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You are here Biopharmaceutical Glossary homepage/Search > Applications > Biopharmaceutical -Omes & -omics - biopharmaceutical -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 Google = about 38, Nov 5, 2005. about 65 Oct. 25, 2006 behaviourome: Behaviourome/ Mental Map Project, Eubios Ethics Institute, 2003 http://www2.unescobkk.org/eubios/menmap.htm
Google = about 160 August 9, 2005, about 369 Oct. 25, 2006 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] Google = about 76 July 11, 2002; about 297 Sept. 10, 2003, about 729 August 9, 2005, about 321,000 Oct. 25, 2006 bibliomics: A subset of high quality and rare information, retrieved and organized by systematic literature- searching tools from existing databases, and related to a subset of genes functioning together in '-omic' sciences. Rihn BH, Vidal S, Nemurat C, Vachenc S, Mohr S, Mazur F, Houdry P, Grandjean F, Visvikis S, Ducloy J., From transcriptomics to bibliomics, Medical Science Monitor. 2003 Aug; 9(8): MT89- 95 Google = about 80 Nov. 11, 2003l, about 10,200 August 9, 2005, about 288,000 Oct. 25, 2006 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. Google = about 96,700 July 11, 2002, about 500,000 Aug. 9, 2005, about 1,490,000 Oct. 25, 2006 BIOME, University of Nottingham, UK http://biome.ac.uk/ A consortium of content providers collaborating on a catalogue of Internet resources, database hosting. 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 Google = about 662 Aug.9, 2005, about 16,900 Oct.25, 2006 cancer fragmentomics, cancer genomics, cancer immunome, cancer immunomics, cancer proteomics, cancer transcriptomes- human: Cancer genomics glossary Google = about 41,800 Aug. 9, 2005, about 177,000 Oct. 25, 2006 cardiogenomics, Cardiome Project: Molecular Medicine glossary Google = about 259 July 11, 2002 about 4,090 July 14, 2003, about 49,000 Aug. 9, 2005, about 148,000 Oct. 25, 2006 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 glossary; Functional genomics glossary cellomics: Studying cell function and drug impact at the level of the cell. [E. Russo "Merging IT and biology" Scientist 14(23): 8 Nov. 27, 2000] Cellomics™ information: Investigation of molecules and their interactions within cells to create knowledge of cell functions. [Cellomics, Inc.] 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 Google = about 34,800 Aug. 10, 2005, about 5,840 Oct. 25, 2006 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 Google = about 495 Nov 5, 2005, about 503 Oct. 25, 2006 Related terms: chemical proteomics, chemiproteomics: Chemistry & biology glossary CHOmics: Global studies of carbohydrates. [Snowdeal.org {bio,medical}informatics. Sept. 14, 2001] http://snowdeal.org/section/informatics/archives/2001_09_09_index.html chromatinomics:
The field of stem cell biology is currently being redefined. Stem cell
(hematopoietic and non-hematopoietic) differentiation has been considered
hierarchical in nature, but recent data suggest that there is no progenitor/stem
cell hierarchy, but rather a reversible continuum. The stem cell (hematopoietic
and non-hematopoietic) phenotype, the total differentiation capacity
(hematopoietic and non-hematopoietic), gene expression as well as other stem
cell functional characteristics (homing, receptor and adhesion molecule
expression) vary throughout a cell-cycle transit widely. This seems to be
dependent on shifting chromatin and gene expression with cell-cycle transit. The
published data on DNA methylation, histone acetylation, and also RNAi, the major
regulators of gene expression, conjoins very well and provides an explanation
for the major issues of stem cell biology. … We are entering a new era of stem
