View a Printer-Friendly Version of this Web Page!

Related glossaries include Functional Genomics, Genomics, Pharmacogenomics,  Proteomics, Structural Genomics

biological atlas: Maps, genomic & genetic glossary

biome: A major regional community of plants and animals with similar life forms and environmental conditions. .. Due to similar pressures of natural selection, species in different parts of a biome may converge in their appearance and behaviors, even when they do not share the same ancestors.  [ML Corn “Report for Congress,  Ecosystems, Biomes, and Watersheds: Definitions and Use, Congressional Research Service, July 1993] http://www.cnie.org/nle/biodv-6.html#BIOMES: DEFINITION AND EXAMPLES

This is the oldest of the "-ome" suffix series. Coined in 1916, It refers to an ecological community of organisms and environments. The ability of genes or alleles to affect the representation of the host organism in a biome is an operational definition for the "function" of the gene (in that context). [George Church Lab, Harvard University, US]  http://arep.med.harvard.edu/ome.html

May also be used in the more specialized sense of  the environments for a yeast culture or other model organism.

BIOME, University of Nottingham, UK http://biome.ac.uk/   A consortium of content providers collaborating on a catalogue of Internet resources, database hosting.

biomics: Perhaps someday all things biological will be classified and jammed into an enormous database -- leading to some hypothetical metadiscipline called biomics.  [Gary Styx “Parsing Cells” Scientific American 281 (1): 35-36 July 1999] http://www.sciam.com/1999/0799issue/0799techbus1.html

BioNome: Biology Network of Modeling Efforts.  A web- based repository of bio- computational models and observational data. The initial focus areas are in signal transduction and cardiovascular science. [BioNome Resource, San Diego Supercomputer Center, CA, US]    http://bionome.sdsc.edu

cancer immunome: The entire panel of expressed genes and gene products with a proven cancer associated immunogenicity. [Ozlem Türeci, Cancer Research Institute, Universitätskliniken des Saarlandes, Germany] http://www.cancerresearch.org/immune99/ozlem_tureci.html

Related terms Expression glossary  

cellome: The entire complement of molecules and their interactions within a cell. It is the information held within the cellome that defines the temporal and spatial interactions of cellular components, and thus normal and abnormal functions. The knowledge base of the cellome will be built by connecting layers of these interactions into the pathways and networks that govern all aspects of cellular life. Just as automated genome analysis and database tools are pushing the genomics era to a conclusion, automated cell analysis using High- Content Screening and cellular bioinformatics systems are the requisite exploration tools to commence the era of the cell and the definition of the cellome. [Cellomics, Inc. website] http://www.cellomics.com/html/about/vision.htm  Related terms Functional genomics glossary  Cell biology glossary

cellomics: Studying cell function and drug impact at the level of the cell. [E. Russo "Merging IT and biology" Scientist 14(23): 8 Nov. 27, 2000]

Cellomics™  information: Investigation of molecules and their interactions within cells to create knowledge of cell functions. [Cellomics, Inc.]

chronome: Derived from chronos (time), nomos (rule, law) and in the case of biological chronomes, chromosome, describes features in time, just as cells characterize the spatial organization of life. The chronome complements the genome (derived from gene and chromosome). The chronome consists of 1) a partly genetic, partly developmental, partly environmentally influenced or synchronized spectrum of rhythms; 2) stochastic or deterministic chaos; 3) trends with growth, development, maturation and aging in health and/or trends with an elevation of disease risk, illness and treatment in disease; and 4) unresolved variability. The chronome is genetically coded: it is environmentally synchronized by cycles of the socio- ecologic habitat niche and it is influenced by the dynamics of the interplanetary magnetic field. The chronome constituents, the chrones, algorithmically formulated endpoints, are inferentially statistically validated and resolved by the computer. Chronomes and their chrones 1) quantify normalcy, allowing an individualized positive health quantification; 2) assess, by their alterations, the earliest abnormality, including the quantification of an elevated risk of developing one (or several) disease(s), chronorisk, by the alteration of one or several chrones; and 3) provide, by the study of underlying mechanisms, a rational basis in the search for measures aimed at the prevention of any deterioration in properly timed, mutually beneficial environmental-organismic interactions. [Franz Halberg et. al "The Story Behind: Chronome/chrone" Neuroendocrinology Letters 20: 101 1999] http://www.nel.edu/20_12/nel20_12%20Chronome%20Chrone.htm

Gubin D, Halberg F. et. al, "The human blood pressure chronome: a biological gauge of aging" In Vivo 1997 Nov- Dec;11 (6): 485-94

chronomics: Technology allows the monitoring of ever denser and longer serial biological and physical environmental data. This in turn allows the recognition of time structures, chronomes, including, with an ever broader spectrum of rhythms, also deterministic and other chaos and trends. Chronomics thus resolves the otherwise impenetrable "normal range" of physiological variation and leads to new, dynamic maps of normalcy and health in all fields of human endeavor, including, with health care, physics, chemistry, biology, and even sociology and economics. [F. Halberg et. al. "Essays on chronomics spawned by transdisciplinary chronobiology. Witness in time: Earl Elmer Bakken" Neuroendocrinology Letters 22 (5): 359- 84 Oct. 2001]

crystallomics: Production of highly purified protein samples and diffraction quality crystals. [Joint Center for Structural Genomics, Oct. 2000]  http://bioinfo-core.jcsg.org/bic/links/crystallomics.htm Related terms NMR & X-ray crystallography glossary.

