eebweb.arizona.edu/faculty/birky/ResearchHistory.html Related term: Cell biology glossary organelles ; Narrower term: mitochondrial genes Compare nuclear genes orphan genes: Putative open reading frames (ORFs) that have no resemblance to known protein coding sequences. Since there are no identified homologs to these orphan genes in other species, it is unknown whether these hypothetical sequences are actually expressed. Promega Product Focus RT-PCR eNotes http://www.promega.com/enotes/incite/in0013_tabs.htm Putative ORFs without any resemblance to previously determined protein- coding sequences…While theoretical evolutionary arguments support the reality of genes when homologues are found in a variety of distant species, this is not the case for orphan genes … Our results suggest that a vast majority of E. coli ORFs presently annotated as “hypothetical” correspond to bona fide genes. J Alimi et al “RT-PCR validation of 25 “orphan” genes” Genome Research 2000 Jul; 10 (7): 959- 966 Predicted genes which have no significant similarities to genes of known function, or genes with unknown function. European Commission press release “Towards the first complete analysis of a plant genome”, 29 Jan.1998 http://europa.eu.int/comm/research/press/1998/pr2901en.html 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" Univ. of Turku, Finland, 2000 http://www.bentham.org/cg1-1/portin/P.Protin.htm pangenes: Research on adult stem cells found in the skin hints at a new class of genes – dubbed pangenes – that can both govern a stem cell's fate and put a hold on future differentiation until the time is right. Wellcome Trust, Stem cell fate, How the Body Works 2005 http://genome.wellcome.ac.uk/doc_WTD020790.html 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 glossary parasitome plasmid genes: In microbial genomes, most often there is a single circular or linear chromosome and there are may be many extra- chromosomal, self- replicating, linear or circular DNA known as plasmids. In eukaryotic genomes, the chromosomes are within the nucleus and the extra chromosomal DNA is in the mitochondria as well as plastids in plants. In our genome projects of organisms that contain plasmids, i.e., Borrelia borgdorferi, Methanococcus jannaschii, and Deinococcus radiodurans, the sequencing, finishing and annotation are done for the entire genome, chromosome and plasmids. "What place do microbial plasmids have in defining the genome of microbes? It seems as though the term "microbial genome" refers solely to the microbial chromosome. How are plasmid genes, that often define key traits, included, or are they not included?" Question from FAQ, TIGR, US http://www.tigr.org/about/faq.shtml 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 In silico & molecular Modeling glossary "gene prediction" processed genes: See under pseudogenes. promoter genes: See promoter, promoter region Sequencing DNA & beyond glossary 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 glossary 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. RNA genes: See In silico & Molecular Modeling glossary RNA computational molecular archaeology See also RNA glossary 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: Some genes are 'silent' - they can be deleted with no apparent effect. To obtain clues about the role of these silent genes the researchers can measure the concentrations of various metabolites within the cell in the genes' presence and absence. This is analysis of the metabolome. Steve Oliver, Exploring and Exploiting the Small Scale, Yeast Cells, BBSRC Biotechnology and Biological Sciences Research Council http://www.bbsrc.ac.uk/life/small-look/oliver.html 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" Univ. of Turku, Finland, 2000 http://www.bentham.org/cg1-1/portin/P.Protin.htm 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 glossary tumor suppressor gene susceptibility genes: Molecular Medicine glossary syntenic genes: See under Gene definitions: synteny transposons: Sequences, DNA & beyond tumor suppressor gene: Cancer glossary virulence genes: Most pathogenic microorganisms encounter a great variety of environments during their pathogenic life cycle. Survival in these different environments often requires the expression of different virulence factors. Therefore, it is not surprising that microorganisms have evolved very sophisticated means of sensing their environment and regulating the expression of virulence genes. There are also a lot of commonalities in the general design of the regulatory mechanisms used by different microorganisms to regulate the expression of virulence genes. Jorge Benach "General objectives for Pathogenic Bacteriology" SUNY- Stonybrook, NY, US 2001 http://www.umc.sunysb.edu/microbiology/bacintro.html wild-type: SNPs & other genetic variations glossary Bibliography How to look for other unfamiliar terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
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