cell biology the era of Google = about 4 Nov 5, 2005, about 59 Oct. 25, 2006 chromonome: 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] Google = about 1 Apr 22, 2003 about 7 July 14, 2003; about 3 April 11, 2005, about 6 Aug. 10, 2005, about 81 Oct. 25, 2006 chromonomics: The Genome Project will give us the genetic sequence, but understanding how that raw data is used in the body will require a better understanding of chromosomes, said speaker Huntington Willard of Case Western Reserve University. Willard spoke of his attempts to build artificial human chromosomes, emphasizing how much is left to learn about how chromosomes work. Only half- joking, Willard suggested the most exciting field in genetics is not genomics, but "chromonomics." Institute of Genetic Medicine Symposium, Health Sciences Campus, Univ. of Southern California, 1998 http://www.usc.edu/hsc/info/pr/1vol4/403/igm.html Google = about 5 Apr. 22, 2003. about 20 Aug. 10, 2005, about 81 Oct. 25, 2006 chronome, chronomics: Molecular Medicine glossary Google = chronome about 380
July 11, 2002, about 920 Aug. 10, 2005, about 18,400 Oct. 25, 2006 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) Google = about 115 Nov 5, 2005, about 182 Oct. 25, 2006 clinomics: Molecular Medicine glossary Google = about 119 July 11, 2002, about 663 Aug. 10, 2005, about 642 Oct. 25, 2006 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 Google = about 136 July 11, 2002 about 75 July 14, 2003, about 212 Aug. 10, 2005, about 386 Oct. 25, 2006 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 Google = about 68 Aug. 10, 2005, about 125 Oct. 25, 2006 Broader term: RNomics 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 Google = about 5 Nov 5, 2005, about 17, Oct. 25, 2006 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 Google = about 30 July 11, 2002 about 42 July 14, 2003; about 66 June 7, 2004, about 149 Aug. 10, 2005, about 309 Oct. 25, 2006 Related terms: NMR & X-ray crystallography glossary. cytochromics: Consisted
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 Google = about 11 July 11, 2002 about 28 July 14, 2003, about 97 Aug. 10, 2005, about 218 Oct. 25, 2006 Related term: Cell biology glossary 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 Google = about 267 July 11, 2002 about 790 July 14, 2003, about 7,200 Aug. 10, 2005, about 37,900 Oct. 25, 2006 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 Google = about 49 July 14, 2003; about 560 Apr. 25, 2005, about 580 Aug. 10, 2005, about 822 Oct. 25, 2006 degradomics: 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 http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrm/journal/v3/n7/abs/nrm858_r.html Google = about 30 July 11, 2002 about 168 July 14, 2003; about 242 April 25, 2005, about 367 Aug. 10, 2005, about 641 Oct. 25, 2006 Related term: Microarrays categories substrate chips diagnomicsTM: Molecular Medicine glossary Google = about 106 July 11, 2002 about 80 July 14, 2003, about 156 Aug. 10, 2005, about 575 Oct. 25, 2006 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. economics: An important aspect of the "omics" family as well. Business of biopharmaceuticals glossary ecotoxicogenomics: Genomics categories eicosanomics: M Balazy, Eicosanomics: targeted lipidomics of eicosanoids in biological systems, Prostaglandins Other Lipid Mediat. 73(3-4): 173- 180, April 2004 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15287150&query_hl=25 But what does eicosanomics mean? Google = about 44, Nov. 5, 2005, about 92 Oct. 25, 2006 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 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11711195&query_hl=2 Google = about 4180 Nov. 7, 2005, about 3,250 Oct. 25, 2006 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 Google = about 116, Nov. 5, 2005, about 294 OCt. 25, 2006 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] Google = about 4 July 11, 2002; about 19 