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Functional genomics glossary & taxonomy
Evolving Terminology for Emerging Technologies
Suggestions? Comments? Questions? Mary Chitty  mchitty@healthtech.com
Last revised March 05, 2014 

 



Functional assessment of every gene in the mammalian cell is an on-going challenge. Understanding, not only the function of each gene in isolation but the complexity of functional networks and control systems is of particular importance for discovery of novel and valid drug targets. Answering complex biological questions in this context necessitates high- throughput gene functional characterization using an array of genomic, proteomic and in silico- based tools and technologies.  

Guide to terms in these glossaries    Site Map
Related glossaries include Sub-categories Metabolic engineering, Phylogenomics 
Applications Drug discovery & development, Proteomics  
Informatics Bioinformatics, Drug discovery & development informatics   Genomic informaticProtein informatics
Technologies Genomic technologiePCR, Genetic Manipulation & disruptionMicroarrays
Biology Cell biology, Chemistry & biology  Expression  Gene Definitions, SNPs & genetic variations Nomenclature
, particularly of genes in humans and in Model & other Organisms is an increasing challenge as comparing completed genomes becomes increasingly possible.  -Omes & omics

age: The time period elapsed since an identifiable point in the life cycle of an organism. (If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting). MIAME Glossary, MGED http://www.mged.org/Workgroups/MIAME/miame_glossary.html 

A good illustration of the challenges inherent in cross species comparisons. 

animal models: Model & other organisms

biochemical function: My research is concerned with the three-dimensional structures of proteins and their biochemical functions. Gregory Petsko, Brandeis University, 2007 http://www.bio.brandeis.edu/faculty01/petsko.html

biochemical genomics: Chemistry & biology
biochemical networks, biochemical systems theory: Metabolic profiling

biological function: One key problem in this discussion involves the definition of "biological function".  Geneticists, cellular biologists, structural biologists, bioinformaticians, and biophysical chemists use this term to mean different things.  Some speakers used the word "function" to refer to the general biochemical activity of the gene produce (e.g. kinase activity), others referred to the cellular process in which the gene product is involved, while to others "function" meant an understanding of the details of the atomic mechanism of catalysis or recognition.  Still others referred to function in the genetic sense of a generalized phenotype.  This lack of consensus in defining what aspect of function one might learn about from an examination of protein structure prevented the group from reaching a consensus on the role that large scale structural genomics will have in the related area of functional genomics.  G. T. Montelione and S. Anderson, Report to the National Science Foundation:  Workshop on Structural Genomics - Understanding Proteins Universal to Life" Advanced Photon Light Source, Argonne Natl. Laboratories, Jan. 23 - 25, 1998  Related terms: biological process, Gene Ontology (GO)

biological process: A biological objective to which the gene or gene product contributes. Gene Ontology Consortium "Gene Ontology: tool for the unification of biology Nature Genetics 25: 25-29 May 2000

A biological process is accomplished via one or more ordered assemblies of molecular functions. Usually there is some temporal aspect to it, although a process event may be essentially instantaneous. It often involves transformation, in the sense that something goes into a process and something different comes out of it. ...  A biological process is not equivalent to a pathway. We are specifically not capturing or trying to represent any of the dynamics or dependencies that would be required to describe a pathway. [The semantic distinction between a biological process and a molecular function can, at times, be hard to draw, and GO takes a pragmatic, rather than dogmatic, approach: As a general rule a process must have >1 distinct steps.] Gene Ontology Consortium General Documentation, 2001  http://www.geneontology.org/doc/GO.doc.html

cellular signaling networks: Metabolic profiling
chemical genetics, chemical genomics,  chemogenomics: Drug discovery & development
chemical mutagenesis: Chemistry & biology

comparative genomics: "We believe that the problem of the genome- phenotype connection, which, in a sense, is the central theme of biology, can be solved only through an experimental program strategically planned on the basis of comparative- genomic results. Much of the biological research of the next few decades is likely to develop along these lines. E. Koonin et al "The Impact of Comparative Genomics on our Understanding of Evolution" Cell 101:573-576 June 9, 2000 

