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-Omes and -omics glossary
& taxonomy
With 35,000 genes and hundreds of thousands of protein states to identify, correlate, and
understand, it no longer suffices to rely on studies of one gene, gene product, or process at a
time. We have entered the "omic" era in biology. But
large- scale omic studies of cellular
molecules in aggregate rarely can answer interesting questions without the assistance of
information from traditional hypothesis- driven research. The two types of science are
synergistic. John N. Weinstein, Searching for pharmacogenomic markers: the synergy between omic and
hypothesis- driven research, Disease Markers 17(2): 77- 88, 2001
alleome: A collection of different allotypes or allelic protein variants, a new type of protein library. Greg Weiss, Univ. of California, Irvine, personal communication, Oct. 2005
allergenome: Putative proteinous allergens. Allergenomics, Div of Medical Devices, National Institute of Health Sciences, Japan, http://dmd.nihs.go.jp/latex/allergenomics-e.html
allergenomics: Rapid and comprehensive analysis of putative proteinous allergens (allergenome) by applying such a proteomic strategy With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. Allergenomics, Div of Medical Devices, National Institute of Health Sciences, Japan, http://dmd.nihs.go.jp/latex/allergenomics-e.html
bibliome: Scientific literature
L. Grivell "Mining the bibliome: searching for a needle in a haystack?: New computing tools are needed to effectively scan the growing amount of scientific literature for useful information."
EMBO Rep 2002 Mar;3(3): 200- 203, Mar. 2002; DB. Searls "Mining the
bibliome: Pharmacogenomics Journal 1 (2): 88- 89, 2001
biome: 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.
biomics: The Erasmus Center for Biomics was initiated in 2002 as a central Dutch facility at Erasmus M[edical C[enter] as a concerted action of all Departments. The Center aims to contribute to the progress of science using Genomics, Proteomics and Bioinformatics. Erasmus MC, Univ. Medical Center, Rotterdam, Netherlands, 2004 http://www.erasmusmc.nl/biomics/index2.html
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
An acronym for a research program in Sweden on "Biomimetic Materials Science". Bo Liedberg, IFM, Linköpings universitet, Swedish Foundation for Strategic Research, personal communication, Jan. 2002
cancer fragmentomics, cancer genomics, cancer immunome, cancer immunomics, cancer proteomics, cancer transcriptomes- human: Cancer genomics
cardiogenomics, Cardiome Project: Molecular Medicine
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. Cellomics, Inc. website http://www.cellomics.com/html/about/vision.htm Related terms: Cell biology; Functional genomics
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.
chaperome: The goal of the "All Chaperome" project is to characterize the molecular chaperones of C. elegans. We have identified approximately 170 chaperones corresponding to the major classes of chaperones and co-chaperones conserved in S. cerevisiae, and vertebrates. Taking advantage of the lineage analysis of C. elegans, we are determining the expression pattern of each chaperone gene to establish a basis for network interactions and tissue specificity during development and aging. Morimoto Laboratory, All Chaperome Project, 2007 http://www.biochem.northwestern.edu/ibis/morimoto/research/research_chap2.html Thanks to Heike Aßmus, University of Rostock for alerting me to this -ome.
chemogenomics: Chemistry & biology glossary
chemoproteomics: The use of biological information to guide chemistry--offers a highly efficient alternative to small-molecule characterization that can accelerate drug discovery. Beroza P, Villar HO, Wick MM, Martin GR. Chemoproteomics as a basis for post-genomic drug discovery, Drug Discov Today, 7(15): 807- 814, Aug 1, 2002 Related terms: chemical proteomics, chemiproteomics: Chemistry & biology
approaches to biology
for carbohydrates John
N. Weinstein "Pharmacogenomics: Teaching Old Drugs New Tricks" New
England Journal of Medicine 343: 1408-1409, http://discover.nci.nih.gov/host/2000_pharmecogenomics.jsp
As is the case with most
higher eukaryotes, only small parts of human Chromosome 17 have been sequenced.
For partially sequenced chromosomes, NCBI has collected several genetic and
physical maps. placed them onto a common coordinate system, and aligned any
shared markers (shown in Entrez by green connecting lines). In this example, the
Map view shows the alignment of the MIT physical map the NCBI transcript
map, the CHLC linkage map, the Genethon linkage map, and the GDB cytogenetic
map. Note that Stanford radiation hybrid maps will also be added as they become
available: currently the Chromonome 4 map is in Entrez. Biological
Computing Division Newsletter, Weizmann Institute of Science, Israel No. 1 May
1996 no longer on the web April 2005
chronome, chronomics: Molecular Medicine
chromosomics: The term "chromosomics'' is introduced to draw attention to the three-dimensional morphological changes in chromosomes that are essential elements in gene regulation. Chromosomics deals with the plasticity of chromosomes in relation to the three-dimensional positions of genes, which affect cell function in a developmental and tissue-specific manner during the cell cycle. It also deals with species-specific differences in the architecture of chromosomes, which has been overlooked in the past. Chromosomics includes research into chromatin-modification-mediated changes in the architecture of chromosomes, which may influence the functions and life spans of cells, tissues, organs and individuals. It also addresses the occurrence and prevalence of chromosomal gaps and breaks. U Claussen, Chromosomics, Cytogenet Genome Res 2005;111:101-106 (DOI: 10.1159/000086377
clinomics: Molecular Medicine
combinatorial peptidomics: Is the first generic methodology applicable to protein expression profiling, that is independent of the physical properties of proteins and does not require any prior knowledge of the proteins. Alternatively, a specific combinatorial strategy may be designed to analyse a particular known protein on the basis of that protein sequence alone or, in the absence of reliable protein sequence, even the predicted amino acid translation of an EST sequence. Combinatorial peptidomics is especially suitable for use with high throughput micro- and nano-fluidic platforms capable of running multiple depletion reactions in a single disposable chip. Mikhail Soloviev et. al, Combinatorial peptidomics: a generic approach for protein expression profiling, Journal of Nanobiotechnology 1:4 doi:10.1186/1477-3155-1-4, 2003 http://www.jnanobiotechnology.com/content/1/1/4 Broader term: peptidomics
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
computational RNomics: The first step toward this goal [Rnomics] is the development of versatile and reliable computational methods that can detect and classify functional RNAs, preferably within a single genome, or in case this proves impossible, from a very small set of related genomes. We propose here to develop a suite of bioinformatics methods that are specifically geared toward detecting, verifying, and classifying functional RNAs. Our comprehensive approach to "Computational RNomics" will provide improved algorithms for RNA secondary structure prediction, improved alignment algorithms for nucleic acid sequences, novel approaches to compare and align RNA structures, extensions of existing RNA algorithms to deal with genome- size data sets, a database system specifically designed for RNA structures. The first step toward this goal is the development of versatile and reliable computational methods that can detect and classify functional RNAs, preferably within a single genome, or in case this proves impossible, from a very small set of related genomes. Peter F. Stadler, Computational RNomics: The Quest for RNA Genes, 2002 http://www.tbi.univie.ac.at/research/RNomics.html Broader term: RNomics
connectome: The connection matrix of the human brain
(the human "connectome") represents an indispensable foundation
for basic and applied neurobiological research. However, the network of
anatomical connections linking the neuronal elements of the human brain is still
largely unknown. Sporns O, Tononi G, Kötter R
(2005) The Human Connectome: A Structural Description of the Human Brain. PLoS
Comput Biol 1(4): e42. doi:10.1371/journal.pcbi.0010042 http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0010042
cross-omics: In addressing the core technological issue of this endeavor namely integration of toxicogenomic data with conventional toxicological endpoints researchers face several technological and methodological limitations .... Kurt Zingler, Cross-Omics and Systems Toxicology, BioIT World 6 (9): 25, Nov 2007 http://www.bio-itworld.com/issues/2007/nov/cross-omics-and-systems-toxicology/ Related term: Drug safety & pharmacovigilance systems toxicology
cryobionomics: Cryopreservation for the long-term conservation of in vitro germplasm results in the exposure of tissues to physical, chemical and physiological stresses causing cryoinjury. Although, the effects of cryoinjury upon the genome are often unknown, any accumulative DNA polymorphisms may not be induced by cryopreservation per se but are the result of the whole culture-cryoprotection-regeneration process. It is desirable to assess the genetic integrity of plants surviving cryogenic storage to determine if they are 'true to type' after cryopreservation. This can be done at the phenotypic, histological, cytological, biochemical and molecular levels. The relevance of these approaches to stability investigations is discussed with their limitations. This review provides a definition for 'Cryobionomics' - a novel term describing the re-modelled concept of genetic stability and the re-introduction of cryopreserved plants into the environment. Keith Harding, Genetic integrity of cryopreserved plant cells: A review, CryoLetters 25, 3-22, 2004 http://www.cryoletters.org/Abstracts/vol_25_1_2004.htm
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.