July 14, 2003, about 89 Aug. 10, 2005, about 75 Oct. 25, 2006 epigenome: A set of what may be hundreds of genes whose function is determined by [genetic] imprinting. [Post Gazette News Bar Harbor, Maine genetics seminar, July 26, 2000] http://www.post-gazette.com/healthscience/20000726heredity1.asp Cytosine methylation [Stephan Beck, Alexander Olek, The Epigenome: Molecular Hide and Seek, Wiley, 2002 http://www.wiley.com/cda/product/0,,3527304940,00.html Epigenome Network of Excellence http://www.epigenome-noe.net/ Research groups and teams from 10 European countries, under a 12.5 MC grant from the European Union Framework 6 Programme Google = about 200 July 11, 2002; about 604 July 14, 2003; about 2,940 June 23, 2004, about 12,500 Aug. 10, 2005, about 111,000 OCt. 25, 2006 epigenomics: A whole genome approach to epigenesis and epigenetics. “An approach that views these [imprinting, metabolic networks, genetic hierarchies in embryonic development, and epigenetic mechanisms of gene activation in cancer] and other complex phenotypes from the genomic level down, rather than from the genetic level up, can provide powerful insights into the functional interrelationships of genes in health and disease. [S Beck, A Olek and J Walter “From genomics to epigenomics” Nature Biotechnology 17 (12):1144 Dec 1999] Takes a whole-genome approach to studying environmental or developmental epigenetic effects, primarily DNA methylation, on gene function. Thus, epigenomics focuses on those genes whose function is determined by external factors. Brush up on your 'omics, Chemical & Engineering News, 81(49): 20, Dec. 2003 http://pubs.acs.org/cen/coverstory/8149/8149genomics1.html Google = about 3050 July 11, 2002; about 8,090 June 22, 2004, about 84,100 Aug. 10, 2005, about 204,000 Oct. 25, 2006 Related terms: Expression glossary; Gene definitions epigenetics epigenotype:
Patients with disorders involving imprinted genes such
as Angelman syndrome (AS) and Prader- Willi syndrome (PWS) can have a mutation in
the imprinting mechanism. Previously, we identified an imprinting center (IC)
within chromosome 15q11-ql3 and proposed that IC mutations block resetting of
the imprint, fixing on that chromosome the parental imprint (epigenotype) on
which the mutation arose. [S Saitoh, "Minimal definition of the imprinting
center and fixation of chromosome 15q11-q13 epigenotype by imprinting
mutations" Google = about 143 July 11, 2002 about 350 July 14, 2003; about 831 June 22, 2004, about 830 Aug. 10, 2005, about 18,000 Oct. 25, 2006 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/ Google = about 94, Apr. 22, 2003 about 87 July 14, 2003; about 974 June 22, 2004, about 16,200 Aug. 10, 2005, about 173,000 Oct. 25, 2006 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 Google = about 71, Nov 6, 2005, about 108 Oct. 25, 2006 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 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. Google = about 5 Aug. 21, 2002 about 20 July 14, 2003; about 42 June 22, 2004, about 602 Aug. 10, 2005, about 643 Oct. 25, 2006 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 Google = about 118 Oct. 25, 2006; about 333 Oct 26, 2007 fluxome: A recently developed methodology for metabolic flux ratio (METAFoR) analysis ... can also directly reveal active metabolic pathways. Generation of fluxome data arrays by use of the METAFoR approach is based on two- dimensional 13C-1H correlation nuclear magnetic resonance spectroscopy with fractionally labeled biomass and, in contrast to metabolic flux analysis, does not require measurements of extracellular substrate and metabolite concentrations. [U. Sauer "Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism" Journal of Bacteriology 181 (21): 6679- 88, Nov. 1999] Google = about 10 July 11, 2002; about 156 June 7, 2004, about 449 Aug. 