Insights can be biochemical, genetic, metabolic or physiological. The practice of uncovering the functions of human genes and other DNA regions by studying their parallels in nonhumans. 
Related terms: biological process, molecular function,  Gene Ontology Consortium; Cell biology cellular components; Maps genomic & genetic comparative genome mapping; Model & other organisms; Phylogenomics comparative proteomics, evolutionary genomics,  Narrower terms: comparative plant genomics, vertebrate comparative genomics
Background on Comparative Genomic Analysis, NHGRI, 2007 http://www.genome.gov/10005835  
Wikipedia http://en.wikipedia.org/wiki/Comparative_genomics   

comparative metabolomics: Omes & omics

comparative plant genomics: With the publication of two draft  sequences of the complete rice genome (Science 296 ( ): 76, 92, 5 April 2002), in addition to Arabidopsis (Model & other organisms) the possibility of comparative plant genomics is upon us. 

comparative proteomics: Proteomics categories

deductive genomics:  deductive genomics, or large-scale forward genetics, bridges the gap between sequence and function by providing a function-driven in vivo screen of a highly orthologous mammalian model genome for medically relevant physiological functions and drug targets. This approach allows drug discovery to move beyond the focus on sequence-driven identification of new members of classical drug-able protein families towards the biology-driven identification of innovative targets and biological pathways. Deductive genomics: a functional approach to identify innovative drug targets in the post-genome era. Stumm G, Russ A, Nehls M., Am J Pharmacogenomics. 2(4): 263- 271, 2002 

forward genetics, forward genomics: Genetic manipulation & disruption

function: The vagueness of the term 'function' when applied to genes or proteins emerged as a particular problem, as this term is colloquially used to describe biochemical activities, biological goals and cellular structure. Gene Ontology Consortium "Gene Ontology: tool for the unification of biology Nature Genetics 25: 25-29 May 2000 Narrower terms:  biological function, gene function; Proteomics protein function. Related terms: Gene Ontology TM Omes & omics functome, transcriptome

functional bioinformatics: Bioinformatics

functional genome annotation: Functional annotation of the genome is primarily hampered by the lack of a unified transcript index. Current transcript information still largely consists of anonymous and highly redundant ESTs. The situation is further complicated by extensive splicing variation and elusive gene expression. To address these problems, the Ensembl consortium relies initially on computational prediction, followed by confirmation with EST/ protein alignments... We have found evidence for a large number of transcriptional units (65,000- 75,000) and performed initial annotation and classification. The effective study of transcription and protein function requires the compilation of all available evidence of transcription and protein homology. FA Wright et. al. A draft annotation and overview of the human genome, Genome Biology 2(7): 2001 http://genomebiology.com/2001/2/7/research/0025 

functional genomics:  The development and application of global (genome- wide or system- wide) experimental approaches to assess gene function by making use of the information and reagents provided by structural genomics [in the original more limited sense of construction of high- resolution genetic, physical and transcript maps of an organism]. It is characterized by high throughput or large- scale experimental methodologies combined with statistical and computational analysis of the results. The fundamental strategy is to expand the scope of biological investigation from studying single genes or proteins to studying all genes or proteins at once in a systematic fashion. Phil Hieter and Mark Boguski "Functional Genomics: It's All How You Read It" Science 278: 601- 602, October 24, 1997

