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Metabolic profiling glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty MSLS
Last revised January 07, 2020

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biochemical feedback: A mechanism of communication among life processes to coordinate development, reproduction, and homeostasis. In humans, feedback loops are especially important for communication between organs that are spatially separated. Virtually all hormones from the nervous and endocrine systems are under feedback control: by peripheral hormones, cations, metabolites, osmolarity or extracellular fluid volume. MeSH, 2002

biochemical networks: Biochemical networks are the central processing units of life. They can perform a variety of computational tasks analogous to electronic circuits. Their design principles, however, are markedly different: in a biochemical network, computations are performed by molecules that chemically and physically interact with each other. Biochemical Networks group, AMOLF, Amsterdam, Netherlands 

biochemical pathways: Traditionally, the term biochemical pathways has principally referred to metabolic pathways. These are the pathways by which a cell converts compounds that enter it into cellular components (e.g., small molecules and macromolecules including proteins, nucleic acids, storage carbohydrates, and fatty acids), and by which the cell derives energy. Allan Haberman, 2002 
Related term: pathway determination    
Boehringer Mannheim Biochemical Pathways
wall chart, Roche, Expasy

BioPAX: Biological Pathways Exchange  a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. 

cellular pathways:  The 20 microns between the cell membrane and the genetic material in the cell nucleus is the playground of the molecules of signal transduction, of the intricate and multifaceted redundancy of the pathways that take signals from the membrane and convert them into the exquisitely selective control of our genes. Within these pathways, the regulation of gene transcription is carried out by a multitude of hormones and growth factors, which in turn are affected by environmental stresses and a host of other phenomena. "UCSD's Michael Karin follows the cellular pathways" ScienceWatch, Mar-Apr. 1999   See also under metabolic engineering

cell signaling (cell signalling in British English) is part of any communication process that governs basic activities of cells and coordinates all cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity, as well as normal tissue homeostasis. Errors in signaling interactions and cellular information processing are responsible for diseases such as cancerautoimmunity, and diabetes.[1][2][3] By understanding cell signaling, diseases may be treated more effectively and, theoretically, artificial tissues may be created.[4]   Traditional work in biology has focused on studying individual parts of cell signaling pathways. Systems biology research helps us to understand the underlying structure of cell signaling networks and how changes in these networks may affect the transmission and flow of information (signal transduction).  Wikipedia accessed 2018 Feb 16  

disproportionate drug metabolite: A metabolite present only in humans or present at higher plasma concentrations in humans than in the animals used in nonclinical studies. In general, these metabolites are of interest if they account for plasma levels greater than 10 percent of total drug-related exposure, measured as area under the curve at steady state. Glossary Safety Testing of Drug Metabolites Guidance for Industry - FDA

functional metabolics: Related terms: metabolic profiling; Expression; Omes & omics metabolome, metabolomics, metabonome, metabonomic

gene regulatory pathways: The association of a particular gene regulatory pathway with a disease process may lead to the identification of critical targets within these pathways. ... A considerable body of evidence already suggests that transcription factors themselves (i.e., key components of gene regulatory pathways) can be disease- gene products and/ or drug targets  , Allan B. Haberman,  2002

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

in vitro screens -- drug metabolism:  Predicting how a drug will behave in humans before clinical testing requires a battery of sophisticated in vitro tests that complement traditional expensive in vivo safety assessments. In vitro assays attempt to mimic in vivo conditions but always involve an element of uncertainty. One approach to solving this problem has been the use of in vitro screens to identify early on the characteristics of a new chemical entity (NCE), particularly with the respect to its metabolism.  Early drug metabolism models help predict a compound's elimination from the body, or metabolic stability, which affects its duration of action. More elaborate in vitro models can identify which enzyme systems play a role in elimination, which help predict drug- drug interactions, as well as the potential for the compound of interest to induce enzyme systems to eliminate other drugs. Finally, experimental design, standardized assays and assay conditions allow researchers to pool data and develop new predictive models.