of a light microscope (Diaplan: (Leitz, Germany), video camera (Bosch), image
card (PIP 1024: (Matrox), IBM PC compatible 486 computer with program Visilog (Noesis)
supplemented with self-elaborated algorithms utilizing transformations of
mathematical morphology Hruby, Smolska, Filipowski, Rabczyn'ski, Cies'lar &
Kopec', The importance of tubulointerstitial injury in the early phase of
primary glomerular disease, Journal of Internal Medicine 243 (3): 215
-, March 1998, doi:10.1046/j.1365-2796.1998.00277.x
cytomes Cellular systems/ organs/ body. [G. K. Valet, Predictive Medicine by Cytomics" Max- Planck- Institut für Biochemie, Martinsreid, Germany, 2001] http://www.biochem.mpg.de/valet/cytomics.html Related term: Imaging flow cytometry
cytomics: Multiparameter cytometric analysis of the cellular heterogeneity of cytomes, ... access a maximum of information on the apparent molecular cell phenotypes, resulting from cell genotypes and exposure. Molecular cell phenotypes in the naturally existing cellular and cell population heterogeneity of disease affected body cytomes contain the information on the future development (prediction) as well as on the present status (diagnosis) of a disease. [G. K. Valet, Predictive Medicine by Cytomics" Max- Planck- Institut für Biochemie, Martinsreid, Germany, 2008 http://www.classimed.de/cytomics.html
The bulk of our knowledge concerning the plant cytoskeleton has come primarily from the use of techniques and probes derived from animal research. However, in comparison with animal tissues, relatively few plant cytoskeleton proteins have been identified. We presume this is not because the plant cytoskeleton is really made up of such few proteins, but rather that only rarely have attempts been made to identify plant- specific cytoskeleton proteins, using plant- specific methods. Here we outline methods that we have developed both for the isolation and identification of novel cytoskeleton proteins as well as for the visualization of novel filamentous structures in plant cells, and we describe several novel cytoskeleton proteins and two novel cytoskeleton structures, 'nanofilaments' and 'nanotubules'. We postulate that use of such approaches will lead to a rapid expansion of our knowledge of the plant cytoskeleton. E. Davies et. al. "Novel components of the plant cytoskeleton: a beginning to plant 'cytomics'" Plant Science 160(2): 185- 196, Jan. 5, 2001 Related/narrower? term: nucleome
degradome: The entire protease complement of human cells and tissues. Santiago Cal, Víctor Quesada, Cecilia Garabaya and Carlos López-Otín, Polyserase-I, a human polyprotease with the ability to generate independent serine protease domains from a single translation product PNAS | August 5, 2003 | vol. 100 | no. 16 | 9185- 9190 http://www.pnas.org/cgi/content/full/100/16/9185
The application of genomic and proteomic
approaches to identify the protease and protease- substrate repertoires, or 'degradomes',
on an organism-wide scale promises to uncover new roles for proteases in
vivo. This knowledge will facilitate the identification of new pharmaceutical
targets to treat disease. Here, we review emerging degradomic techniques and
concepts. Protease Degradomics: A New Challenge for Proteomics, Carlos Lopez-
Otin & Christopher M. Overall, Nature Reviews Molecular Cell Biology 3, 509
-519, 2002
diagnomicsTM: Molecular Medicine glossary
differential transcriptome: The differential transcriptome represents the set of genes that are differentially expressed during a cellular transition. The static transcriptome is the set of genes that does not change expression under that particular condition. Koen J. Dechering, The transcriptome's drugable frequenters, Drug Discovery Today 10?12/24, 857- 864, June 15, 2005 and cites Mark Gerstein's http://bioinfo.mbb.yale.edu/what-is-it/omes/ as the originator of this phrase.
diseasome: Molecular Medicine
economics: An important aspect of the "omics" family as well. Business of biopharmaceuticals glossary
ecotoxicogenomics: Genomics categories
eicosanomics: analysis
of eicosanoids present in a biological sample (eicosanomics), which requires the
power of chromatographic separation coupled with mass spectrometric detection to
quantitate subpicomolar levels of these arachidonate metabolites generated after
cellular activation. Working
towards an exegesis for lipids in biology, H
Alex Brown and Robert
C Murphy Nat
Chem Biol. Sep 2009; 5(9): 602606. doi: 10.1038/nchembio0909-602
embryogenomics: Fundamental questions in developmental biology are: what genes are expressed, where and when they are expressed, what is the level of expression and how are these programs changed by the functional and structural alteration of genes? Genomics needs developmental biology because one of the goals of genomics -- collection and analysis of all genes in an organism -- cannot be completed without working on embryonic tissues in which many genes are uniquely expressed. However, developmental biology needs genomics -- the high-throughput approaches of genomics generate information about genes and pathways that can give an integrated view of complex processes. MS Ko, Embryogenomics: developmental biology meets genomics, Trends in Biotechnology. 19(12): 511- 518, Dec. 2001
envirome: See under enviromics
enviromics: The envirome is the total complement of environmental characteristics, conditions, and processes required for life form viability and successful adaptation. The genome dwells within environment, and genomic expression shapes and is shaped by environment. James. C. Anthony, Michigan State Univ. School of Medicine, Highly Cited Authors, ISI http://hcr3.isiknowledge.com/author.cgi?id=1613&cb=1353
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
epigenonomics: SNPs & other genetic variations
epitome: Monoclonal antibody technology has generated invaluable tools for both the analytical and clinical sciences. However, standard immunization approaches frequently fail to provide monoclonal antibodies with the desired specificity. Subtractive immunization provides a powerful alternative to standard immunization and allows for the production of truly unique antibodies. With the intent of targeting specific epitopes within the proteome, subtractive immunization has been broadly and successfully implemented for the production of monoclonal antibodies otherwise unobtainable by standard immunization. A Zijlstra, JE Testa, JP Quigley, Targeting the proteome/ epitome, implementation of subtractive immunization, Biochem Biophys Res Commun 303(3): 733- 744, Apr. 11, 2003
epitomics: A new field of science that studies all epitopes of the proteome in an organism. The understanding of epitope reveals the functions of these proteins. The word Epitomics derives from the combined words of epitope and omics. An epitope is a functional recognition site that binds by a specific monoclonal antibody. Epitomic, Inc. http://www.epitomics.com/
ethnogenomics: The main task of ethnogenomics is to study the characteristics of genomic polymorphism and genomic diversity of various groups of population: separate communities, ethnoses, and ethnoterritorial communities. Khusnutdinova EK, The ethnogenomics and genetic history of eastern European peoples, HERALD OF THE RUSSIAN ACADEMY OF SCIENCES 73 (4): 365-372, 2003 http://www.garfield.library.upenn.edu/histcomp/cavallisforza_all_auth-citing/index-so-46.html
exome: The exome is the 1% of the genome most easily interpreted and most likely to cause noticeable phenotypes. George Church, Nature Genetics "Question of the year" http://www.nature.com/ng/qoty/index.html
exposome: the full catalogue of a person's environmental exposures throughout their life. Epidemiology: Every bite you take "how to measure everything" Nature News Published online 16 February 2011 | Nature 470, 320-322 (2011) | doi:10.1038/470320a http://www.nature.com/news/2011/110216/full/470320a/box/1.html
expressome: Expressome is a slightly larger concept than transcriptome. Transcriptome is the set of transcripts, while expressome includes transcripts, proteins and other ligands (how much concentration). Wikipedia accessed Aug. 15, 2005 http://en.wikipedia.org/wiki/Expressome
Refers to the whole set of gene expression in a cell, tissue, organ, organisms, and species.
expressomics: Expressomics has two major branches. One is RNA expression represented by transcriptomics and protein expression by proteomics (or translatomics if you insist). Expressomics, omics.org wiki http://omics.org/index.php/Expressomics
Strives to couple information from genomes, transcriptomes, proteomes,
metabolomes and metagenomes to the long-established practice in crop science of
conducting field trials as well as to adapt current strategies for recording and
analysing field metadata to facilitate integration with -omics data.
Dan Jacobson, researcher, Institute for Wine Biotechnology, Stellenbosch
University, South Africa, Erik Alexandersson, PhD Dept of Plant Protection
Biology, Swedish University of Agricultural Sciences http://www.plantlink.se/en/news/news/124-plg0036-field-omics-3-ects.html
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"
of Bacteriology 181 (21): 6679- 88, Nov. 1999
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
Human Genome is essentially complete, and yet the impact on how we understand
physiological processes such as cellular force transduction has been minimal in
part because of our inability to work from known sequence to structure, i.e. the
Foldome. In order to specifically identify cytoskeletal proteins that change
conformation or assembly in stressed versus static cells, in situ labeling of
sterically-shielded or 'cryptic' cysteines with fluorophores is analyzed by
quantitative mass spectrometry, sequential two-dye labeling, and fluorescence
imaging. Within red blood cells, shotgun labeling shows that shielded cysteines
in the two isoforms of the cytoskeletal protein spectrin are increasingly
labeled as a function of shear stress and time, indicative of forced unfolding
of specific domains. Conf
Proc IEEE Eng Med Biol Soc. 2009;:3341-2.
doi: 10.1109/IEMBS.2009.5333197. The Foldome in cellular force transduction. Discher
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 See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome Research 11 (9): 1484- 1502, Sept. 2001
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
what we're really looking at is fragmentomics -- fragments of proteins that are
the true biomarkers. We don't actually know what the true protein is doing. It's
fragments of these things that are going up and down. -- sometimes whole
proteins too. But it might be ill advised to design an antibody based on
what the fragment is doing when it cross reacts with the parent protein and the
parent protein may not be the true diagnostic test. Kevin Rosenblatt, Biomarker
Discovery for Clinical Assays , In Focus April 8, 2004 http://www.bio.com/file_temp/BiomarkerDiscovery04.3.pdf;jsessionid=JFXFPFYT14ZJ3R3FQLMSFEWHUWBN...
cancer: has been used to characterize the protein
fragments that are potential biological markers of cancer diseases [45].