Functional genomics aims to discover the biological function of particular genes and to uncover how sets of genes and their products work together in health and disease. In its broadest definition, functional genomics encompasses many traditional molecular genetic and other biological approaches. Google = 199,000 Feb. 4, 2004,  = about 2,080,000 Nov 7, 2005, about 1,640,000 July 24, 2007 Related terms: biological process,  genome function,  molecular function, Metabolic profiling networks, pathways,  physiological genomics;  Phylogenomics comparative genomics, homology, phylogenomics,

functional genomics data: A useful way to tackle noise and complexity of functional genomics information is to average the data from many different genes into broad 'omic categories (Jansen & Gerstein 2000. For instance, instead of looking at how the level of expression of an individual gene changes over a time- course, we can average all the genes in a functional category (e.g. glycolysis) together. This gives a more robust answer about the degree to which a functional system changes over the time- course. Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of  Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdfRelated terms: Omes & omics

functional genomics technologies: Conditional or tissue- specific gene expression in animal models is a major area of interest. Other increasingly popular methods of downregulating gene expression, in order to study function, include antisense, ribozyme, and zinc finger protein (ZFP) approaches. In addition, a limited number of companies have developed chemical- genetics methods. Include gene disruption, gene manipulation, gene shuffling, gene targeting, gene trapping, knockdowns, knockins, knockouts, mutagenesis, phage display, positional cloning, Post Translational Gene Silencing PTGS; Genetic Manipulation & Disruption RNA interference RNAi.  Related terms chemical genetics, chemical genomics

functional glycomics: Glycosciences Google = about  742  Feb. 4, 2004, about 389,000 July 24, 2007

functional homology: Sequence homology does not necessarily indicate functional homology. A number of labs are working with yeast and other non-human organisms to try to determine what the relationship between sequence and function might be, if there is any.  Google = about 4,260  Feb. 4, 2004, about 109,000 July 24, 2007

functional imaging: Molecular Imaging
functional informatics:
Bioinformatics  Google = about 36  Feb. 4, 2004, about 1,010 July 24, 2007
functional maps: Maps: genomic & genetic

functional metabolics: Metabolic profiling  Google = about 9  Feb. 4, 2004, about 7 July 24, 2007  Related terms: metabolic profiling; Expression gene and proteinOmes & omics metabolome, metabolomics, metabonome, metabonomics

functional profiling:  Linking genes and proteins to disease. 

functional proteomics: Proteomics Google = about 8,480  Feb. 4, 2004, about 167,000 July 24, 2007
functome, functomics : -Omes & -omics

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gene function: A chart from NCBI’s Cluster of Orthologous Groups (COGs) of proteins database lists as functional annotation descriptions: in Functional Screens for Drug Safety Testing May 21-22, 2014 • Boston, MA Program | Register | Download Brochureormation storage and processing (translation, ribosomal structure and biogenesis, transcription, DNA replication, recombination and repair) Cellular processes (cell division and chromosome partitioning, post- translational modification, protein turnover, chaperones, cell envelope biogenesis, outer membrane, cell motility and secretion, inorganic ion transport and metabolism, signal transduction mechanisms) metabolism (energy production and conversion, carbohydrate transport and metabolism, amino acid transport and metabolism, nucleotide transport and metabolism, coenzyme metabolism, lipid metabolism) and poorly characterized.  NCBI, COG website   http://www.ncbi.nlm.nih.gov/COG/  

The lack of a common language for gene functions is … proving to be a serious problem. E Pennisi "Seeking common language in a Tower of Babel" Science 286 (5439): 449 Oct. 15 1999

The nature of gene function was substantially specified by George W. Beadle and Edward Tatum [19] and Adrian M. Srb and Norman H. Horowitz [20] when they showed, using Neurospora crassa (Ascomycetes) as their experimental organism, that genes control the synthesis of enzymes, and in particular that each individual gene is responsible for the synthesis of one single enzyme. This one gene - one enzyme hypothesis was the culmination of the classical view of the gene. ... The classical concept of the gene started to break down as soon as it had been completely formulated.  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  Related terms: biological function, function, genome function, molecular function; protein function Proteomics

Gene OntologyTM (GO):  The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. … GO terms are organized in structures called directed acyclic graphs (DAGs), which differ from hierarchies in that a child, or more specialized, term can have many parent, or less specialized, terms. http://www.geneontology.org/