Metabolic Engineering ME:
Methods and techniques used to genetically modify cells' biosynthetic product output and develop conditions for growing the cells as BIOREACTORS. MeSH Year introduced: 2012

For purposes of this solicitation, ME is defined as follows: An approach to the understanding and utilization of metabolic processes. As the name implies, ME is the targeted and purposeful alteration of metabolic pathways found in an organism in order to better understand and utilize cellular pathways for chemical transformation, energy transduction, and supramolecular assembly. ME typically involves the redirection of cellular activities by the rearrangement of the enzymatic, transport, and regulatory functions of the cell through the use of recombinant DNA and other techniques. Much of this effort has focused on microbial organisms, but important work is being done in cell cultures derived from plants, insects, and animals. Since the success of ME hinges on the ability to change host metabolism, its continued development will depend critically on a far more sophisticated knowledge of metabolism than currently exists. This knowledge includes conceptual and technical approaches necessary to understand the integration and control of genetic, catalytic, and transport processes.  . National Science Foundation, Interagency Opportunities in Metabolic Engineering,   

metabolic fingerprinting: For functional genomic or plant breeding programmes, as well as for diagnostic usage in industrial or clinical routines, it might not be necessary to determine the levels of all metabolites individually.  Instead, a rapid classification of samples according to their origin or their biological relevance might be more adequate in order to maintain a high throughput.  This process can be called metabolic fingerprinting.  Oliver Fiehn "Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks" Comparative and Functional Genomics 2: 155-168, 2001

metabolic networks: To further test the biological relevance of hypotheses gained from metabolomic data sets, these data should be compared to predictions made either by searching connections to known biochemical pathways, or by using prediction models based on mathematical calculations from biochemical kinetics or stoichiometries. Oliver Fiehn "Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks" Comparative and Functional Genomics 2: 155-168, 2001 

metabolic network modelling: Wikipedia 
metabolic pathway:

metabolic pathway:  In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes.[1] In most cases a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, set products are considered waste and removed from the cell[2]. Wikipedia accessed 2018 Feb 16

metabolic phenomics: Omes & omics

metabolic profiling:  In the context of drug research or pesticide metabolism, the term metabolic profiling is frequently used to describe the metabolic fate of an administered drug. Oliver Fiehn "Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks" Comparative and Functional Genomics 2: 155-168, 2001
Related terms: functional metabolics; Expression metabolite expression, metabolite systems biology, molecular profile; Omes & omics metabolomics, metabonomics;
Broader term profiling Narrower terms: in vitro screens for drug metabolism, metabolic flux profiling

metabolism: In case of heterotrophic organisms, the energy evolving from catabolic processes is made available for use by the organism.   IUPAC Medicinal Chemistry

The sum of chemical changes that occur within the tissues of an organism consisting of anabolism (BIOSYNTHESIS) and catabolism; the buildup and breakdown of molecules for utilization by the body. MeSH

Metabolism, The three main purposes of metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for proteinslipidsnucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter for example, the breaking down of glucose to pyruvate, by cellular respiration, and anabolism, the building up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes.  Wikipedia, accessed Mar 22 2018 distinguishes between total metabolism, specific metabolism, cell metabolism and other types of metabolism. 
Narrower term: metabolism- medicinal chemistry

metabolite: Any intermediate or product resulting from metabolism. IUPAC Biotech

A compound derived from the parent drug through Phase I and/or Phase II metabolic pathways. Glossary Safety Testing of Drug Metabolites Guidance for Industry - FDA

metabolite profiling: For investigators of selected biochemical pathways, it is also often not necessary to view the effects of perturbation on all branches of metabolism. Instead, the analytical procedure can be focused on a smaller number of pre- defined metabolites. Sample preparation and data acquisition can be focused on the chemical properties of these compounds with the chance to reduce matrix effects. This process is called metabolite profiling (or sometimes metabolic profiling). Oliver Fiehn "Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks" Comparative and Functional Genomics 2: 155-168, 2001  See also metabonomics

metabolomics: -Omes & -omics; Pharmacogenomics

metabolon: The coordinated channelling of substrates through tightly connected enzyme complexes. Oliver Fiehn "Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks" Comparative and Functional Genomics 2: 155-168, 2001