complexome: It has become evident over the past few years that many complex cellular processes, including control of the cell cycle and ubiquitin- dependent proteolysis, are carried out by sophisticated multi- subunit protein machines that are dynamic in abundance, post- translational modification state, and composition. To understand better the nature of the macromolecular assemblages that carry out the cell cycle and ubiquitin- dependent proteolysis, we have used mass spectrometry extensively over the past few years to characterize both the composition of various protein complexes and the modification states of their subunits. [Raymond J. Deshaies et. al "Charting the protein 'complexome' in yeast by mass spectrometry" Molecular and Cellular Proteomics, Nov. 21, 2001] http://www.mcponline.org/cgi/content/abstract/R100001-MCP200v1

diagnomics^TM: Molecular diagnostics with highly enhanced prognostics, diagnostics and therapeutic benefits. Combined with advanced genomic and proteomic technologies, MPMx [Millennium Predictive Medicine] is developing proprietary products that will shift medical care from current  symptom- based therapeutics to those tackling the root causes, or pathogenesis, of diseases. [Millennium Pharmaceuticals News, 1997] http://www.mlnm.com/news/1997/12-2--0.html Related terms Clinical genomics glossary

enzymome: A biochemical genomics has already been described in which all proteins predicted from a proteome can be assayed for potential enzymatic activities (Martzen et. al, 1999). So far, only a few enzymatic reactions have been tested but it is likely that with increasing automation, large numbers of conditions will become testable. It is conceivable that a complete set of proteome's proteins could be tested, for the ability to modify post- translationally the same set of proteins with the goal of defining a complete "enzymome" [Marc Vidal "A Biological Atlas of Functional Maps" Cell 104: 333-339, Feb. 9, 2001] 

A comprehensive set of enzymatic reactions [Marc Vidal, personal communication, Dec. 2001]

epigenome: A set of  what may be hundreds of genes whose function is determined by [genetic] imprinting. [Post Gazette News Bar Harbor, Maine genetics seminar,  July 26, 2000]  http://www.post-gazette.com/healthscience/20000726heredity1.asp

epigenomics: A whole genome approach to epigenesis and epigenetics. “An approach that views these [imprinting, metabolic networks, genetic hierarchies in embryonic development, and epigenetic mechanisms of gene activation in cancer] and other complex phenotypes from the genomic level down, rather than from the genetic level up, can provide powerful insights into the functional interrelationships of genes in health and disease. [S Beck, A Olek and J Walter “From genomics to epigenomics” Nature Biotechnology 17 (12):1144 Dec 1999]

By detecting DNA methylation patterns, the "on" and "off" signs for genes, Epigenomics can create a digitized readout (Digital Phenotype®) for each tissue. The comparison of healthy and sick tissue enables an exact diagnosis of disease at a very early stage and opens up new therapeutic opportunities. [Epigenomics website, Corporate profile] http://www.epigenomics.com/p1.htm  

Related terms Expression glossary; Gene definitions epigenetics

epigenotype: 'Digital phenotype'. [derived from first] genome- scale mapping of epigenetic parameters such as DNA- methylation; secondly, identification and analysis of epigenomic loci in some of the most interesting regions of the human genome; and thirdly, comparative analysis of epigenomic information from different organisms. [Human Epigenome consortium, Berlin PRNewswire, December 7, 1999] http://www.findarticles.com/m4PRN/1999_Dec_7/58049826/p1/article.jhtml

fluxome: A recently developed methodology for metabolic flux ratio (METAFoR) analysis ... can also directly reveal active metabolic pathways. Generation of fluxome data arrays by use of the METAFoR approach is based on two- dimensional ¹³C-¹H correlation nuclear magnetic resonance spectroscopy with fractionally labeled biomass and, in contrast to metabolic flux analysis, does not require measurements of extracellular substrate and metabolite concentrations. [U. Sauer "Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism"  Journal of Bacteriology181 (21): 6679- 88, Nov. 1999]

fluxomics: Integration of metabolic pathway engineering and fermentation production technologies is necessary for the successful commercial production of chemicals. The 'toolbox' to do pathway engineering is ever expanding to enable mining of biodiversity, to maximize productivity, enhance carbon efficiency, improve product purity, expand product lines, and broaden markets. Functional genomics, proteomics, fluxomics, and physiomics are complementary to pathway engineering, and their successful applications are bound to multiply product turnover per cell, channel carbon efficiently, shrink the size of factories (i.e., reduce steel in the ground), and minimize product development cycle times to bring products to market. [G. Chotani et. al. "The commercial production of chemicals using pathway engineering" Biochim Biophys Acta 1543 (2): 434- 455, Dec. 29, 2000].

foldome: The population of gene products classified through their tertiary structure. [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.pdf.

A number of projects are currently being launched to determine the three- dimensional structure of most protein folds or "foldome" of several proteomes [Marc Vidal "A Biological Atlas of Functional Maps" Cell 104: 333-339, Feb. 9, 2001]

A comprehensive set of protein folds. [Marc Vidal, personal communication, Dec. 2001] See also NIGMS Structural Genomics Initiatives http://www.nigms.nih.gov/funding/psi.html

Related terms: Structural genomics glossary

functional maps: Maps: genomic & genetic glossary

functome: What functions an organism has the potential to perform. What substances (metabolome) are available? What proteins are currently (proteome) or potentially (transcriptome, genome) available to utilise them? Narrower sense of “potential functions encoded by the genome”. [Stuart Rison "Functomics!?" Dept. of Biochemistry, University College, London, 16 Feb. 2000]  http://www.biochem.ucl.ac.uk/~rison/Presentations/biochem_gp_talk_16_02_2000/tsld004.htm