A collaborative effort to address the need for consistent descriptions of gene products in different databases. The project began as a collaboration between three model organism databases: FlyBase (Drosophila), the Saccharomyces Genome Database (SGD) and the Mouse Genome Database (MGD) in 1998. Since then, the GO Consortium has grown to include many databases, including several of the world's major repositories for plant, animal and microbial genomes. An introduction to the Gene Ontology http://www.geneontology.org/GO.doc.shtml
Gene Ontology: tool for the unification of biology
. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29 http://www.geneontology.org/GO_nature_genetics_2000.pdf
Gene Ontology Faq-O-Matic
Gene Ontology Consortium
GO Term definitions
, Gene Ontology Consortium TM http://www.geneontology.org/ontology/GO.defs

Gene Ontology Annotation Project: Gene Ontology controlled vocabulary will be applied to a non- redundant set of proteins described in the Swiss- Prot, TrEMBL and Ensembl databases that collectively provide complete proteomes for Homo sapiens and other organisms.  European Bioinformatics Institute, UK http://www.ebi.ac.uk/GOA/  Related terms: biological process, molecular function; cellular component Cell biology; Computers & computing controlled vocabulary; Broader terms: Information management & interpretation: ontology, taxonomy

GO slims: Cut-down versions of the Gene Ontology [GO] ontologies containing a subset of the terms in the whole GO. They give a broad overview of the ontology content without the detail of the specific fine-grained terms… Are particularly useful for giving a summary of the results of GO annotation of a genome, microarray, or cDNA collection when broad classification of gene product function is required without the detail of the specific fine grained terms. http://www.geneontology.org/GO.slims.shtml   

genome function: Efficient interpretation of the functions of human genes and other DNA sequences requires that resources and strategies be developed to enable large- scale investigations across whole genomes. A technically challenging first priority is to generate complete sets of full- length cDNA clones and sequences for human and model- organism genes. Other functional genomics goals include studies into gene expression and control, creation of mutations that cause loss or alteration of function in nonhuman organisms, and development of experimental and computational methods for protein analyses. [Oak Ridge National Lab, Human Genome Management Information Services, US] http://www.ornl.gov/hgmis/resource/function.html

genome integrity: Maintaining the integrity of genetic information is fundamental for the life of a cell and the survival of a species. Cells can encounter DNA damage as a consequence of normal cellular metabolism or as a result of exposure to chemical or physical agents. Humpath.com http://www.humpath.com/genome-integrity  Related term: DNA repair

genotype to phenotype: Pharmacogenomics

homolog, homologue, homologous: Used by geneticists in two different senses: (1) one member of a chromosome pair in diploid organisms, and (2) a gene from one species - -for example, the mouse - -that has a common origin and functions the same as a gene from another species -- for example, humans, Drosophila, or yeast. [NHLBI]  Related terms: Phylogenomics lateral genomics, ortholog, orthologous, paralog, paralogous, synologous, xenolog, xenologous; Model organisms; Structural genomics homology modeling

This is different from homologue as defined in the Pharmaceutical biology

homology:  The relationship among sequences due to descent from a common ancestral sequence. An important organizing principle for genomic studies because structural and functional similarities tend to change together along the structure of homology relationships. When applied to nucleotide or protein sequences, means relationship due to descent from a common ancestral sequence. Two DNA molecules (or regions thereof) are homologous if they both "descended" through a series of replication from a single DNA strand … The terms "homology" and "similarity" are often, incorrectly, used interchangeably.