10, 2005, about 961 OCt. 25, 2006 fluxomics: Integration of metabolic pathway engineering and fermentation production technologies is necessary for the successful commercial production of chemicals. The 'toolbox' to do pathway engineering is ever expanding to enable mining of biodiversity, to maximize productivity, enhance carbon efficiency, improve product purity, expand product lines, and broaden markets. Functional genomics, proteomics, fluxomics, and physiomics are complementary to pathway engineering, and their successful applications are bound to multiply product turnover per cell, channel carbon efficiently, shrink the size of factories (i.e., reduce steel in the ground), and minimize product development cycle times to bring products to market. [G. Chotani et. al. "The commercial production of chemicals using pathway engineering" Biochim Biophys Acta 1543 (2): 434- 455, Dec. 29, 2000]. Google = about 5 July 11, 2002; about 32 July 14, 2003, about 177 Aug. 10, 2005, about 571 Oct. 25, 2006 foldome: The population of gene products classified through their tertiary structure. [Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001] http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf 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 See also NIGMS Structural Genomics Initiatives http://www.nigms.nih.gov/funding/psi.html Google = about 14, July 11, 2002; about 22 July 14, 2003, about 68 Aug. 10, 2005, about 122 Oct. 25, 2006 Related terms: Protein structure glossary, Structural genomics glossary foldomics: Google = about 9, Aug. 10, 2005, about 59 Oct. 25, 2006 fragmentome: Low molecular weight metabolite, protein and peptide fragments being explored as potential cancer biomarkers. Google = about 22 June 7, 2004, about 52 Aug. 10, 2005, about 136 Oct. 25, 2006 fragmentomics: 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 fragmentomics http://abstracts.imsc2006.org/abstract.php?ID=1037 Google = about 3 Oct. 25, 2006 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 Google = about 87 Nov 5, 2005, about 138, Oct. 25, 2006 Broader term: lectinomics 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 Google = about 20 July 11, 2002; about 37 July 14, 2003; about 54 May 25, 2004, about 437 Aug. 10, 2005, about 4,980 Oct 25, 2006 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 Google = about 7 July 11, 2002; about 14 July 14, 2003; about 147 May 25, 2004, about 850 Aug. 10, 2005, about 451 Oct. 25, 2006 functionomics: Sometimes used as a synonym for functional genomics, has been trademarked by Regeneron Pharmaceuticals FunctionomicsTM Google = about 131 Aug. 10, 2005 galectinomics: Cancer genomics glossary genome, genomics: Genomics glossary Google = genome about 1,710,000
July 11, 2002, about 3, 680,000 July 14, 2003, about 22,400,000 Aug. 15, 2005,
about 80,700,000 Oct. 25, 2--6 glycogenomics,
glycome, glycomics: Glycosciences glossary Google = glycome about 73
July 11, 2002, about 242 July 14, 2003, about 870 Aug. 15, 2005, about 19,900
Oct. 25, 2006 GPCRomics: The GPCR family of proteins has traditionally provided the pharmaceutical industry with a rich source of targets for drug discovery. The recent sequencing of the human genome has led to the compilation of the complete catalog of human GPCRs. Current GPCR research focuses on (1) determining which members of this family represent opportunities for therapeutic intervention and (2) how to efficiently identify small molecule modulators of these targets for drug development. GPCRomics is defined as the application of a wide range of technologies to this research effort. GPCRomics: Comprehensive Target Evaluation of a Protein Family, Dr. Marvin Bayne, Vice President, Discovery Technologies, Schering- Plough Corporation GPCRs: From Orphan to Blockbuster, June 9-10, 2003, Boston MA Google = about 11 Aug. 10, 2005, about 40 Oct. 25, 2006; about 12 Apr 6. 