Related terms: Functional genomics function, gene function,  Gene Ontology 

functomics: A comparison of annotation schemes for genomes. [Stuart Rison "Functomics!?" Dept. of Biochemistry, University College, London, 16 Feb. 2000]  http://www.biochem.ucl.ac.uk/~rison/Presentations/biochem_gp_talk_16_02_2000/sld001.htm

genome, genomics: Genomics glossary

glycome: Carbohydrate components of the cell. Analogous to the terms that characterize the genome and proteome, we define the glycome as the total carbohydrate complement.  Where glycomics is an analysis of their patterns of expression as modulated by the environment and the physiological state of the organism.  [Center for Structural Biology, Univ. of New Hampshire, US, 2000] http://glycome.unh.edu/

glycomics: The cascade of genetic information does not terminate with proteins but with glycans … diverse glycan structures are significantly related to various biological phenomena … glycans have potential to exhibit structural diversity, whose complexity is far greater than that of nucleic acids or proteins … Unless we adopt a global strategy involving the genome, proteome and glycome, we will never achieve an understanding of the glyco- code, which is probably based on a completely different system from those governing nucleic acids and proteins. [J. Hirabayashi, J and K. Kasai “Glycomics, Coming of Age! Trends in Glycosciences and Glycobiology 12  (63): 1-5 Jan 2000]  http://www.gak.co.jp/TIGG/63PDF/GF.pdf 

Related terms Biomolecules glycans, glycobiology, glycotechnology; Functional genomics: functional glycomics

immunome: The sum total of the immunodominant proteins in an organism. [Parasitology Group,  University of Wales, Aberystwyth UK, April 2000]  http://www.aber.ac.uk/~mpgwww/Proteome/Proteome.html

The totality of rearranged antibody and antigen receptor genes present in all living humans. The presently chronicled set of all sequenced human immunoglobulin and antigen receptor gene rearrangements and mutations if of course an infinitesimally small subset of the total human immunome, and can thus be thought of as the “working immunome’. To the extent that somatic  gene rearrangements may also be discovered someday in other, non- lymphoid cells, ...  the immunome should properly be regarded as a specific, though probably major, case with in the broader concept of the “somatonome”. [T Pederson “The immunome” Molecular Immunology 36 (15-16): 1127-1128 Oct.- Nov. 1999]

Narrower term cancer immunome

immunomics: Collective endeavors by many labs to read the DNA or mRNA sequences of as many immunoglobulins and antigen receptors as can be marshalled … dynamic biology in the cells of today’s humans.  [T Pederson “The immunome” Molecular Immunology 36( 15-16) : 1127-1128 Oct. - Nov. 1999]

Immunomics ™  has been trademarked by Beckman Coulter, referring to cellular immune response to achieve direct ex vivo quantitation of antigen- specific T cells. http://www.beckmancoulter.com/Immunomics/default.asp

interactome: A complete set of macromolecular interactions, physical and genetic are included.  Current usage of  the word tends to refer to a comprehensive set of protein- protein interactions. [Marc Vidal, personal communication, Dec. 2001]

Systematic screens were recently described for large sets of proteins that lead to interesting clusters of potential protein interaction networks indicative of functional relationships between products including those of uncharacterized genes (Schwikowski et al., 2000; Walhout et al., 2000a). Here again a physical interaction mapping concept emerges as a two- dimensional matrix in which all pairwise combinations of possible interactions between the proteins of a proteome need to be tested with the goal of generating a physical "interactome" map. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001] http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11239391&dopt=Abstract

FlyNets- list is a very simple and more general databank, the long- term goal of which is to report on any published molecular interaction occurring in the fly, giving direct web access to corresponding s in Medline and in FlyBase. In the context of genome projects, databases describing molecular interactions and genetic networks will provide a link at the functional level between the genome, the proteome and the transcriptome worlds of different organisms. Interaction databases therefore aim at describing the contents, structure, function and behaviour of what we herein define as the interactome world. [C. Sanchez et. al  "Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database" Nucleic Acids Research 27 (1): 89- 94, Jan. 1, 1999]

Related terms phenome, transcriptome; Proteomics glossary protein- DNA interactions, protein- RNA interactions, protein-protein interactions

interactome map: Maps: genomic & genetic glossary

interactomics: With the biology which has already emerged, we have proper targets for looking at cancer. Genomics and the things which are emerging from genomics like proteomics, which is actually looking at the products of the genes and the way that they interact, which you can call interactomics if you want, are just as important. It is the gene expression which is critical. We have to learn about that as well. Genomics is the beginning and then there is a whole series of things which spread from them. [Dr. George Blackledge, Select Committee on Science and Technology, House of Commons, UK, 12 April 2000] http://www.parliament.the-stationery-office.co.uk/pa/cm199900/cmselect/cmsctech/332/0041204.htm

lipoproteomics: A new analysis protocol directed toward developing new markers for the detection and treatment of cardiovascular disease. A component of the protocol is the use of MALDI  [mass spectrometry] to identify isoforms and mutations of the protein domains associated with lipoprotein particles. It involves the analysis of protein mixtures with a MW [molecular weight] range of 5kDa to 80 kD.  [Ronald D. Macfarlane et. al. "Lipoproteomics" American Society of Mass Spectrometry Annual Conference, Chicago IL, 2001]  http://www.inmerge.com/aspfolder/ASMS2001Schedule2.asp

localizome: Refers to the presence or absence of proteins in particular cells or cellular compartments. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001] http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11239391&dopt=Abstract

The primitive goal of mapping projects of the localizome is to generate information about where various proteins can be found in what cellular compartments. With computational approaches, we have recently constructed a prediction system (SubLoc) to determine protein subcellular localization using sequence information. [Sujon Hua, "Current Research" Institute of Bioinformatics, Tsinghua Univ., China, 2001] http://www.bioinfo.tsinghua.edu.cn/~huasj/Research/Research.htm

Related terms Gene definitions localize, locus Narrower term: localizome maps:

localizome maps: Maps, genomic & genetic glossary

metabolome: The quantitative complement of all the low molecular weight molecules  present in cells in a particular physiological or developmental state.  [Parasitology Group,  University of Wales, Aberystwyth UK, April 2000] http://www.aber.ac.uk/~mpgwww/Metabol/Metabol.html