Homology has been used by various people with different meanings, even though similarity was a common denominator among these meanings. The two most important of these meanings related homology to similar structures and/ or to similar functions. By structures I mean both molecular sequences and morphology. Life would have been simple had phylogenetic homology necessarily implied structural homology or either of them necessarily implied functional homology. However, they map onto each other imperfectly and my definition of homology includes all forms of characters. We could reduce confusion by always indicating the kind of homology we are referring to when using the tern. Walter Fitch "Homology a personal view on some of the problem" Trends in Genetics 16 (5): 227-231 May 2000

Note that homology can be genic, structural, functional or behavioral.  Related terms: Drug targets target homology  Phylogenomics evolutionary homology, orthology, paralogy, similarity; Proteomics;  regulatory homology;  Sequencing sequence homology;  Structural genomics homology modeling, structural homology
Wikipedia http://en.wikipedia.org/wiki/Homology_%28biology%29 

horizontal gene transfer: See xenology; Related term: microbiome Omes & omics

Human Ontology Resources: SOFG Standards and Ontologies for Functional Genomics, http://www.sofg.org/   

hypomorph: Loss of function.  Related term: null mutation

interactions- molecular: Related terms: Biomolecules  biomolecular interactions; Omes & omics interactome; Proteomics protein- DNA interactions, protein- protein interactions, protein- RNA interactions; RNAi: RNA- RNA interactions

knockout mice: Model & other organisms  Knockout-mouse technology is considered an essential and standard technique in functional genomics and target validation. 

metabolic engineering, metabolite: Metabolic Profiling
metabolite expression; metabolite systems biology: Expression

molecular function: The biochemical activity including specific binding to ligands or structures) of a gene product. This definition also applied to the capability that a gene product (or gene product complex) carries as a potential. It describes only what is done without specifying where or when the event actually occurs.  Gene Ontology Consortium "Gene Ontology: tool for the unification of biology Nature Genetics 25: 25-29 May 2000

There is a potential for semantic confusion between a gene product and its molecular function, because very often these are described in exactly the same words. For example, "alcohol dehydrogenase" can describe what you can put in an Eppendorf tube (gene product) or it can describe the function of this stuff. There is, however, a formal difference -- a "product" has a (potentially) many- to- many relationship with a "molecular function."  Gene Ontology Consortium General Documentation, 2001 http://www.geneontology.org/GO.doc.html  
Related terms: biological function, biological process, function, gene function, Gene OntologyTM; Cell biology cellular component Gene definitions gene product 

OBO Foundry Ontologies http://obofoundry.org/ 

ortholog (orthologue): That relationship where sequence divergence follows speciation, that is, where the common ancestor of the two genes lines in the cenancestor of the taxa from which the two sequences were obtained … There is a tendency to wish that there could be only one ortholog in an organism. This is frequently not the case. Walter Fitch “Homology a personal view on some of the problem” Trends in Genetics 16 (5): 227-231 May 2000  Narrower term: Phylogenomics super- orthologs

orthologous: Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function. NCBI Bioinformatics

paralog (paralogue): That condition where sequence divergence follows gene duplication. Such genes might descend and diverge while existing side by side in the same lineage. Walter Fitch “Homology a personal view on some of the problem” Trends in Genetics 16 (5): 227-231 May 2000  Narrower term: Phylogenomics ultra- paralogs

paralogous: Homologous sequences within a single species that arose by gene duplication. NCBI Bioinformatics Related term:  SNPs & Genetic variations duplication  

Pathogen Functional Genomics Resource Center PFGRC: A centralized facility providing the research community with resources necessary to conduct functional genomics research on human pathogens and invertebrate vectors of infectious diseases. The PFGRC provides scientists with genomic resources and reagents such as microarrays, protein expression clones, genotyping and bioinformatics services. The PFGRC supports the training of scientists in the latest techniques in functional genomics and emerging genomic technologies. PFGRC, NIAID, NIH, 2005 http://www.niaid.nih.gov/dmid/genomes/pfgrc/default.htm   

pathways: Metabolic profiling 
phenotype to genotype: Pharmacogenomics
phenotypic screening: Assays & screening
phylogenomics: Phylogenomics    phylome: Phylogenomics