However, this definition of fragmentomics is rather limited, as there are
numerous biological processes where fragments of larger molecules are involved.
A natural fragmentation of proteins, nucleic acids, carbohydrates, and other
natural molecules is well known. For example, the peptide molecules excised from
specialized precursors are fragments. This is characteristic of both the
oligopeptide regulators and large protein structures. Fragmentomics:
a New Insight into Structures and Functions of the Natural Oligopeptide
Diversity Proceedings
of the 2nd WSEAS International Conference on BIOMEDICAL ELECTRONICS and
fragonomics: The use of smaller molecules (fragments) in the drug discovery process has led to success in delivering novel leads for many different targets. ER Zartler, MJ Shapiro, Fragonomics: fragment-based drug discovery, Current opinion in chemical biology, 9 (4): 366- 370, Aug 9, 2005
functional lectinomics: Encompasses,
among other activities, intra- and intercellular transport processes, sensor
branches of innate immunity, regulation of cell-cell (matrix) adhesion or
migration and positive/negative growth control with implications for
differentiation and malignancy. HJ Gabius, S Andre, H Kaltner, HC Siebert, The
sugar code: functional lectinomics. Biochim Biophys Acta. 1572(2-3): 165- 177,
Sept 19, 2002 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12223267&dopt=Abstract
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/Presentatios....
The whole set of functional entities in a cell, tissue, organ, organism, and specie. ...
The functome is usually used in the context of enzyme functions. However, the discipline is broadening to encompass other aspects of biological functions. Functome is the next step of metabolome and regulome. It represents biological functions rather than chemical of cells. So, a whole metabolic pathway can be an example of a functomic entity. Wikipedia, accessed Aug. 10, 2005 http://en.wikipedia.org/wiki/Functome Related terms: Functional genomics function, gene function, Gene Ontology; Proteomics protein function
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...
The scientific discipline of studying the functional entities in biological cells. Functomics encompasses enzyme, cells, and higher level of biological entities and functions. Wikipedia, accessed Aug. 10, 2005 http://en.wikipedia.org/wiki/Functome
The challenge of characterizing ESTs linked to complex diseases is like interpreting sharp images on a blurred background and therefore requires a multidimensional screen for functional genomics ("functionomics") in tissues, mice and zebra fish model, which intertwines various approaches and readouts to study development and homeostasis of a system. In summary, the post-genomic era of functionomics will facilitate to narrow the bridge between correlative data and causative data by quaint hypothesis-driven research using a system approach integrating "intercoms" of interacting and interdependent disciplines forming a unified whole as described in this review for Arthritis. MG Attur et. al A system biology" approach to bioinformatics and functional genomics in complex human diseases: Arthritis Current Issues in Molecular Biology 4(4): 129- 146 Oct. 2002
functionomics: Sometimes used as a synonym for functional genomics, has been trademarked by Regeneron Pharmaceuticals FunctionomicsTM
galectinomics: Cancer genomics glossary
genome, genomics: Genomics glossary
glycome, glycomics: Glycosciences glossary
Even in the case of well-characterized variants that confer a significant
disease risk, more healthy individuals carry the variant, with no apparent ill
effect, than those who manifest disease. ... we examine the
'Hemostaseome,' and more specifically focus on DNA sequence changes pertaining
to those human genes known to impact upon hemostasis and thrombosis that can be
analyzed coordinately, and on an individual basis, to interrogate how specific
combinations of variants act to confer disease predisposition. As a first step,
we delineate known members of the Hemostaseome and explore the nature of the
genetic variants that may cause disease in individuals whose hemostatic balance
has become shifted toward either a prothrombotic or anticoagulant phenotype.
human microbiome: Therapeutic indications infectious
hygienomics: Integrated hygiene and food safety management systems in food production can give rise to exceptional improvements in food safety performance, but require high level commitment and full functional involvement. A new approach, named hygieneomics, has been developed to assist management in their introduction of hygiene and food safety systems. For an effective introduction, the management systems must be designed to fit with the current generational state of an organisation. GD Armstrong, Towards integrated hygiene and food safety management systems: the Hygieneomic approach, Int J Food Microbiol. 50(1-2): 19-24, Sept 15, 1999
proportion of genes with intense and selective expression in specific tissues,
cells, or systems are still almost completely uncharacterized with respect to
biological function? In what ways do these functionally enigmatic genes differ
from well-studied genes? To address these two questions, we devised a
computational approach that defines so-called ignoromes. Pandey AK, Lu L, Wang X, Homayouni R, Williams RW (2014)
Functionally Enigmatic Genes: A Case Study of the Brain Ignorome. PLoS ONE 9(2):
e88889. doi:10.1371/journal.pone.0088889 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088889
"ignorome" concept http://bit.ly/1oCa3aE
applies across omics "Real knowledge is to know the extent of one's
ignorance" Eric Topol, Twitter https://twitter.com/EricTopol/status/435065444139925504
immunogenomics: Molecular Medicine glossary
immunome: 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 genomics glossary cancer immunome
immunomics: Study of the molecular functions associated with all immune- related coding and non- coding mRNA transcripts. To unravel the function, regulation and diversity of the immunome requires that we identify and correctly categorize all immune- related transcripts. The importance of intercalated genes, antisense transcripts and non- coding RNAs and their potential role in regulation of immune development and function are only just starting to be appreciated. C. Schonbach, From immunogenetics to immunomics: functional prospecting of genes and transcripts. Novartis Found Symp. 2003; 254: 177-88; discussion 189-92, 216-22, 250-2.
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 todays humans. T Pederson The immunome Molecular Immunology 36 (15-16): 1127-1128 Oct. - Nov. 1999
immunoproteomics: The mammalian immune system has evolved to display fragments of protein antigens derived from microbial pathogens to immune effector cells. These fragments are typically peptides liberated from the intact antigens through distinct proteolytic mechanisms that are subsequently transported to cell surface bound to chaperone like receptors known as Major Histocompatibility Complex (MHC) molecules. These complexes are then scrutinised by effector T cells that express clonally distributed T cell receptors with specificity for specific MHC- peptide complexes. In normal uninfected cells, this process of antigen processing and presentation occurs continuously, with the resultant array of self-antigen derived peptides displayed on the surface of these cells. Changes in this peptide landscape of cells act to alert immune effector cells to changes in the intracellular environment that may be associated with infection, malignant transformation or other abnormal cellular processes, resulting in a cascade of events that result in their elimination. Because peptides play such a crucial role in informing the immune system of infection with viral or microbial pathogens and the transformation of cells in malignancy, the tools of proteomics, in particular mass spectrometry, are ideally suited to study these immune responses at a molecular level. Immunoproteomics: Mass spectrometry based methods to study the targets of the immune response, AW Purcell, JJ Gorman, Immunoproteomics: Mass spectrometry based methods to study the targets of the immune response. Molecular and Cellular Proteomics 3(3): 193- 208, March 2004 Epub 2004 Jan 12
in silico transcriptomics: Immunotherapy approaches to fight cancer are based on the principle of mounting an immune response against a self- antigen expressed by the tumor cells. In order to reduce potential autoimmunity side- effects, the antigens used should be as tumor- specific as possible. A complementary approach to experimental tumor antigen discovery is to screen the human genome in silico, particularly the databases of "Expressed Sequence Tags" (ESTs), in search of tumor- specific and tumor- associated antigens. The public databases currently provide a massive amount of ESTs from several hundreds of cDNA tissue libraries, including tumoral tissues from various types. We describe a novel method of EST database screening that allows new potential tumor- associated genes to be efficiently selected. C. Vinals et. al, "Using in silico transcriptomics to search for tumor- associated antigens for immunotherapy" Vaccine 19(17-19): 2607- 2614 Mar 21, 2001
Genomic medicine is poised to offer a broad array of new genome-scale
screening tests. However, these tests may lead to a phenomenon in which multiple
abnormal genomic findings are discovered, analogous to the incidentalomas
that are often discovered in radiological studies. If practitioners pursue these
unexpected genomic findings without thought, there may be disastrous
consequences. The Incidentalome A
Threat to Genomic Medicine, Isaac
S. Kohane, MD, PhD; Daniel R. Masys, MD; Russ B. Altman, MD, PhD,
JAMA. 2006;296(2):212-215. doi:10.1001/jama.296.2.212. http://jama.jamanetwork.com/article.aspx?articleid=211038
inflammasome: The adapter molecules ASC, Ipaf and Cryopyrin/Nalp3 have each been proposed to regulate caspase-1 within a multi-protein complex called the "inflammasome". Activation of caspase-1 leads to the cleavage and activation of pro-inflammatory cytokines such as interleukin (IL)-1beta and IL-18. The analysis of mice deficient in ASC, Ipaf and Cryopyrin/Nalp3 has revealed that the inflammasome is a dynamic entity that is assembled from different adapters in a stimulus-dependent manner. ASC, Ipaf and Cryopyrin/Nalp3: bona fide intracellular adapters of the caspase-1 inflammasome. S Mariathasan, Microbes Infect 2007 Apr 9 (5): 664- 671. Epub 2007 Jan 27
information from all the omes thrown into one pot for an integrated analysis,
along with any other relevant data for good measure.