The entire complement of all the small molecular weight metabolites inside a cell suspension (or other sample) of interest.  [Douglas Kell, Metabolomics in Aberystwyth,  University of  Wales, Aberystwyth UK] http://gepasi.dbs.aber.ac.uk/dbk/metabol.htm

Total metabolite pool ("metabolome") analysis offers a means of revealing novel aspects of cellular metabolism and global regulation. [H. Tweeddale "Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis" Journal of  Bacteriology 180 (19): 5109- 5116, Oct. 1998] 

Related terms Cell biology glossary metabolite; Molecular modeling glossary: in silico cell, virtual cell

metabolomics: Rapid analysis of metabolites at the whole cell level, using methods such as Pyrolysis mass spectrometry, Fourier-Transform Infrared Spectrometry, Raman spectrometry, and most recently Electrospray mass spectrometry. [Metabolomics in Aberystwyth, University of Wales, Aberystwyth UK] http://gepasi.dbs.aber.ac.uk/dbk/metabol.htm

metabonome: Total small molecule complement of a cell. [Jeremy K. Nicholson, J.C. Lindon & E. Holmes. "Metabonomics": understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29, 1181-1189, 1999]

metabonomics: The quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification. This concept has arisen from work on the application of  ¹H-NMR spectroscopy to study the multicomponent measurement of biofluids, cells, and tissues. [J.K. Nicholson, J.C. Lindon & E. Holmes, "Metabonomics" understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29, 1181-1189, 1999]

A powerful tool for the evaluation of drug toxicity and clinical disease processes based on the proton NMR spectroscopic analysis of biological fluids and intact tissue samples. Chemometric and bioinformatic methods are used to construct mathematical models of the complex NMR patterns which reflect the activities of many linked biochemical pathways. This technology is highly complementary to genomic and proteomic methods for toxicological assessment and can also be used in furthering the understanding of functional genomics and transgenic models of human disease processes. [Jeremy Nicholson, University of London, CHI NMR conference Oct. 24-26, 2000, McLean VA]  Related terms Functional genomics, Pharmacogenomics

methylome: The complete set of DNA methylation modifications of a cell - has its own life cycle, and alterations in the methylome may be linked to aging and cancer, as well as polymorphic variation in populations. [Andrew Feinberg, Nature Genetics 27 (1): 9-10, Jan. 2001] http://www.psychiatry.wustl.edu/Resources/LiteratureList/2001/January/Feinberg-A.html

The methylation pattern of the genome. It comprises all positions of methylated cytosine (mC) on healthy DNA. [Epigenomics AG, Germany, Glossary] http://www.epigenomics.com/glossary.htm

Related term: Proteins methylation

methylomics: Our research investigates the role of genetic and epigenetic alterations in the development of sporadic cancers, with a focus on brain tumors. Most sporadic cancers have been described by molecular pathways involving gain and loss of chromosomal regions corresponding to oncogene activation and tumor suppressor gene inactivation, respectively. Such genetic characterizations of sporadic tumors do not take into account epigenetic alterations that may similarly result in abnormal loss or gain of gene activity. Methylation of cytosine in DNA is such a modification that can influence gene expression and chromosome stability. Although DNA methylation patterns can be significantly altered in human cancers, such changes are not detected by typical genetic screening methods. [Joseph Costello, Univ. of California- San Francisco Neurosurgery Faculty 2000] http://www.som.ucsf.edu/neuros/faculty/bios/costello.htm

microbiome: Our understanding of the microorganisms that inhabit the human body is woefully inadequate. The diversity, abundance, and activities of these microorganisms are all matters of both importance and ignorance. This might seem surprising given that the human body contains far more microbial cells than it contains human cells. The repercussions of our information deficit are extensive: many of these poorly- characterized microbes probably play critical roles in maintaining human health, and some microbes, both transient and permanent members of our microflora, play necessary roles in disease. In particular, compelling evidence suggests that disruption of the endogenous intestinal microbial ecosystem contributes to a number of diseases, such as inflammatory bowel disease, tropical and celiac sprue and antibiotic- associated diarrhea, with major impact on global health. [David A. Relman, Senior Scholar Award in Global Infectious Disease, Ellison Medical Foundation, 2000]  http://www.ellison-med-fn.org/emf_award.jsp?award_id=128

morphome: The quantitative description of anatomical structure, chemical and biochemical composition, and material properties of an intact organism, including its genome, proteome, cell, tissue and organ structures up to those of the whole intact being. [JB Bassingthwaighte, National Simulation Resource, Univ. of Washington, personal communication, May 2000] 

See also JB Bassingthwaighte "Strategies for the physiome project" Annals of  Biomedical Engineering 28 (8): 1043- 1058, Aug. 2000] 

Related terms Cell biology morphometry; Functional genomics;, Pharmacogenomics

-ome:  According to Merriam-Webster Online from the Latin for "mass". http://www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=ome

According to the Oxford English Dictionary this is an Anglicized version of the suffix "oma", primarily found in botanical terms and usually  meaning normal, in contrast to the pathology implied by "oma".