positional candidates: The positional candidate approach relies on a three- step process that saves time and effort: (1) localizing a disease gene to a chromosomal subregion, generally by using traditional linkage analysis; (2) searching databases for an attractive candidate gene within that subregion; and (3) testing the candidate gene for disease- causing mutations. ... Since 1990, scientists have used this approach to find genes implicated in such conditions as Marfan syndrome, inherited nonpolyposis colon cancer, retinitis pigmentosa, long QT syndrome, Jackson-Weiss syndrome, Crouzon syndrome, Alzheimer's disease, and several others. "Positional Cloning Approach Expedites Gene Hunts" Human Genome News, Mar.-Apr. 1995; 6(6): 1  http://www.ornl.gov/hgmis/publicat/hgn/v6n6/1kuska.html  Related terms: functional cloning, positional cloning.

positional cloning: Involves using a genetic map to determine the location of a disease gene. Researchers use such maps to analyze genetic markers in extended families that include individuals affected by a heritable disease, and to pinpoint regions of the genome that are associated with the disease. They then use that information to isolate the DNA from the region, and to identify and sequence the disease gene and identify mutations. 

A process which, through gene mapping techniques, is able to locate a gene responsible for a disease when little or no information is known about the biochemical basis of the disease. [NHGRI] cloning requires a genetic map with a large number of markers (especially in the region of interest), and the use of physical mapping and DNA sequencing technologies to isolate and sequence the targeted gene. A disease gene is usually identified from among candidate genes in the region of interest by showing that affected individuals carry mutations within that gene. 

Positional cloning was incorrectly called "reverse genetics" early on. Reverse genetics in its purest definition refers to the analysis of gene function by assaying proteins expressed from gene variants. "[Positional cloning] is not "reverse" at all, but rather genetics in its purest form, unadulterated by any influences of biochemistry, cell biology or physiology." ( Francis S Collins "Positional cloning: Let’s not call it reverse anymore" Nature Genetics. 1: 3-6, 1992) The term "positional cloning" was coined by Francis Collins.  Related terms: functional cloning, positional candidate approach;  Genetic variations and SNPs candidate gene approach; Maps- genomic & genetic

protein function: Protein informatics
regulatory networks: See under networks.
Related terms: Omes & omics regulatory, regulome, regulomics
robogenomics: -Omes & -omics
sequence homology: Sequencing
signal transduction: Metabolic engineering 

similarity: how related one nucleotide or protein sequence is to another. The extent of similarity between two sequences is based on the percent of sequence identity and/or conservation. DOE, Glossary of Bioinformatics Terms, 2002 http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/genejargon.shtml Related term: homology

siRNA Small interfering RNA: RNA May be useful in assessing gene function Related terms: Genetic manipulation & disruption RNAi, Post-Transcriptional Gene Silencing PTGS

standards and ontologies - functional genomics: Standards and ontologies for functional genomics,  http://www.sofg.org/

transcriptome, transcriptomics: Omes & omics
transgenic: Model & other organisms
translatome:-Omes & omics
transposon: Gene definitions

xenology (xenologous): That conditional (horizontal transfer) where the history of the gene involves an interspecies transfer of genetic material. It does not include transfer between organelles and the nucleus.  It is the only form of homology in which the history has an episode where the descent is not from parent to offspring but, rather, from one organism to another … Gogarten has proposed a special term, synology, for those xenologs that arise, not by the transfer of a gene between two species, but by a hybridization of two species.  Walter Fitch “Homology a personal view on some of the problems” Trends in Genetics 16 (5): 227-231 May 2000

Bibliography
Comparative & Functional Genomics Fact Sheet,  Human Genome Project Information, Oak Ridge National Lab, 2007 http://www.ornl.gov/sci/techresources/Human_Genome/faq/compgen.shtml 
Science Magazine "Functional Genomics" website http://www.sciencemag.org/feature/plus/sfg/  Archived since Feb 2005

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