2007 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 Google = about 12 Nov 7, 2005, about 20 Oct. 25, 2006 immunogenomics: Molecular Medicine glossary Google = about 211 May 8, 2003; about 600 Apr. 28, 2004; about 17,300 Nov. 7, 2005, about 33,700 Oct. 25, 2006 immunome: The sum total of the immunodominant proteins in an organism. [Parasitology Group, University of Wales, Aberystwyth UK, April 2000] http://www.aber.ac.uk/~mpgwww/Proteome/Proteome.html The totality of rearranged antibody and antigen receptor genes present in all living humans. The presently chronicled set of all sequenced human immunoglobulin and antigen receptor gene rearrangements and mutations if of course an infinitesimally small subset of the total human immunome, and can thus be thought of as the “working immunome’. To the extent that somatic gene rearrangements may also be discovered someday in other, non- lymphoid cells, ... the immunome should properly be regarded as a specific, though probably major, case with in the broader concept of the “somatonome”. [T Pederson “The immunome” Molecular Immunology 36 (15-16): 1127-1128 Oct.- Nov. 1999] Google = about 74 July 11, 2002; about 340 July 14, 2003, about 827 Aug. 15, 2005, about 33,900 Oct. 25, 2006 Narrower term: Cancer genomics glossary cancer immunome Google = about 75 July 14, 2003, about 280 Aug. 15, 2005, about 824 Oct 25, 2006 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 today’s humans. [T Pederson “The immunome” Molecular Immunology 36 (15-16): 1127-1128 Oct. - Nov. 1999] Immunomics ™ has been trademarked by Beckman Coulter, referring to cellular immune response to achieve direct ex vivo quantitation of antigen- specific T cells. http://www.beckmancoulter.com/Immunomics/default.asp Google = about 171 July 11, 2002; about 389 July 14, 2003, about 856 Aug. 15, 2005, about 32,200 Oct. 25, 2006 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 Google = about 631 Aug. 15, 2005, about 10,100 Oct. 25, 2006 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 Google = about 26, Aug. 15, 2005, about 51 Oct. 25, 2006 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 inomics: The study of inositol signaling molecules (ISMs) and their role in regulating cellular functions. Inologic, Inc. http://www.inologic.com/company.html integromics: High-throughput, multiplexed technologies – including microarrays -- are changing the way we think about development of new diagnostics and new therapeutic agents. But the most profound changes will come from use of such technologies in combination to obtain an integrated picture at the DNA, RNA, protein, tissue, and pharmacological levels. Microarrays in biomedical research: Genomics, proteomics, and bioinformatics. Dr. John N. Weinstein, Senior Research Investigator, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health Microarrays in Biomedical Research, Microarrays in Medicine, April 26-27, 2004, Boston MA [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, May 2004, accessed Apr. 5, 2005 http://discover.nci.nih.gov/host/weinsteinmain.html A Spanish life sciences informatics company http://www.integromics.com/index.php Google = about 87 July 3, 2003; about 245 Mar. 22, 2004, about 457 Aug. 15, 2005, about 755 Oct. 25, 2006 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] Google = about 272 July 11, 2002; about 1,430 July 14, 2003, about 44,200 Aug. 10, 2005; about 237,000 Oct. 25, 2006 Related terms: phenome, transcriptome; Proteomics glossary 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 Google = about 23 July 11, 2002; about 182 July 14, 2003, about 2,320 Aug. 10, 2005, about 24,400 Oct. 25, 2006 invariome: 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 : http://genomebiology.com/2007/8/12/R265 Google = about 28 Jan.