-omes, integrating: George Church Lab chart with links to genome (DNAs), transcriptome (RNAs), proteome (proteins), physiome (metabolites) and biome (environments). http://twod.med.harvard.edu

A key approach in genomic research is to divide the cellular contents into distinct sub- population, each given an -omic term. Broadly, these 'omes can be divided into those that represent a population of molecules, and those that define their actions. ... Once the individual sub- populations are defined and analyzed, we can then try to reconstruct the full organism by interrelating them, eventually allowing for a full and dynamic view of the cell. ... A problem in comparing the different 'omes' is that each represents a different set of genes. [Mark Gerstein "What is Bioinformatics?" MB&B 474b3, 2001] http://bioinfo.mbb.yale.edu/what-is-it.html

See also 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.pdf.

omics:  Joshua Lederberg and Alexa T. McCray "'Ome Sweet 'Omics: A Genealogical Treasury of Words" Scientist 15 (7): 8 April 2, 2001] http://www.the-scientist.com/yr2001/apr/comm_010402.html

operome projects: Characterization of unknown protein in biological function. [Akira TSUGITA, “Proteome the state of the art and future projections” Proceedings 8th Codata/DSAO Meeting and workshop Nov. 25-26, 1997, Korea R&D Information Center] http://codata.kordic.re.kr/proceeding/6-1.html Related terms Proteomics glossary.

operomics: The profiling of tissues and cell populations at the genomic, transcriptomic and proteomic levels. The molecular analysis of tissues at all three levels. [SM Hanash "Operomics: molecular analysis of tissues from DNA to RNA to protein" Clin Chem Lab Med 38 (9): 805-13 Sep. 2000]

The whole operation of molecular analysis of a cell, extending from DNA to RNA to protein. [“Proteomics, transcriptomics: what's in a name?” Nature 402:715 Dec 16, 1999]  Related terms Cell biology, Expression, Functional genomics,  Proteomics

A correspondent has suggested that this term is linked to operons (Gene definitions) but I have not been able to find any evidence for (or against). Any insights would be welcomed.

ORFeome: Complete sets of open reading frames (ORFs), or "ORFeomes," need to be cloned into various expression vectors.  [J. Reboul et. al Open- reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans.  Nat Genet 2001 Mar; 27 (3): 332-6] 

But the gene number question is really just a footnote to [Marc] Vidal's larger purpose: to create clones of the entire collection of ORFs - the ORFeome - of the C. elegans genome. Beyond simply identifying a gene, the ORFs will provide information about intron and exon structure. "It's okay to know where genes are, but at the end of the day you want to have a good idea of exactly what the ORF looks like after splicing, improving our knowledge of what kind of protein comes out," said Vidal.  ["Human Genome Tally: Is Recount in Order?" Harvard Medical School Focus, Mar. 23, 2001] http://www.med.harvard.edu/publications/Focus/2001/Mar23_2001/genetics.html

ORFeome Project link http://www.hms.harvard.edu/dms/bbs/fac/vidalma.html

Related terms  translatome; Gene definitions ORF, ORESTES

orgeomic profiling: Low molecular weight molecule profiling [SurroMed, Inc. website, 2001] http://www.surromed.com/Technology.html

pathogenomics: Our project utilizes a combination of informatics, evolutionary biology, microbiology and eukaryotic genetics to identify pathogen genes which are more similar to host genes than expected, and likely to interact with, or mimic, their host’s gene functions. In addition, potential pathogenicity islands in genomes are being identified. A database of these genes is being built, which will be updated in an automated fashion, based on the increasing number of pathogen genomes being sequenced. Candidate functions identified by our informatics approach will be tested in the laboratory to investigate their role in pathogen infection and host interaction. Tests will include studies of both the pathogen gene and any homologous C. elegans gene, as C. elegans will be used as a model host organism for some pathogens. Public databases of all analyses used and all genes identified using our approach will be made available on this website. [Pathogenomics, British Columbia, Canada, 2001]  http://www.pathogenomics.bc.ca/

peptidome: Biologically active peptides are one of the most important substances that transmit and regulate bio- information in the circulatory and neuronal systems. In order to elucidate and identify the mechanism in the pathogenesis and development of cardiovascular and related diseases, we are trying to identify new biologically active peptides and analyze their molecular mechanism in the regulation of circulation system. ... We have also developed the highly sensitive techniques for the measurement of biological activity of peptides and for the separation and sequence determination of peptides with ultra- low abundance. Indeed, we have applied these methods to the screening of unidentified peptides. We have also started the "Peptidome" project that is aimed to construct fact- databases of all peptides that exist in the tissue or body. These databases are expected to be utilized for developing new drugs and therapy as an intellectual infrastructure. [Naoto Minamino, Takeshi Katafuchi and postdocs, Laboratory of Development and Evaluation of Biomedical Instruments and Systems (LDEBIS), National CardioVascular Center NCVC, Japan] http://www.ncvc.go.jp/english/res/LDEBIS.html

peptidomics: Peptide profiles of the pars intercerebralis and the corpora cardiaca  [of insects, the endocrinological equivalent of the hypothalamus- pituitary system of vertebrates] were characterized using simple sampling protocols in combination with MALDI- TOF and electrospray ionization double quadrupole time of flight (ESI-Qq-TOF) mass spectrometric technologies. The results were compared with earlier results of conventional sequencing methods and immunocytochemical methods. In addition to many known peptides, several m/z signals corresponding to putative novel peptides were observed in the corpora cardiaca and/or pars intercerebralis. Furthermore, for a number of peptides evidence was provided about their localization and MALDI- TOF analysis of the released material from the corpora cardiaca yielded information on the hormonal status of particular brain peptides. [E. Clynen "Peptidomics of the pars intercerebralis- corpus cardiacum complex of the migratory locust, Locusta migratoria" Eur J Biochem 2001 Apr;268(7):1929-39]  

Related terms Drug discovery & development glossary peptidomimetic; Proteins peptides