Michael Snyder, a
geneticist at Stanford University in California, published his personal
integrome7 (although he called
it an integrative personal omics profile and others dubbed it the
narcissome), combining data for his genome, transcriptome, proteome and
metabolome (see Nature
http://doi.org/hrq; 2012)
[John Weinstein's]
research program is 50% experimental, 50% theoretical. The experimental part
centers on mRNA expression profiling (with cDNA microarrays, oligonucleotide
chips, and RT-PCR), proteomic profiling (with 2D-gels and reverse-phase lysate
arrays), and DNA profiling (with SNP chips, array- CGH, SKY, and methylation
sequencing) of cancer cells in the NCI drug discovery program. The bioinformatic
and chemoinformatic tools of his research include those of classical statistics,
computer-intensive statistics, neural computing, genetic algorithm, data mining,
computer- aided drug design, and bioinformatic interpretation. The idea is to
create, splice together, and mine large databases of information on the
molecular structures, patterns of activity, and biochemical targets of potential
anticancer agents. Included are what he has termed .integromicTM.
studies combining information at the DNA, RNA, protein, functional, and
pharmacological levels. His group also develops professional- grade, freely
available bioinformatics software packages for public use. John N.
Weinstein, MD, PhD, Brief Biography, National Cancer Institute, NIH http://discover.nci.nih.gov/weinstein.jsp
A Spanish life sciences informatics company http://www.integromics.com/index.php
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
The interactome is less well defined than the genome and the transcriptome, as different communities use the term protein interaction to refer to anything from physical interactions to broadly defined functional interactions, such as neighbors in metabolic networks. Even if restricted to physical interactions, it is important to discriminate between stable interactions and transient interactions. Lars J. Jensen, Peer Bork, Quality analysis and integration of large- scale molecular data sets. Drug Discovery Today: Targets, 3(2): 51-56.
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
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,... 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 protein- DNA interactions, protein- RNA interactions, protein- protein interactions
interactome map: See under interactome
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
the complement of genes in an organism whose level of expression does not change
significantly from condition to another, i.e. they are invariantly expressed.
Ben Sidders personal communication Jan 12, 2008 and Sidders et. al
Quantification of global transcription patterns in prokaryotes using spotted
microarrays, Genome Biology 2007, 8:R265doi:10.1186/gb-2007-8-12-r265
kinome: Phosphorylation by protein kinases is the most widespread and well-studied signaling mechanism in eukaryotic cells. Phosphorylation can regulate almost every property of a protein and is involved in all fundamental cellular processes. Cataloging and understanding protein phosphorylation is no easy task: many kinases may be expressed in a cell, and one-third of all intracellular proteins may be phosphorylated, representing as many as 20,000 distinct phosphoprotein states. Defining the kinase complement of the human genome, the kinome, has provided an excellent starting point for understanding the scale of the problem. The kinome consists of 518 kinases, and every active protein kinase phosphorylates a distinct set of substrates in a regulated manner. Sam A Johnson & Tony Hunter, Kinomics: methods for deciphering the kinome, Nature Methods 2, 17 - 25, 2005 Published online: 21 December 2004; | doi:10.1038/nmeth731 http://www.nature.com/nmeth/journal/v2/n1/full/nmeth731.html
Full complement of human protein kinases. http://kinase.com/human/kinome/
Protein Kinase Complement of the Human Genome,
G Manning et. al. Science 298: 1912-1934, Dec. 6, 2002, Human Kinome supplement,
SUGEN http://www.kinase.com/human/kinome/
kinomics: It is not sufficient to state an interaction between biomolecules - You need to know how your biomolecule is interacting with its binding partner kinetically. Those kinetics are described in a new part of functional Genomics or Proteomics sometimes referred to as Kinomics. [Biaffin GmbH & Co. KG homepage] http://www.biaffin.com/
In this review, we describe and
evaluate modern techniques for studying the protein kinases, or, in other words,
state-of-the-art kinomics. Sam A Johnson & Tony Hunter, Kinomics:
methods for deciphering the kinome, Nature Methods 2, 17 - 25, 2005
Published online: 21 December 2004; | doi:10.1038/nmeth731 http://www.nature.com/nmeth/journal/v2/n1/full/nmeth731.html
lectinomics: Carbohydrate-binding
proteins, excluding sugar-specific antibodies, receptors of free mono- or
disaccharides for transport or chemotaxis and enzymes modifying the bound
carbohydrate. HJ Gabius, S Andre, H Kaltner, HC Siebert, The sugar code:
functional lectinomics. Biochim Biophys Acta. 1572(2-3): 165- 177, Sept 19, 2002
ligandomics: Complete set of organic small molecules. Glen A. Evans "Designer Science and the 'omics revolution" Nature Biotechnology 18 (2): 127, April 2000
an inventory of the thousands of individual lipid molecular species
Lipidomics Gateway, NIGMS http://www.lipidmaps.org/about/about_consortium.html
lipidomics: Mass
spectrometry-based analysis of lipids, called lipidomics, presents a number of
opportunities not only for understanding the cellular processes in health and
disease but also in enabling personalized medicine. Lipidomics in its most
advanced form is able to quantify hundreds of different molecular lipid species
with various structural and functional roles. Unraveling this complexity will
improve our understanding of diseases such as atherosclerosis at a level of
detail not attainable with classical analytical methods. Lipidomics: A Tool for Studies
of Atherosclerosis, Ekroos K, Jänis M, Tarasov K, Hurme R, Laaksonen R., Zora
Biosciences Oy, Curr Atheroscler Rep. 2010 Apr 28. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/20425241
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
In recent years large-scale
determination of protein localization, localizome analysis, has been
investigated in yeast and certain organella in higher Eukaryotic cells. This
information augments the long accumulation of small- scale experiments which
have determined the localization of various proteins under specific conditions.
Together these findings have begun to reveal the complexity of protein
localization. A Knowledge base for the Protein Localizome, Mitsuteru Nakao et.
al, poster Intelligent Systems for Molecular Biology, 2004
localizome maps: Maps, genomic & genetic
membranome: The plasma membrane mediates a
wide variety of basic biological functions including signal transduction,
molecular transport, membrane trafficking, cell migration, cell-cell
interactions, intercellular communication and even drug-resistance. Plasma
membrane-associated proteins, especially integral membrane proteins (IMP) that
traverse the lipid bilayer, are key elements mediating these vital biological
processes. Developing a map of the proteins present at the luminal surface of
vascular endothelial cells (a membranome) will shed new light on the function of
these cells in vivo. Additionally, because these cells form a vital interface
between the blood and tissue, defining the membranome will reveal new tissue-
and disease-specific targets. Mass Spectrometry, Proteogenomics Research
Institute for Systems Medicine, San Diego http://www.prism-sd.org/facilities_massspec.html
In the human body, all biological components from individual genes to
entire organs work together to promote normal development and sustain health.