31, 2008 [4 in English, none for invariomics] Google = about 161 Oct. 10, 2003, about 283 Aug. 15, 2005, about 1,170 Oct. 25, 2006 ionomics: We describe here the use of mineral nutrient and trace element profiling as a new tool to determine the biological significance of connections between a plants genome and its elemental- profile. Using inductively- coupled plasma mass spectrometry (ICP-MS) we have quantified Li, Na, Mg, P, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd and Pb in shoots of 8,300 fast neutron mutagenized Arabidopsis thaliana plants consisting of 4747 M2 plants (representing 2373 M1 parental lines) and 320 M3 families selected in the M2 generation for their modified elemental- profiles. B Lahner et. al., Arabidopsis Ionomics Database, Center for Plant Stress Physiology, Purdue Univ., US http://hort.agriculture.purdue.edu/ionomics/database.asp Google = about 418 Oct. 10, 2003, about 455 Aug. 15, 2005, about 2,530 Oct. 25, 2006 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://www.kinase.com/ 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/ Google = about 869 July 14, 2003, about 8,750 Aug. 15, 2005, about 58,100 Oct. 25, 2006 Related terms: Proteomics categories kinase proteomics Protein categories protein kinases 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 Google = about 21 July 11, 2002; about 42 July 14, 2003, about 352 Aug. 15, 2005, about 793 Oct. 25, 2006 Related term: Protein categories protein kinases 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 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12223267&dopt=Abstract Google = about 100 Nov 5, 2005, about 196 Oct. 25, 2006 Narrower term: functional lectinomics ligandomics: Complete set of organic small molecules. Glen A. Evans "Designer Science and the 'omics revolution" Nature Biotechnology 18 (2): 127, April 2000 Google = about 8 July 11, 2002; about 19, July 14, 2003, about 168 Aug. 15, 2005, about 2,830 lipidomics:
A rapidly expanding research field in which multiple techniques are utilized to
quantitate the hundreds of chemically distinct lipids in cells and determine the
molecular mechanisms through which they facilitate cellular function. Recent
developments in electrospray ionization mass spectrometry (ESI/MS) have made
possible, for the first time, the precise identification and quantification of
alterations in a cell's lipidome after cellular perturbations. X Han, RW Gross,
Global analyses of cellular lipidomes directly from crude extracts of biological
samples by ESI mass spectrometry: a bridge to Lipidomics, Journal of Lipid
Research 44(6): 1071- 1079. Epub 2003 Apr 1; June 2003 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12671038&query_hl=34 Google = about 22,000 Nov. 5, 2005, 51,100 Oct. 25, 2006 lipoproteomics: Molecular Medicine glossary Google = about 4 July 11, 2002; about 11 July 14, 2003, about 36 Aug. 15, 2005, about 245 Oct. 25, 2006 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 http://www.iscb.org/ismb2004/posters/nakao-mitsuteruATaist.go.jp_879.html Google = about 19 July 11, 2002; about 55 July 14, 2003, about 218 Aug. 15, 2005, about 541 Oct. 25, 2006 Related terms: Gene definitions gene
localization, localize, locus; Proteins: protein
localization; Proteins: subcellular localization localizome maps: Maps, genomic & genetic glossary metabolic phenomics: Schilling CH et. al. "Towards Metabolic Phenomics: Biotechnology Progress 15:288 -295, 1999 Google = about 77 July 14, 2003, about 103 Aug. 15, 2005, about 162 Oct. 25, 2006 metabolome: The quantitative complement of all the low molecular weight molecules present in cells in a particular physiological or developmental state. [Parasitology Group, University of Wales, Aberystwyth UK, April 2000] http://www.aber.ac.uk/~mpgwww/Metabol/Metabol.html The entire complement of all the small molecular weight metabolites inside a cell suspension (or other sample) of interest. Metabolomics, Douglas Kell, Bioanalytical Sciences Group, Univ of Manchester http://dbk.ch.umist.ac.uk/metabol.htm Total metabolite pool ("metabolome") analysis offers a means of revealing novel aspects of cellular metabolism and global regulation. [H. Tweeddale "Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis" Journal of Bacteriology 180 (19): 5109- 5116, Oct. 1998] Google = about 948 July 11, 2002; about 2, 350 July 14, 2003, about 26,100 Aug. 10, 2005, about 153,000 Oct. 25, 2006 Related terms Cell biology glossary metabolite; In silico & Molecular modeling glossary: in silico cell, virtual cell metabolomics: The study of the