Proteomics has established itself as a highly valuable technology for producing functionally related data in an unparalleled fashion, but is methodologically restricted to the analysis of proteins with higher molecular masses (>10 kDa). The development of a technology which covers peptides with low molecular weight and small proteins (0.5 to 15 kDa) was necessary, since peptides, amongst them families of hormones, cytokines and growth factors, play a central role in many biological processes. To summarise the technologies used for this approach the term "peptidomics” is introduced. In this article, we present the rationale and first results of a novel, universal peptide display approach for the analysis and visualisation of peptides and small proteins from biological samples. [Peter Schulz- Knappe et. al. "Peptidomics: The Comprehensive Analysis of Peptides in Complex Biological Mixtures" Combinatorial Chemistry & High- Throughput Screening 4 (2): 207-217, 2001] http://www.bentham.org/cchts/cchts4-2.htm##link8

pharmacogenome: I am very optimistic about pharmacogenome drugs reaching the market within the next 10 or 12 years. [Ken Rubenstein, BioOnline, Feb. 9, 2000]  http://www.talkcity.com/transcripts/BioOnline/2-9-2000-4.htmpl

pharmacogenomics: Pharmacogenomics glossary

phenome: The digital system depicted for the phenome refers to the presence or absence of particular phenotypes conferred by gene knockout. [Marc Vidal "Biological Atlas of Functional Maps" Cell 104: 333­ 339, February 9, 2001]    

Perhaps the "phenome" or phenotype lies between morphome and physiome, in recognition of the importance of the qualitative identification of form and function derived from the gene, though lacking in the quantitative, integrative definition. [JB Bassingthwaighte, National Simulation Resource, Univ. of Washington]   http://nsr.bioeng.washington.edu/NSR/physiome/files/Petrodvoret.1997/abstracts/jbb.html

See also note on variant meanings for genome, genotype and phenotype in Genomics glossary under genome citing M. Mahner, M. Kary "What exactly are genomes, genotypes and phenotypes? And what about phenomes?" Journal of  Theoretical Biology 186 (1): 55- 63, May 1997]

Mouse Phenome Project, Jackson Labs, US. http://aretha.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/introducing

Related terms interactome; Functional genomics Gene Ontology^TM Consortium  Narrower term: Maps glossary phenome maps

phenome maps: Maps: genomic & genetic glossary

phenomics: Phenomics can be defined as the identification of a gene's function. With completion of the Human Genome Project in sight, Phenomics will become the focal point of tomorrow's drug discovery effort by allowing pharmaceutical and biotechnology companies to rapidly validate genes as potential targets for drug discovery.  At present, researchers use genomic knockouts and antisense approaches to determine the biological function of a gene. Unfortunately, neither foretell, with any degree of accuracy, the outcome of modest changes in the biological activity of a gene's protein product. As diseases are related to subtle changes in protein activity rather than to complete loss or gain in any one protein, a method is needed to produce varying changes in protein activity to determine a gene's relation to the specific disease process. [DGI Biotechnologies, Inc.] See also Genetic Engineering News June 1, 2000] http://www.dgibt.com/science.htm

Study of phenotypes with knowledge of the genotypes ... will have an important theoretical component through mathematical model building and computer simulation. [B. Palsson "The challenges of in silico biology" Nature Biotechnology 18:1147-1150, Nov. 2000]  

In the case of microorganisms, there are accumulation of studies on phenotypic characters such as morphological, physiological, and biochemical. Let us call them 'phenomics'. Integration between phenomic analysis and molecular phylogenetic analysis using rRNA sequences has been conducted for organismal taxonomy studies that are essential for biodiversity studies. We now need a new integration between phenomics and genomics in which evolutionary scenarios are estimated through comparison of complete genomic sequences.   [DNA DataBank of Japan, “Genomics and Phenomics” DDBJ Report  March 1999]  http://www.ddbj.nig.ac.jp/ddbjnew/dcr99/dcr1999-e.html#GenandPhen

Complex or multifactorial diseases are defined as diseases that are ultimately determined by a number of genetic and environmental factors. Although there are many technologies and strategies that can be used to detect genetic factors influencing complex diseases, these technologies and strategies have inherent limitations. ... Ultimately, both the detection and precise characterization of a factor's contribution to a complex disease are difficult undertakings, because the effect of any one factor may be obscured or confounded by other factors. However, the genetic dissection of complex diseases can be greatly facilitated by paying heed to two very basic distinctions. The first distinction is between complexity at the level of individuals and complexity at the level of populations. The second distinction is between the two sequentially pursued components of gene discovery paradigms: gene identification and gene effect characterization. Although genetic epidemiology, as a research field, is oriented to both components of gene discovery for complex diseases, it is suited to gene effect characterization at the population level more than anything else. This paper reviews the origins of the genetic basis of complex traits, as well as the problems plaguing genetic epidemiologic analysis strategies, with the hope of showing how greater attention to these distinctions, as well as a greater integration of relevant knowledge, can alleviate confusion and shape future investigations. In addition, a new discipline, "phenomics" or "phenometrics," could be initiated that would complement genomic research as presently performed. [Nicholas J. Schork "Genetics of complex disease: approaches, problems, and solutions" American Journal of Respiratory & Critical Care Medicine 156 (4 Pt 2): S103-109, Oct. 1997]

Ciphergen has coined the term "Phenomics" to describe the system’s applications for protein research and biomarker discovery when a single, integrated biochip platform can be used for protein discovery through functional analysis. [Ciphergen’s FAQ, US]  http://www.ciphergen.com/tech_doc5.html

Phenomics ® is also an automated technology trademarked by Proteus SA. http://www.proteus.fr/Phenomics/phenomics_home.htm and a linguistics term.