This amazing feat of biological teamwork is made possible by an array of
intricate and interconnected pathways that facilitate communication among genes,
molecules, and cells. While some of the biological pathways have already been
discovered, many more remained to be found. Further research is needed to
understand how these pathways are integrated in humans and other complex
organisms, as well as to determine how disturbances in these pathways may lead
to disease and what might be done to restore disturbed pathways to their normal
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 through- put. This process can be called metabolic finger- printing. Such approaches have occasionally been termed metabonomics, which on the one hand could be mixed up with the completely different goal of metabolomics, and on the other hand with the earlier defined concept of the 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 April, 2001 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447208/
The presented data illustrate the potential of the
NMR technique for (1) fast initial screening
of biodegradative pathways, i.e. for studies on metabolomics in newly
isolated microorganisms, and (2) identification of relatively unstable pathway
intermediates like fluoromuconolactones and fluoromaleylacetates. MG Boersma
"19F NMR metabolomics for the elucidation
of microbial degradation pathways of fluorophenols"
Journal of
Industrial Microbiol Biotechnol 26 (1/2): 22- 34 Jan 2001
metabonome: 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]
Metabolic control and regulation ... in the intact system at multiple levels over time. Jeremy K. Nicholson, Imperial College, Univ. of London "Metabonomics: Understanding the Metabolic Signature of Disease in the Post- Genomic Age" at Northeastern Univ, US, Oct. 30, 2001 http://www.med.ic.ac.uk/divisions/1/metabo.htm
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]
metallome: The study of the entirety of the content of inorganic species within a cell or tissue-type. .. deciphering a metallome will inform us about Where metals are within a given cellular type, What biomolecules those metals are associated with (whether small ligands such as siderophores, or larger proteins), What concentrations do they exist at, How are they speciated throughout the cell, and, perhaps most importantly, How do all of these pieces of information change as a function of time. Sean Elliott, Research interests of the Elliott Group, Bioinorganic Chemistry - Bioelectrochemistry - Biophysical Chemistry, Boston Univ., US http://people.bu.edu/elliott/sjeresearch.html
Wikipedia http://en.wikipedia.org/wiki/Metallome
cites Williams, R.J.P. (2001). "Chemical
selection of elements by cells". Coordination Chemistry Reviews 216217:
583595 accessed Oct. 25, 2006
metaproteome: See under metaproteomics
metaproteomics: Our method enabled the successful extraction and purification of the entire proteome from a laboratory- scale activated sludge system optimized for enhanced biological phosphorus removal, its separation by two-dimensional polyacrylamide gel electrophoresis and the mapping of this metaproteome. Highly expressed protein spots were excised and identified using quadrupole time-of-flight mass spectrometry with de novo peptide sequencing. We propose the term "metaproteomics" for the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time. P Wilmes, PL Bond, The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms, Environ Microbiol. 6(9): 911- 920, Sept 2004 Google = about 518 Nov 5, 2005, about 1,100 Oct. 25, 2006
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/Feil Related term: Proteins methylation
methylomics: The modern era of Methylomics had its origins in the fields of genetics and embryology. It began in 1939 with Conrad Waddingtons concept of the epigenotype, a character whose mode of impression was over and above, or in addition to, the classical genotype (8). Waddington used this descriptor in terms of interrelated developmental pathways, a view which culminated in his famous description of the Epigenetic Landscape. Epigenetics moved from a genetics-based, to a methylation-based, to a CpG island-based, and more recently to genome-wide Methylomics, initiated by the seminal articles of Art Riggs, Robin Holliday and Adrian Bird and their associates(9-13). Human Genetic Signatures, Historical Profile http://www.geneticsignatures.com/3LinkD.php
AP Feinberg, Methylation meets
genomics, Nature Genetics, 27, 9-10, 2001
I've coined a new word: microbiome. I suggest we broaden our horizons by thinking of the multicellular being as a superorganism, with an extended genome comprising: a) karyome ? chromosome set b) chondriome - mitochondria or b') plastidome ? chloroplasts (in plants) c) microbiome - the entourage of microbial flora that we carry in and on us, perhaps as endosymbionts like mitochondria or chloroplasts, but also on our skin, gut lumen, mucosal surfaces, and elsewhere. Each of these components can have an impact on the outcome of our encounters with infection (and reinfection), as well as on nutrition. Microbiome is a microbial community. You may wince and say, ?Josh, do we need another word?? but microbes have a big part to play in our destiny. And new words will facilitate the change in metaphor we need. Joshua Lederberg correspondence with Jack Woodall, "Friendly Fire: Make Love Not War: A new approach to epidemics "Praxis Post, 2001
MicrobeLibrary, American Society of Microbiology http://www.microbelibrary.org/
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 Google = about 227 July 11, 2002; about 340 July 14, 2003; about 667 June 7, 2004, about 877 Aug. 15, 2005, about 21,200 Oct. 25, 2006 Related terms: Cell biology morphometry; Functional genomics; Pharmacogenomics
morphomics: (biology) The identification of the totality of the morphological features of species Wiktionary http://en.wiktionary.org/wiki/morphomics Google = about 78 Oct. 25, 2006, about 752 Feb 16 2011
Medicine Google = neurogenome about 4,
July 11, 2002; about 12 July 14,
2003; about 24 June 7, 2004, about 121 Aug. 15, 2005, about 150 Oct. 25, 2006
nucleome: Over the last decade, a variety of technological innovations have accelerated the acquisition of knowledge concerning the regulation of gene expression. In particular, techniques have been devised that permit analysis of the behavior of essentially all genes contained within the genome. Nonetheless, we still confront the problem of dissecting the different patterns of gene expression that occur within the frequently complex interspersions of individual cell types within the tissues and organs of higher eukaryotes. This lecture will outline recent progress in the global analysis of cell- specific gene expression within complex tissues, drawing on developments in analytical cytology, particularly microarray technologies, Fluorescent Protein targeting to the nucleus, and flow cytometry. David Galbraith, Univ. of Arizona Cancer Center, International Society for Analytical Cytology, May 6-9, 2002, San Diego US http://www.isac-net.org/congresses/ISACFA/PlenarySessions.html
Google = about 12 July 11, 2002; about 31 July 14, 2003; about 24, June 7, 2004, about 53 Aug. 15, 2005, about 253 Oct. 25, 2006
-ome: According to Merriam-Webster Online from the Latin for "mass". http://www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=ome
In physics, probably starting with Faraday's ion, cation, anion, the -on suffix has tended to signify an elementary particle, later materially focused on the photon, electron, proton, meson, etc., whereas -ome in biology has the opposite intellectual function, of directing attention to a holistic abstraction, an eventual goal, of which only a few parts may be initially at hand. 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
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?" Molecular Biology & Biochemistry 474b3, Yale Univ. 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
See also D. Greenbaum et. al.
-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
An English neologism
referring to a field of study in biology,
ending in the suffix -omics such as genomics
or proteomics.
Wikipedia, accessed Feb. 20, 2006 http://en.wikipedia.org/wiki/-omics
oncogenomics: Cancer Google = about 333 July 11, 2002; about 1,070 July 14, 2003; about 3,080 June 7, 2004, about 10,600 Aug. 15, 2005, about 50,300 Oct. 25, 2006
The characterization of proteins with unknown biological function.
Gerstein Lab, Bioinformatics, Omes Table, Molecular
Biology & Biochemistry, Yale Univ. http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html
operomics: Our group has embarked on a major effort to integrate genomics transcriptomics and proteomics for the profiling of cancer tissue, an approach we refer to as Operomics. Our major goals are the molecular classification of tumors and the identification of markers for the early detection of cancer. S.M. Hanash, University of Michigan Medical Center "Integrating Genomics and Proteomics in the Post- Genome Era" Michigan State Univ. May 4, 2001 http://www.pa.msu.edu/seminars/ctss/abstracts/20010504.txt
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- 813 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]
ORFeome: The sum total of open reading frames in the genome, without regard to whether or not they code; a subset of this is the proteome. Gerstein Lab, Molecular Biology & Biochemistry, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/figures.pdf.
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. Nature Genetics 27 (3): 332- 336 Mar. 2001
Complete set of
protein-encoding open reading frames (Reboul et al, Nature Genetics,
2003) Marc Vidal, Harvard Medical School faculty
ORFeomics: C. Boone, B. Andrews, ORFeomics: correcting the wiggle in worm genes, Nature Genetics 34 (1): 8- 9, May 2003 Google = about 155 Oct. 25, 2006
paleogenomics: Genomics categories Google = about 234 Nov 6, 2005, about 576 Oct. 25, 2006
parasitome: A subset of the secretome of a parasite that mediates parasitism. Richard S. Hussey et. al,, Brazilian Journal of Plant Physiology 14:183-194, 2002 Google = about 7, Feb. 4, 2003; about 23 July 14, 2003; about 46 June 7, 2004, about 117 Aug. 15, 2005, about 318 Oct. 25, 2006 Narrower term: secretome; Related term: Gene categories parasitism genes
PathoGenome TM: Databases & software directory
pathogenomics, pathome: Molecular Medicine Google = pathogenomics about 271 July 11, 2002; about 1,240 July 14, 2003; about 1,880 June 7, 2004, about 9,580 Aug. 15, 2005, about 52,400 Oct. 25, 2006
pathome: It had become increasingly clear with the completion of the human genome project that genotyping alone will have little impact on the medical treatment of chronic diseases. To accomplish this, a better understanding of the pathophysiology of the subsets that underline many of these conditions is required. For example, subdividing hypertensive patients by intermediate phenotypes - traits that are found to be present in some but not all hypertensive subjects - has the potential to substantially increase the power of such genetic approaches. We have termed the collection of these intermediate phenotypes, a Human Hypertension Pathome Project. Gordon Harold Williams, Brigham & Women's Hospital, Boston, US "Endocrine Renal and Genetic Factors in Human and Experimental Hypertension, 2001 http://research.bwh.harvard.edu/rdbook/en18.htm
pathomics: the study of the molecular basis of infectious disease. It focuses on the changes in protein levels and other molecules that occur when a body has been exposed to a pathogen. Science & Technology Lawrence Livermore Lab, 2004 https://www.llnl.gov/str/June04/NewsJune04.html
peptaibiomics: Isolates were screened for the production of a group of polypeptide antibiotics named peptaibiotics, including its subgroups peptaibols and lipopeptaibols. Fully-grown fungal cultures on potato-dextrose agar were extracted with CH(2)Cl(2)/MeOH, and these extracts were subjected to SPE using C(18) cartridges. The methanolic eluates were analyzed by on-line LC/ESI-MS(n) coupling--a method which is referred to as 'peptaibiomics. Peptaibiomics: screening for polypeptide antibiotics (peptaibiotics) from plant-protective Trichoderma species. T. Degenkolb, et al. Chem Biodivers. 2006 Jun;3(6): 593- 610 Thanks to Willibald Schliemann for telling me about this omics.