Enzymes of metabolic pathways are nowadays thought to be clustered and operate as 'metabolons'.  S. Beeckmans et. al., "Immobilized enzymes as tools for the demonstration of metabolon formation. A short overview" Journal of  Molecular Recognition 6 (4): 195- 204 Dec. 1993] 

metabonomics: -Omes & -omics
molecular networks: 
Molecular networks are composed of pathways
molecular profiling: Expression gene and protein

network dynamics:  Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically 1, 2, 3, 4, 5, 6, 7, 8 . Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information9, 10, 11 and gene-expression data12, 13, 14, 15, 16 for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. Genomic analysis of regulatory network dynamics reveals large topological changes Nicholas M. Luscombe1,5, M. Madan Babu4,5, Haiyuan Yu1, Michael Snyder2, Sarah A. Teichmann4 & Mark Gerstein Nature 431, 308-312 (16 September 2004) | doi:10.1038/nature02782; Received 15 January 2004; Accepted 24 June 2004 

networks: Although there is no consensus definition of "program" or "networks", these terms are most often encountered and understood in the context of the regulatory interactions that link groups of genes and gene products in developmental processes.  Many of these linkages have recently been elucidated in considerable detail for key events in a variety of species. Sean Carroll "Communications breakdown?" (book review) Science 291: 1264-1265, Feb. 16, 2001

The experimental task of mapping genetic regulatory networks using genetic footprinting and [yeast] two- hybrid techniques is well underway, and the kinetics of these networks is being generated at an astounding rate. Technology derivatives of genome data such as gene expression micro- arrays and in vivo fluorescent tagging of proteins through genetic fusion with the GFP [Green fluorescent] protein can be used as a probe for network interaction and dynamics. If the promise of the genome projects and the structural genomics effort is to be fully realized, then predictive simulation methods must be developed to make sense of this emerging experimental data. There are three bottlenecks in the numerical analysis of biochemical reaction networks. The first is the multiple time scales involved. Since the time between biochemical reactions decreases exponentially with the total probability of a reaction per unit time, the number of computational steps to simulate a unit of biological time increases roughly exponentially as reactions are added to the system or rate constants are increased. The second bottleneck derives from the necessity to collect sufficient statistics from many runs of the Monte- Carlo simulation to predict the phenomenon of interest. The third bottleneck is a practical one of model building and testing: hypothesis exploration, sensitivity analyses, and back calculations, will also be computationally intensive. Lawrence Berkeley Lab "Advanced Computational Structural Genomics" Glossary  Narrower terms: biochemical networks, molecular networks  

pathway analysis: Getting Started in Biological Pathway Construction and Analysis PLOS 2008

pathways:  A general term meant to include all forms of  molecular transactions and processes that are part of  biochemical systems. Some of these pathways may involve linear processing, but many involve complex branches, convergences, and even cycles. .... There are several different classes of biochemical pathways: metabolic pathways, signal transduction cascades, genetic networks, and drug metabolism pathways. In addition, protein interaction data  links protein data objects, and can therefore also be conceptualized as graphs. Although the relationship of  protein- interaction maps with biochemical pathways is undeniable, it is not obvious. ... the design of  adequate models for bio- process representation, manipulation and simulation is still a very open field of research. In conclusion, we will need to examine and discuss the relationships between all pathway information, protein interaction data, and biological process information in order to successfully produce informatics specifications for any of these kinds of  data.  Biopathways Consortium "Definition"

The routes or processes by which genes and their products function in cells, tissues, and organisms. Pathways involving a particular gene or its product may be determined by two major types of methods. One involves identifying other proteins that specifically interact with the product of the gene of interest. The other involves carrying out specific genetic studies with model organisms.