Related terms Functional genomics glossary function; Genomics glossary complex diseases; Molecular modeling glossary phenotypic screening

physiogenomics: A new field of study that is dedicated to understanding the function and interaction of genes. As The Jackson Laboratory develops new mouse models for hundreds of human diseases and disorders-including Alzheimer's disease, epilepsy, deafness, atherosclerosis and high blood pressure-new, high-technology measuring techniques are needed to detect the subtle physiological differences that signal susceptibility or resistance to those diseases. Physiogenomics matches that physiological information with genetic data, making each new mouse model a powerful tool for researchers at The Jackson Laboratory and the worldwide biomedical research community.  [Jackson Laboratory, Bar Harbor, Maine, US, Aug. 13, 2001]  http://www.jax.org/pubinfo/media/releases/collins_plaque.html

physiome: The quantitative description of the physiological dynamics or functions of the intact organism. ...We need to be able to predict phenotype from genotype, but cannot because the influences of environment and happenstance on growth, development and disease rival the influences of inheritance via the gene. ...  "physiome" is coined from "physio", life or nature, and "ome", as a whole entity.  [JB Bassingthwaighte, Physiome Project, National Simulation Resource, Univ. of Washington personal communication Oct. 2000] and  http://nsr.bioeng.washington.edu/NSR/physiome/   Related terms Functional genomics glossary.

physiomics: Knowledge of the complete physiology of an organism, including all interacting metabolic pathways, structural and biochemical scaffolding, the proteins and accessories that make them up, and the gene interactions and cues that control them. [Mark Lesney "Finding New Targets" Modern Drug Discovery 4(9): 34-36 Sept. 2001] http://pubs.acs.org/subscribe/journals/mdd/v04/i09/html/09lesney.html

postgenomics: "Thinking postgenomics" Nature Genetics 23 (4): 375- 376, Dec. 1999

promoterome: A complete set of promoters. [Marc Vidal, personal communication, Dec. 2001]

proteome, proteomics: Proteomics glossary

pseudogenome: The complement of pseudogenes in the proteome. [Dov Greenbaum "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.pdf.

See also Goro Terai^{1, 2}, Toshihisa Takagi¹, Kenta Nakai "Prediction of co- regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species" Genome Biology 2(11): research0048.1-0048.12, 2001 

pseudogenomics: Five years after completion of the yeast genome sequence, I will give examples of truly "genomic" (global) achievements as well as of other "pseudogenomic" approaches abusively called "postgenomics" or "functional genomics" which use gene sequence information to study specific traits. [André Goffeau (ENS) "Yeast Genomics, Pseudogenomics and Postgenomics" Structures macromoléculaires dans le cadre biologique, mathématique et algorithmique, 6 décembre 2001] http://www.ihes.fr/IHES/Scientifique/Seminaires/Sgenomique2001.html

Surveying "dead" parts. [Mark Gerstein, MB&B Bioinformatics Group, Yale Univ, 2001]  http://bioinfo.mbb.yale.edu/lectures/woodshole/talk.pdf

regulome: Genome- wide regulatory network of the cell. [Harmen Bussemaker "Bioinformatics Homepage" Swammerdam Institute of Life Sciences SILS Univ. of Amsterdam, Netherlands] http://regulome.bio.uva.nl/hjb/  Related terms Functional genomics glossary.

regulomics: The study of gene expression at the level of genetic network regulatory mechanisms. [Mary E. Harper, Chief Scientific Officer, CIStem Molecular Corp. “Regulomics: A New Approach to Discover Gene Circuitry”, Cambridge Healthtech Institute’s Functional Genomics conference, Nov. 13-14, 2000, Boston, MA, US http://www.healthtech.com/conference/00fgn/  

Related terms Expression, Functional genomics; Proteomics regulatory homology

resistome: All those proteins whose expression is altered in drug resistant forms. [Parasitology Group, University of Wales, Aberystwyth UK]  http://www.aber.ac.uk/~mpgwww/Proteome/Proteome.html  Related terms Expression

ribonome: The population of RNA- coding regions of the genome.  [Mark Gerstein "What is Bioinformatics? Omes Table" 2001]  http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html  Related terms riboproteomics; Cell biology ribosomes

ribonomics: Our understanding of RNA in biology is currently limited in part by a lack of structural data, but perhaps more profoundly by limited knowledge of the cast of characters. It is not yet clear how many structured RNAs are expressed in different cell types, what biochemical pathways they participate in and what proteins they bind. Structural genomics of RNA will be most interesting when integrated with experimental and computational methods for identifying novel RNA genes and determining their biological relevance: an approach defined previously as 'ribonomics' [11]. Such an effort would have at least three essential goals: (i) to develop and implement methodologies for identifying and characterizing novel RNA genes; (ii) to develop techniques for high- throughput determination of RNA and RNA- protein structures; and (iii) to create and maintain a centralized database of RNA structures, sequences, functional data and modeling tools. [Jennifer A. Doudna "Structural Genomics of RNA" Nature Structural Biology (7) 11 supp: 954- 956 November 2000] http://www.euchromatin.org/Doudna1.htm#Ribonomics

Functional analysis of genome sequences has largely ignored RNA genes and their structures. We introduce here the notion of 'ribonomics' to describe the search for the distribution of and eventually the determination of the physiological roles of these RNA structures found in the sequence databases. The utility of this approach is illustrated here by the identification in the GenBank database of RNA motifs having known binding or chemical activity. The frequency of these motifs indicates that most have originated from evolutionary drift and are selectively neutral. On the other hand, their distribution among species and their location within genes suggest that the destiny of these motifs may be more elaborate. [V. Bourdeau "The distribution of RNA motifs in natural sequences" Nucleic Acids Research 27 (22): 4457- 4467, Nov. 15, 1999] http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10536156&dopt=Abstract

Related term: Sequences, DNA & beyond RNA

riboproteomics: Riboproteomics^TM is the systematic characterization and annotation of RNA- protein interactions that affect RNA metabolism, including RNA transport, [RNA] splicing, translation and decay. [Anadys Pharmaceutical, Inc."Riboproteomics opportunity" 2000]http://www.iluminausa.com/anadys/riboproteomics.html  

Related terms: Bioinformatics glossary annotation; Proteomics glossary RNA- protein interactions, translation; Sequences, DNA & beyond glossary RNA splicing

secretome: A subset of the proteome that is defined by its action, i.e. it is actively exported from the cell. [Dov Greenbaum "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.pdf.