metabolite profiles in biological samples, is growing amidst the current shift toward translational research. Although there is some debate over what the field should actually be called, scientists are pushing forward to find uses for metabolomic profiling, a clinical option that is comparatively cheap and noninvasive. Charles W. Schmidt, Metabolomics: What's happening downstream of DNA, EHP online Environmental Health Perspectives, Toxicogenomics http://ehp.niehs.nih.gov/txg/members/2004/112-7/focus.html?section=toxicogenomics General aim of metabolomics is to identify, measure and interpret the complex time-related concentration, activity and flux of endogenous metabolites in cells, tissues, and other biosamples such as blood, urine, and saliva; here metabolites include small molecules that are the products and intermediates of metabolism, as well as carbohydrates, peptides, and lipids. CRISP Thesaurus, NIH http://crisp.cit.nih.gov/Thesaurus/00012860.htm Due to pleiotropic effects, the effect of a single mutation may lead to the alteration of metabolite levels of seemingly unrelated biochemical pathways. This is especially liable to happen if genes are constitutively overexpressed or anti- sense inhibited. A comprehensive and quantitative analysis of all metabolites could help researchers understand such systems. Since such an analysis reveals the metabolome of the biological system under study, this approach should be called metabolomics. Analogous to proteins and proteomics, metabolomics, or metabonomics, is the study of all the metabolites of a cell or organism. Identifying and quantifying these components helps to reveal cellular regulation, pathways, activity, and response under normal and other conditions. Brush up on your 'omics, Chemical & Engineering News, 81(49): 20, Dec. 2003 http://pubs.acs.org/cen/coverstory/8149/8149genomics1.html 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.wiley.co.uk/wileychi/genomics/fiehn.pdf Metabolic control and regulation at the single cell level. [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 The presented data illustrate the potential of the 19F 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] Google = about 1670 July 11, 2002; about 4, 960 July 14, 2003; about 16,500 May 28, 2004, about 105,000 Aug. 15, 2005, about 819,000 Oct. 25, 2006 Related terms metabonomics; Functional genomics glossary metabolic profiling; Mass spectrometry glossary, NMR glossary See also Pharmacogenomics glossary metabonomics/metabolomics 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] Wikipedia http://en.wikipedia.org/wiki/Metabonomics Google = metabonome about
18 July 11, 2002, about 55 July 14, 2003, about 161 Aug. 15, 2005, about 479
Oct. 25, 2006 Related terms Functional genomics; Pharmacogenomics See also Metabolic engineering glossary metabonomics Narrower term: pharmacometabonomics: Metabolic engineering glossary See under metabonomics 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 216–217: 583–595 accessed Oct. 25, 2006 Google = about 21, Oct. 10, 2003, about 173 Aug. 15, 2005, about 574 Oct. 25, 2006 metallomics: The study of the entirety of the content of inorganic species within a cell or tissue- type. And whereas a genome tells you what genes are where in an organisms chromosome, 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's Research Interests, Bioinorganic Chemistry, Bioelectrochemistry, Biophysical Chemistry http://people.bu.edu/elliott/sjeresearch.html Google = about 16, Oct. 10, 2003, about 371 Aug. 15, 2005, about 870 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 The methylation pattern of the genome. It comprises all positions of methylated cytosine (mC) on healthy DNA. Epigenomics AG, Germany, Glossary http://www.epigenomics.com/glossary.php Google = about 29 July 11, 2002; about 125 July 14, 2003; about 169 June 7, 2004, about 265 Aug. 15, 2005, about 17,900 Oct. 25, 2006 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 Google = about 7 July 11, 2002; about 88 July 14, 2003; about 151 June 7, 2004; about 203 May 9, 2005, about 256 Aug. 15, 2005, about 406 Oct. 25, 2006 microbiome: The Microbiome is the full collection of microbes (bacteria, fungi, viruses, etc.) that naturally exist within the human body. Initiatives in this area would focus on developing a deeper understanding of these c |
chromatinomics.
We are one step closer to the practical use of cellular therapy for degenerative
diseases. Jan Cerny, Peter J Quesenberry, Chromatin remodeling and stem cell
theory of relativity, J. Cell. Physiol. 201: 1-16, 2004