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
N. Minamino [Peptidome: the fact- database for endogenous peptides Article in Japanese] Tanpakushitsu Kakusan Koso 46 (11 Suppl): 1510- 1517 Aug. 2001
Peptides and small proteins of a
whole organism or a subsystem (peptidome). M Schrader et. al. Peptidomics
technologies for human body fluids, Trends in
Biotechnology 19 (10 Suppl): S55- 60, Oct. 2001
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" European Journal of Biochemistry 268 (7): 1929- 1939, Apr. 2001 Google = about 174 July 11, 2002; about 404 July 14, 2003; about 700 June 7, 2004, about 4,790 Aug. 15, 2005, about 28,100 Oct. 25, 2006 Related terms: Chemistry peptidomimetic; Proteins peptides
pharmacoepigenomics: Pharmacogenomics Google = about 19 Nov 5, 2005, about 38 Oct. 25, 2006
pharmacogenome: custom chips or alternative multiplexed genotyping technologies will undoubtedly be developed for specific diagnostic needs and updated as novel pharmacogenetic variants are discovered. These types of highly multiplexed assays for individual variants provide a view into the `pharmacogenome' of an individual, Pharmacogenetics and personal genomes, Michael Wagner Per Med. 2009 November 1; 6(6): 643652.doi: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826717/ Google = about 4 July 11, 2002; about 10 July 14, 2003; about 11 June 7, 2004, about 18 Aug. 15, 2005, about 66 Oct. 25, 2006
Related terms: Pharmacogenomics pharmacometabonomics Google pharmacogenomics = about 22,400 July 19, 2002; about 37,100 July 14, 2003; about 107,000 June 7, 2004, about 414,000 Aug. 15, 2005, about 1,670,000 Oct. 25, 2006
pharmacomethylomics: John N. Weinstein "Pharmacogenomics: Teaching Old Drugs New Tricks" New England Journal of Medicine 343: 1408-1409, 2000 Google = about 13 July 11, 2002; about 91 July 14, 2003; about 131 June 7, 2004, about 106 Aug. 15, 2005, about 125 Oct. 25, 2006
pharmacophylogenomics: David B. Searls, Pharmacophylogenomics: genes, evolution and drug targets, Pharmacophylogenomics: genes, evolution and drug targets, Nature Reviews Drug Discovery 2(8) : 613- 623 Aug. 2003
Phylogenomics is a new discipline that concentrates on large scale analysis on the whole genome level of phylogeny prediction. Pharmacophylogenomics attempts to apply this knowledge to pharmacological relevant areas like for example ADME-Tox (Absorption, Distribution, Metabolism, Excretion and Toxicology). Bioinformatics, Radboud Univ. Nijmegen, Netherlands http://www.ru.nl/cmbi/english/research/computational_drug/research/item_31154/
Google = about 21 Mar. 3, 2004, about 70 Aug. 15, 2005 ,about 181 Oct. 25, 2006
pharmanome: The pharmaceutically important set of the human genome comprising whole sets of protein families, including secreted factors, all cancer cell surface antigens and small molecule targets. Five Prime Therapeutics press release, 2003 http://www.atvcapital.com/news.php?id=103 Google = about 20, June 22, 2005, about 54 Oct. 25, 2006
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://www.physiome.org/Models/xsim_modeldocs/OLD/Documents/pdf/7.1jun98.pdf
The phenotype of a
comprehensive set of mutants (ideally measuring a comprehensive set
environmental and internal states). A play on the word "phenomenon"
too. George Church Lab,
Harvard Molecular Technology Group & Lipper
Center for Computational Genetics, Harvard http://arep.med.harvard.edu/ome.html
Qualitative identification
of the form and function derived from genes, but lacking a quantitative,
integrative definition Omes Table,
Gerstein Lab, Yale http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html
See also note on variant meanings for genome, genotype and phenotype
in Genomics 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
phenomics: the systematic cataloging of phenotype terms on a genome-wide scaleis still emerging as a scientific field. A critical limitation to its growth is the lack of informatics tools to characterize, manage, and analyze phenotypes. Ontology based approach to Computational Phenomics, 2009 http://www.bioontology.org/node/525
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. 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 systems applications for protein research and biomarker discovery when a single, integrated biochip platform can be used for protein discovery through functional analysis. [Ciphergens FAQ, US] http://www.ciphergen.com/tech_doc5.html
Phenomics ® is also an automated technology trademarked by Proteus SA. http://www.proteus.fr and a linguistics term.
Google = about 544 July 11, 2002; about 1,110 July 14, 2003; about 2,840 June 7, 2004, about 9,220 Aug. 15, 2005, about 46,400 Oct. 25, 2006, about 35,200 Oct 5, 2009 Narrower term: metabolic phenomics Related terms Functional genomics function; Genomics complex diseases; Drug discovery informatics phenotypic screening
Phosphatome gene families. Arena S, Benvenuti S,
Bardelli A, Genetic
analysis of the kinome and phosphatome in cancer, Cell Mol Life Sci. 62(18):
2092- 2099, Sept. 2005
phosphatomics: some websites but no definitions? Google = about 16, Oct. 25, 2006, about 37 Feb 16 2011
phosphoproteomics : Proteomics
phylogenomics, phylome: Phylogenomics
Google =
phylogenome = about 9 July 11, 2002; about 9 June 7, 2004, about 19 Aug. 15,
2005, about 20 Oct. 25, 2006 phylogenomics about 440
July 11, 2002; about 1,260 July 14, 2004; about 3,050 June 7, 2004; about
14,700 Aug. 15, 2005, about 164,000 Oct. 25, 2006
phyloproteomics: Proteomics Google = about 15 July 11, 2002; about 24 July 14, 2003; about 46 June 7, 2004, about 64 Aug. 15, 2005, about 84 Nov 5, 2005, about 158 Oct. 25, 2006
On September 30, 2000, the National Heart,
Lung, and Blood Institute (NHLBI) launched the Programs for Genomic Applications
(PGAs) http://www.nhlbi.nih.gov/resources/pga/.
This program is a major initiative to advance functional genomic research
related to heart, lung, blood, and sleep health and disorders. The MCW program,
termed PhysGen, has been focused on understanding the genetic basis of
fundamental mechanistic pathways of the heart, lung, kidney, blood and
vasculature through development of consomic rat panels and physiological
genomics, using environmental stressors. PhysGen, Medical College of Wisconsin,
US http://pga.mcw.edu/
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
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 Google = about 156 July 11, 2002; about 793 June 7, 2004, about 3,420 Aug. 15, 2005, about 14,200 Oct. 25, 2006
The term 'physionomics' is proposed for this comprehensive physiological
profiling of the plant system, following the parallel terminology of the
molecular and biochemical 'omics' technologies. Physionomics procedures provide
a first clue to the mode of action of a new herbicide that can direct more time-
consuming and costly molecular, biochemical, histochemical or analytical studies
to identify a target site more efficiently. K.
Grossmann, What it takes to get a herbicide's mode of action. Physionomics, a
classical approach in a new complexion, Pest Manag Sci. Jan 20, 2005
Related term: functional
bioassays Google = about 326 Aug.
15, 2005, about 658 Oct. 25, 2006
Various protein
modifications finely tune the cellular functions of each protein. Understanding
the relationship between post- translational modifications and functional
changes ("post- translatomics") is another enormous project, not
unlike the human genome project. Proteomics, combined with separation technology
and mass spectrometry, makes it possible to dissect and characterize the
individual parts of post- translational modifications and provide a systemic
analysis. J Seo, KJ Lee, Post- translational modifications and their
biological functions: proteomic analysis and systematic approaches, J Biochem
Mol Biol. 37(1): 35- 44, Jan 31, 2004
promoterome: A complete set of promoters.