As soil-living microorganisms Bacillus species have a high capacity to secrete degradative enzymes into the environment, enabling them to use alternative nutrient resources. The best-studied representative of this genus is Bacillus subtilis. In particularly, the progress on the characterization of the so-called secretome including the exported proteins and components of protein secretion pathways was facilitated by the availability of the complete genome sequence of B. subtilis (Kunst et al., 1997). Because exported proteins are usually synthesized as precursors with an amino- terminal hydrophobic signal peptide the genome sequence made it possible to predict all secreted proteins of this eubacterium (Tjalsma et al., 2000 Signal peptide- dependent protein transport in Bacillus subtilis: a genome- based survey of the secretome. Microbiol Mol Biol Rev.64, 515-47 (2000). http://microbio1.biologie.uni-greifswald.de:8080/institute/33

Related terms Proteomics glossary secreted proteins

signalome- plant: The identification of all signaling components in all messengers mediated transduction pathways, analysis of their function and regulation, and cross talk among these components - should help in understanding the inner workings of plant cell responses to diverse signals. New functional genomics approaches such as reverse genetics, microarray analyses coupled with in vivo protein- protein interaction studies and proteomics should not only permit functional analysis of various components in Ca(2+) signaling but also enable identification of a complex network of interactions. [A. S. Reddy "Calcium: silver bullet in signaling".  Plant Science 160: 381- 404, 2001 arrayit.com e-library summary]. http://arrayit.com/e-library/r/ReddyAS2001/reddyas2001.html

somatonome: All somatic gene rearrangements, lymphoid plus non- lymphoid. [T Pederson “The immunome” Molecular Immunology 36( 15-16) : 1127-1128 Oct.- Nov. 1999] As of  Dec. 27, 2001  http://www.google.com did not retrieve any websites but this article (and this glossary) when searching for somatonome or somatonomics.

transcriptome: Complement of mRNAs transcribed from a cell’s genome. [“Proteomics, transcriptomics: what's in a name?” Nature 402:715 Dec 16, 1999]

The set of genes expressed from the yeast genome [VE Velculescu et al. “Characterization of the yeast transcriptome” Cell 88: 243-251, 1997]    http://www.sagenet.org/yeast/summary.htm

Related terms interactome, translatome; Expression glossary; Microarrays glossary; Proteomics reverse proteomics.

transcriptomics: Generation of messenger RNA expression profiles. [“Proteomics, transcriptomics: what's in a name?” Nature 402:715 Dec 16, 1999]

The study of  genome- wide mRNA levels (sometimes called transcriptomics) has far outpaced the study of genome- wide protein levels (called proteomics) because of the huge amount of available DNA sequence information, the relative ease with which DNA can be manipulated, and technological advances that allow for analysis of the expression of 100s or 1000s of mRNA species simultaneously. [Chemical Industry Institute of Toxicology, US] http://www.ciit.org/ACT99/ACTIVITIESFEB99/feb99.html

Related terms Expression glossary; Sequences, DNA & beyond transcript; protein transcription.

translatome: The cellular population of proteins expressed in the organism at a given time, explicitly weighted by their abundance. ... Our definition of the translatome is partially motivated by the ambiguities in term proteome, which has two competing definitions. First, broadly favoured by computational biologists, is a list of all the proteins encoded in the genome (Gaasterland 1999, Doolittle 2000). In this context, it is equivalent to what some refer to as the orfeome, i.e. the set of genes excluding non- coding regions. Experimentalists, especially those involved in large- scale experiments such as expression analysis and 2D electrophoresis, favor a second definitions. Here it is used to describe the actual cellular contents of proteins, taking into account the different levels of protein concentrations (Yates 2000). We prefer the former definition for proteome, and use the term translatome for the later.  [Dov Greenbaum "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.pdf

Related terms orfeome, transcriptome; Proteins translation; Proteomics glossary proteome

unknome: At present, a large proportion of genes can only be described as members of the unknome - those with currently no functional information!  [Dov Greenbaum "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.pdf.

vaccinome: Genomics could provide a new way to develop DNA vaccines for malaria, which, if successful, could be applied toward other diseases. "DNA vaccines would offer this flexibility because of the ease of production, stability, and versatility of use," reported Stephen L. Hoffman of the Naval Medical Research Institute. DNA vaccines are fundamentally different from traditional ones, Hoffman notes. "The difference in this approach is that we would be receiving DNA that encodes a substance and asking our bodies to make a protein in response to it. However, this approach, while potentially flexible, is also more complex. It requires assessing potential antigen proteins encoded by the malaria genome, using that "vaccinome" to induce antibodies, judging the accuracy of expression, immunizing mice with each plasmid, and ultimately, developing a multigene DNA vaccine. [Ilene Schneider and Paul Smaglik "Harnessing the Microbial World: Big Info in Small Packages" Scientist 13 (4): 1 Feb. 15, 1999] http://www.the-scientist.com/yr1999/feb/schneider_p1_990215.html

Related terms Pharmaceutical biology glossary antibody, antigen, DNA vaccine, vaccine

vaccinomics: Using bioinformatics and genomics for vaccine development.  [Tom Hollon "Clad against all clades" Scientist 14 (18): 1 Sep. 18, 2000] http://www.the-scientist.com/yr2000/sep/hollon_p1_000918.html

Variome ^TM: Databases & software directory

variomics: Study of variants of DNA, RNA and proteins.

Bibliography

Alpha glossary index

I have tried to determine the status of all words known to be, or are suspected of being, proprietary names or trademarks and to include this information. No judgment concerning the legal status of such words is claimed.