The term biochemical pathways has principally referred to metabolic pathways, which are the pathways by which a cell converts compounds that enter it into cellular components (e.g., small molecules and macromolecules including proteins, nucleic acids, storage carbohydrates, and fatty acids) and by which the cell derives energy. Signaling pathways are biochemical pathways that regulate cellular characteristics and processes such as physiology, proliferation, changes in shape and motility, differentiation, adhesion, and intercellular interactions. High- content screening approaches can be used to help elucidate pathways. 
Narrower terms: biochemical pathways, gene regulatory pathways, metabolic pathways, signaling pathways 

pharmacologically active metabolite: A metabolite that has pharmacological activity at the target receptor. The activity may be greater than, equal to, or less than that of the parent drug. Glossary Safety Testing of Drug Metabolites Guidance for Industry - FDA

phenotypic profiling:  Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life. To start to fill this gap we developed a high-throughput phenotypic screening platform combining potent gene silencing by RNA interference, time-lapse microscopy and computational image processing. We carried out a genome-wide phenotypic profiling of each of the ~21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes. Nature 2010  Related terms: Genomics  phenotype, phenotyping

reaction phenotyping: Knowing how a drug candidate is eliminated by the human body is important in understanding the potential for drug-drug interactions.  Compounds with a single route of elimination have a high victim potential, which is why the FDA requires reaction phenotyping studies. Reaction phenotyping generally involves three types of analysis: correlation analysis, antibody and chemical inhibition, and metabolism by recombinant human CYP enzymes. Each has its advantages and disadvantages, and a combination of approaches is highly recommended.

signal transduction: The intercellular or intracellular transfer of information (biological activation/ inhibition) through a signal pathway. In each signal transduction system, an activation/ inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/ enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA- AMINOBUTYRIC ACID- postsynaptic receptor- calcium ion channel system, the receptor- mediated T-cell activation pathway, and the receptor- mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor- mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway. MeSH, 1989

Any process that helps to produce biological responses to events in the environment or internal milieu (e.g., transduction of light into nerve impulses by the retina or transduction of hormone binding into cellular events by hormone receptors). MeSH, earlier definition

Aberrant signal transduction is the cause of many of the most personally and financially devastating diseases challenged by modern medicine, including cancer, inflammatory diseases, cardiovascular disease and neuropsychiatric disease. In the search for treatments, cures, and preventions for these diseases, in depth understanding of the biology of signal transduction is a prime method for the discovery of appropriate disease targets and in the design of drugs to halt or prevent them. 

The intercellular or intracellular transfer of activation or inhibition signals through a so- called signaling pathway. These signals can be initiated, for example, when a biologically active molecule binds to a receptor. Signal transduction is involved in many cellular processes, including cell proliferation and differentiation. Related terms: pathway determination, physiological genomics
Signaling, Science Magazine  Cellular Signaling

signaling pathways: Biochemical pathways that regulate cellular characteristics and processes such as physiology, proliferation, changes in shape and motility, differentiation, adhesion, and intercellular interactions. Examples include pathways by which hormones, growth factors, and cytokines regulate cellular processes. For instance, factors such as epidermal growth factor and insulin initiate signaling by binding to their specific receptors on the cell surface. Broader terms: pathways, biochemical pathways

signalome- plant: Omes & omics

Metabolic engineering resources
FDA, Guidance for Industry, Safety testing drug metabolites  [PDF]Safety Testing of Drug Metabolites Guidance for Industry - FDA  2016
UCSD Cellular Signaling Molecule Pages:  a database providing essential information on the thousands of proteins involved in cell signaling. 
 Was Alliance for Cellular Signaling AfCS

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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