Marc Vidal, personal
communication, Dec. 2001
proteogenomics: The study of gene expression during the infectious cycle, in mutants or after environmental or chemical stimuli, is a powerful approach towards understanding parasite virulence and the development of control measures. Like other trypanosomatids ... With the impending completion of the Leishmania genome, global approaches surveying mRNA and protein expression are now feasible. Our laboratory has developed the Drosophila transposon mariner as a tool for trapping Leishmania genes and studying their regulation in the form of protein fusions; a classic approach in other microbes that can be termed 'proteogenomics'. SM Beverley et. al., Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling, Mitsubishi Kagaku Institute of Life Sciences (MITILS) Japan, Annual Report, 2001, Philos Trans R Soc Lond B Biol Sci. 357 (1417): 47- 53, Jan. 29, 2002 Google = about 31 July 11, 2002; about 184 June 7, 2004; about 179 March 11, 2005, about 309 Aug. 15, 2005, about 692 Oct. 25, 2006 Related term: small molecules Drug discovery & development
proteome, proteomics: Proteomics Google = proteome about 74,600 July 11, 2002; about 83,500 Sept. 18, 2002; about 159,000 Aug. 18, 2003, about 263,000 Jun 7, 2004, about 268,000 July 14, 2004, about 813,000 Aug. 15, 2005, about 7.720,000 Oct. 25, 2006 Google proteomics = about 138,000 July 11, 2002; about 162,000 Sept. 18, 2002; about 357,000 Aug. 18, 2003; about 776,000 June 7, 2004, about 842,000 July 14, 2004; about 4,680,000 Aug. 15, 2005, about 10,900,000 Oct. 25, 2006
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 D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome Research 11 (9): 1484- 1502, Sept. 2001 See also Goro Terai1, 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 Google = about 8 July 11, 2002; about 28 Jan. 6, 2004, about 58 Aug. 15, 2005, about 235 Oct. 25, 2006
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
psychiatome: Herein,
we investigate the putative relationships among and between biological and
environmental factors in psychiatric diseases, in what we call psychiatome,
inspired by the concept of diseasome. Our approach is to assess
the shared genes (via mining through genetic databanks), shared networks (using
inferred proteomics data) and shared networks of anatomical regions (i.e.
toponomics, exploiting the PubBrain tool) in such a way as to develop a unique
picture of salient inter-relationships that may subserve or be reflected by
psychiatric disorders.
Perhaps the psychiatome will provide an
adequate translational framework for both psychiatric research and practice,
being holistic and broad, rather than narrow and simplistic, even though this
promising paradigm at present is still at an early stage of its development and
implementation. Rethinking psychiatry with OMICS science in the age of
personalized P5 medicine: ready for psychiatome? Nicola Luigi
Bragazzi Philosophy, Ethics, and Humanities in Medicine 2013, 8:4 doi:10.1186/1747-5341-8-4 http://www.peh-med.com/
Google - about 1,070 Dec 2 2013
psychogenomics: Molecular Medicine Google = about 167 Nov 5, 2005, about 442 Oct. 25, 2006
portion of the genome encoding ligand reception. KA O'Connor, BL Roth, "Screening
the receptorome for plant-based psychoactive compounds", Life Sci
2005 Dec 22; 78(5): 506 -511. Epub 2005 Oct 6
Ideally, receptoromics profiling could be utilized both to identify
the molecular targets for endogenous ligands and as a drug
discovery tool. N Armbruster Blaine, Bryan L. Roth, Mining the Receptorome, J.
Biol. Chem., Vol. 280, Issue 7, 5129-5132, February 18, 2005 http://www.jbc.org/cgi/content/full/280/7/5129
The whole set of regulation components in a cell, tissue, organ, organisms, and
species. They are usually used in the context of signal transduction.
"Regulome" Wikipedia http://en.wikipedia.org/wiki/Regulome
regulome maps: Will be established for health and disease, namely, data bases for networks of regulatory gene and protein interactions, with quantitative features and alternative routes incorporated. Such maps will have many uses and will need to be extensive if scientists and physicians; are to be able to chose the best targets for an intervention. Regulomics after Genomics: A Challenge for the 21st Century, Emile Zuckerkandl, Institute of Molecular Medical Sciences, International Union of Biological Sciences http://www.iubs.org/test/bioint/41/16.htm
Inroads into the field of regulomics are already being made in the name of
genomics, proteomics, and functional genomics. Regulomics is constituted by the
study of the totality of specific molecular interactions that determine gene
expression in any given organism, and includes the topological (circuitry)
characteristics of the interaction networks as well as the quantitative
variations of their components. Regulomics after Genomics: A Challenge for
the 21st Century, Emile Zuckerkandl, Institute of Molecular Medical Sciences,
International Union of Biological Sciences http://www.iubs.org/test/bioint/41/16.htm
relevantome: See under ridiculome Google = about 1 Oct. 25, 2006
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
Biologist users and scientists approaching the field
do not have a comprehensive index of bioinformatics algorithms, databases, and
literature annotated with information about their context and appropriate use.
We suggest that the full set of bioinformatics resourcesthe
resourceomeshould be explicitly characterized and organized. A
hierarchical and machine-understandable organization of the field, along with
rich cross-links (an ontology!) would be a useful start. "Time to
organize the bioinformatics resourceome" Nicola Cannata, Emanuela Merelli,
Russ B. Altman*, PLOS Computational Biology, Dec. 2005 DOI:
10.1371/journal.pcbi.0010076 http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010076
ribonome, ribonomics, riboproteomics: RNA
Abnormality of specific ribosomal proteins causes genetic diseases and
tumorigenesis. Also, ribosomal proteins appear to have roles in addition to
those in the translation machinery (extraribosomal functions). Mutants of model
eukaryotic organisms have revealed that many ribosomal proteins are essential
for cell viability. However, the precise structure, functional role, and
regulation of each ribosomal protein in the eukaryotic ribosome are largely
unknown. . Our group has started to analyze the RNA-protein complex, human
ribosome, and its components at the level of genomics, transcriptomics,
proteomics and molecular complex. We have designated this comprehensive study 'ribosomics'.
Daita Nadano, Shinji Irie, Taka-Aki Sato, Ribosomics: A Comprehensive Study of
the Human Ribosome and its Components, 3rd ORCS International
Symposium, 2001 http://www.icube-t.co.jp/orcs2001/past/abstruct/lecture5.html
ridiculome: What does it take to turn a ridiculome into a
The complement of non-coding RNAs
RNomics: The
understanding of functional RNAs and their interactions at a genomic level.
Peter F. Stadler, Computational RNomics: The Quest for RNA Genes,
2002 http://www.tbi.univie.ac.at/research/RNomics.htm
At what biological levels are data from single-celled organisms akin to a
Rosetta stone for multicellular ones?
Gene order is not evolutionarily
Most gene expression is pleiotropic, and deletion studies
reveal that a morphological phenotype is seldom observed when these
genes are removed from the genome. These data pinpoint some general
bottlenecks in functional genomics, and they reveal the acute
emerging difficulties with data transferability above the levels of
genes and proteins, especially with complex human phenotypes. At
these higher levels the Rosetta stone analogy has almost no
applicability. However, newer transgenic technologies in Drosophila
and Mus, combined with coherency pattern analyses of gene
networks, and synthetic neural modeling, offer insights into
organismal function.
We conclude that industrially scaled robogenomics
in model organisms will have great impact if it can be realistically
linked to epigenetic analyses of human variation and to phenotypic
analyses of human diseases in different genetic backgrounds. R.
Maleszka, H. G. de Couet, George L. Gabor Miklos, Data
transferability from model organisms to human beings: Insights from the
functional genomics of the flightless region of Drosophila, PNAS
95(7): 3731-3736, March 31, 1998 http://www.pnas.org/cgi/content/abstract/95/7/3731
saccharomics: Glycosciences Google = about 60 Nov. 15, 2002, about 298 Oct. 25, 2006
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 See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome Research 11 (9): 1484- 1502, Sept. 2001
The recent sequencing of the genome of
B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported
Tjalsma et al., "Signal peptide-
dependent protein transport in Bacillus subtilis:" Microbiol Mol Biol Rev.64: (3) 515-
547 Sept. 2000
secretomics: We present a "differential secretomics analysis" as the most direct approach to identify the underlying alterations. MW Volmer et. al, Tumor suppressor Smad4 mediates downregulation of the anti-adhesive invasion-promoting matricellular protein SPARC: Landscaping activity of Smad4 as revealed by a "secretome" analysis, Proteomics. 4(5): 1324- 1334, May 2004 Google = about 12, Aug. 15, 2005, about 172 Oct. 25, 2006
separomics: Protein purification is one of the most fundamental, yet most challenging, operations in life science research and the biotech industry. Depending on the complexity of the sample, the scale of the process and the characteristics of the target protein, vastly different starting conditions can be encountered. This "universe" of starting conditions can be viewed as the working ground for Separomics: the challenge to provide a simple solution to every purification situation. ... Affinity capture is one of the most attractive procedures for isolating biomolecules from complex mixtures because it offers an efficient purification and concentration of the target in a single step. "Business Areas: Separomics" Affibody AB, Sweden http://www.affibody.se/ Google = about 56, Aug 15, 2005, about 92 Oct. 25, 2006 Related terms: Proteins, Proteomics
seromics: See autoantibodies: Cancer diagnostics & genomics
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, Feb. 5, 2001]
Google = signalome about 9 July 11, 2002; about 38 June 7, 2004, about 63 Aug. 15, 2005, about 187 Oct. 25, 2006
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, July 11, 2002 http://www.google.com did not retrieve any websites but this article (and this glossary) when searching for somatonome or somatonomics. Google = about 11, June 7, 2004 including several which seem to be unattributed copies of this glossary, about 9 Aug.. 15, 2005
static transcriptome: See under differential transcriptome
strainomics: Unbiased analyses of a
total subset of strains isolated from specific soybean-cropping areas (an
approach which could be called "strainomics") can be used to
answer various biological questions. J. Thomas-Oates, et al, A catalogue of
molecular, physiological and symbiotic properties of soybean- nodulating
rhizobial strains from different soybean cropping areas of China, Syst Appl
Microbiol. 26(3): 453- 465, Sept 2003 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14529189&query_hl=40
subcellular proteomics, subproteomics: Proteomics categories
syndromics: Molecular Medicine Google = about 76, Nov 5, 2005, about 92 Oct. 25, 2006
systeome: It
is necessary to study the behavior of the system level in order to understand
biological system as a system. The system level understanding of biological
system is an ultimate challenge in the biology which corresponds in the system
biology directly. This field is the enormous challenge that the equivalent
effort for establishing the base for the scientific research is required, and it
has also exceeded the ability of any single research group by far. Therefore,
the Systeome project was proposed as gland challenge project in the field of the
system biology. The Systeome project has the main engineering project for
measurement and software platform development. The best method is to start as an
international joint project of the scale compatible to the human genome project.
Transitioning from the
identification to the subsequent validation and prioritization of their cognate
proteins as bona fide drug targets using proteomic techniques - -a process that
could appropriately be termed targetomics -- is still very much in its infancy,
with expectations far exceeding present capabilities. M Williams, Target
Validation, Current Opinion in Pharmacology 3(5): 571- 577, Oct 2003 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14559105&dopt=Abstract
toponomics: See Proteomics
categories topological proteomics, toponomics
toxigenomics: Pharmacogenomics
toxicogenomics: Pharmacogenomics Google = about 9,650 Sept. 10, 2003; about 27,700 June 7, 2004, about 1,050 Aug. 15, 2005, about 689,000 Oct. 25, 2006
An omics field to study the totality of toxic chemicals in
cells. http://omics.org/index.php/Toxicomics.
toxome, human: the full scope of industrial pollution in humanity. HTP scientists use cutting edge biomonitoring techniques to test for industrial chemicals. Environmental Working Group, Human Toxome Project http://www.ewg.org/sites/humantoxome/
transcriptome: The population of mRNA transcripts in the cell, weighted by their expression levels. Gerstein Lab, Molecular Biology & Biochemistry, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/figures.pdf.
Complement of mRNAs transcribed from a cells genome. Proteomics, transcriptomics: what's in a name? Nature 402:715 Dec 16, 1999
The full complement of activated genes, mRNAs, or transcripts in a particular tissue at a particular time http://www.ornl.gov/TechResources/Human_Genome/glossary/glossary_t.html
The set of genes expressed from the yeast
genome, VE Velculescu et al. Characterization of the yeast transcriptome Cell 88: 243-251,
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.
transductome: We call this superset of signalling pathways the transductome. Institute of Biotechnology, University of Helsinki, Finland, 2005 http://ekhidna.biocenter.helsinki.fi:9801/research Google = about 18, Oct. 25, 2006
Transgenome: Our
new resource, TRANSGenomeTM provides an overall annotation of the human genome
with emphasis on its regulatory characteristics. We show that the occurrence of
sequence patterns with regulatory potential may be supported by, but cannot be
fully explained by either the GC content of a whole chromosome or its putative
promoter regions, nor by the information content of the patterns. Composition-
sensitive analysis of the human genome for regulatory signals, O.V. Kel-
Margoulis, D. Tchekmenev et. al., In Silico Biol. 2003;3 (1-2):145- 171
transgenomics: Transgenomics Initiative (TGS) is a program that concentrates on developing novel traits and agriculturally relevant characteristics where novel phenotypes are generated through changes in gene regulation. Transgenomics is a three-step process. First, we capture a large number of rice genomic regions using an Enhancer Trap system that employs a transcriptional activator to generate Tran activator Facilitated Enhancer Trap (TAFFETA) lines. Second, we insert into the rice genome a number of copies of an Upstream Activating Sequence (US) that is the target for binding by the Tran activator. Third, crosses between the TAFFETA lines and the US lines are expected to change expression patterns of a plants own genes resulting in Gain of Function mutations. The controlled manipulation of expression of practically any gene in rice offers an opportunity to develop and test specific hypotheses of linkages between gene expression and the resulting phenotype. Sri Kermit et. al, Transgenomics: Novel Technology for Genomics and Crop Improvement, Plant, Animal & Microbe Genomes X Conference, Jan 12-16, 2002, San Diego CA http://www.intl-pag.org/10/abstracts/PAGX_P128.html Google = about 260 Apr. 22, 2003; about 444 June 7, 2004, about 513 Aug. 15, 2005, about 958 Oct. 25, 2006
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 favored by computational biologists, is a list of
all the proteins encoded in the genome (Wasteland 1999, Do little 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
See also D. Greenbaum et. al. Interrelating different types of genomic
data, from proteome to secretome: 'oming in on function" Genome
Research 11 (9): 1484- 1502, Sept. 2001
transportome: The population of the gene products that are transported; this includes the secretome. Mark Gerstein "What is Bioinformatics? Omes Table" Molecular Biology & Biochemistry 474b3, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html Google = about 14 July 11, 2002; about 40 June 7, 2004, about 140 Aug. 15, 2005, about 367 Oct. 25, 2006 Narrower term: secretome
unfoldome: a set of unstructured proteins in a proteome. Intrinsically Disordered Proteins Gordon Research Conferences 2010 http://www.grc.org/programs.aspx?year=2010&program=intrinsic Related terms: foldome, Protein structures: intrinsically disodered proteins, protein folding
is the field that focuses on the unfoldome. The unfoldome is the set of IDPs,
which are also known as natively unfolded proteins, hence the unfoldome. We are
also using unfoldome to cover segments or regions of proteins that remain
unfolded in the functional state. Unfoldomics considers not only the identities
of the set of proteins and protein regions in the unfoldome of a given organism,
but also their functions, structures, interactions, evolution, etc. Because IDPs
and IDRs are highly abundant in nature (~50% eukaryotic proteins are either
entirely disordered or contain long disordered regions), have amazing structural
variability and possess a very wide variety of functions, we thought it
appropriate to name this realm of proteins the unfoldome, with unfoldomics
reflecting the totality of the phenomena associated with IDPs and IDRs.
[Intrinsically disordered proteins (IDPs) and intrinsically disordered
regions (IDRs)] BMC
Genomics. 2009; 10(Suppl 1): S7. Published online 2009 July 7. doi: 10.1186/1471-2164-10-S1-S7
PMCID: PMC2709268 Unfoldomics of human diseases: linking protein
intrinsic disorder with diseases Uversky VN et. Al. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709268/
unknome: At present, a large proportion of genes can only be described as members of the unnamed - 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 See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome Research 11 (9): 1484- 1502, Sept. 2001 Google = about 81 Aug. 15, 2005, about 164 Oct. 25, 2006
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 "vaccinate" to induce antibodies, judging the accuracy of
expression, immunizing mice with each plasmid, and ultimately, developing a cultigens
DNA vaccine. [Ilene Schneider and Paul Shavlik "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
vaccinomics: Using bioinformatics and genomics for vaccine development. Tom Hollow "Clad against all cades" Scientist 14 (18): 1 Sep. 18, 2000 http://www.the-scientist.com/yr2000/sep/hollon_p1_000918.html Google = about 24 July 11, 2002; about 44 June 7, 2004, about 222 Aug. 15, 2005, about 120 Oct. 25, 2006
variome: Wikipedia
Variome TM:
is/was a structural pharmacogenomics database.
variomics: Study of variants of DNA, RNA and proteins. How/ does this relate to population genomics? Related terms: SNPs & other genetic variations Google = about 20, Aug. 15, 2005, about 110 Oct. 25, 2006
VeloceGenomics: The aim of this study is to test the predictive power of in vivo multigrain RNA expression profiling in identifying the biologic activity of molecules... a strategy of coupling in vivo compound testing with genomic technologies. The process enables prediction of the mechanism of action and, coupled with other relevant data, prediction of the suitability of compounds for advancement in the drug development process. R. Papuan et. al, "VeloceGenomics: An Accelerated in Vivo Drug Discovery Approach to Rapidly Predict the Biologic, Drug- Like Activity of Compounds, Proteins, or Genes" Pharma Res. 2005 Aug 13; [Epub ahead of print] Google = about 96 Oct. 25, 2006
Refers to the use of viruses and viral gene transfer to explore the complexity
arising from the vast array of new targets available from the human and murine
genomes. Indeed, access to large numbers of genes using viral vectors is a key
tool for drug discovery and drug delivery. . During the last 12 years alone,
there have been over 26,000 publications on virus vectors. Many of them have
been found useful in target validation, assay development, and evaluation in in
vivo models and gene therapy. MT Lotze, TA Kost, Viruses
as gene delivery vectors: application to gene function, target validation, and
assay development, Cancer Gene Therapy 9(8): 692- 699, August 2002
yeast localizome: See under Proteins protein localization
Omics Gateway http://www.nature.com/omics/index.html
Current content http://www.nature.com/omics/current/subject/index.html
biology: The omes puzzle, Monya Baker
494, 416419, (28 February 2013) doi:10.1038/494416a 27
February 2013 http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484
How to look for other unfamiliar terms
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.
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