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-Omes and -omics glossary & taxonomy
Evolving terminology for emerging technologies

Comments? Revisions? Suggestions?
Mary Chitty MSLS
Last revised July 10, 2019

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

Drug discovery & development term index: Finding guide to terms in these glossaries  Site Map
Related glossaries include Functional Genomics, Genomics, Pharmacogenomics,  Proteomics, Structural Genomics

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,

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,  

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

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 

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

a community of plants and animals that have common characteristics for the environment they exist in. They can be found over a range of continents. Biomes are distinct biological communities that have formed in response to a shared physical climate.[1][2] "Biome" is a broader term than "habitat"; any biome can comprise a variety of habitats. While a biome can cover large areas, a microbiome is a mix of organisms that coexist in a defined space on a much smaller scale. For example, the human microbiome is the collection of bacteria, viruses, and other microorganisms that are present on or in a human body.[3] A 'biota' is the total collection of organisms of a geographic region or a time period, from local geographic scales and instantaneous temporal scales all the way up to whole-planet and whole-timescale spatiotemporal scales. The biotas of the Earth make up the biosphere. Wikipedia accessed 2018 Sept 4

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

biomics: Perhaps someday all things biological will be classified and jammed into an enormous database -- leading to some hypothetical metadiscipline called biomics.  Gary Styx “Parsing Cells” Scientific American 281 (1): 35-36 July 1999 

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   

cardiogenomics, Cardiome Project: Molecular Medicine  

cellome: is the whole set of biological entities within cells and their interactions in the cell, and the totality of biological cells. They are both physical and informational. Proteins are major components of the cellome. The cellome concept is derived from the understanding that cells as a whole, rather than simply their DNA or RNA, can be used for therapeutic purposes. As a distinct group concept, cellome refers to cells and their genetic materials kept as a resource for biotechnology
Related terms: Cell biologyFunctional 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

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 Thanks to Heike Aßmus, University of Rostock for alerting me to this -ome. 

chemogenomics: Chemistry  

CHOmics: comprehensive approaches to biology … for carbohydrates  John N. Weinstein "Pharmacogenomics: Teaching Old Drugs New Tricks" New England Journal of Medicine 343: 1408-1409, 

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 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   

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 

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

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  

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  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]  

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    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 

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   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  

crystallomics:  Production of highly purified protein samples and diffraction quality crystals. [Joint Center for Structural Genomics, Oct. 2000]  

Related terms: NMR & X-ray crystallography.

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

cytome:  the cellular systems, subsystems, and functional components of the body. The cytome is the collection of the complex and dynamic cellular processes (structure and function) underlying physiological processes. It describes the structural and functional heterogeneity of the cellular diversity of an organism. Wikipedia accessed 2018 Feb 25   
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 

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  

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   
Related term: Microarrays categories substrate chips

diagnomics: Molecular diagnostic testing that provides patient-specific information for use in decision-making;  diagnomics are also defined as molecular diagnostic markers with prognostic and economic 
 Segen's Medical Dictionary. © 2012 Farlex, Inc.

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 as the originator of this phrase. 

economics: An important aspect of the "omics" family as well. Business of biopharmaceuticals

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): 602–606. 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:  Envirome In genetic epidemiology, an envirome the total set of environmental factors, both present and past, that affect the state, and in particular the disease state, of an organism.[1] The study of the envirome and its effects is termed enviromics. The term was first coined in the field of psychiatric epidemiology by J.C. Anthony in 1995.[2][3] More recently, use of the term has been extended to the cellular domain, where cell functional enviromics studies both the genome and envirome from a systems biology perspective.[4]   Wikipedia accessed 2018 Feb 18

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   

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: Efforts toward the development of early detection assays for cancers have traditionally depended on single biomarker molecules. Current technologies have been disappointing and have not resulted in diagnostic tests suitable for clinical practice. Using a high-throughput cloning method, a panel of epitopes/antigens that react with autoantibodies to tumor proteins in the serum of patients with ovarian cancer have been isolated…. This technology of global epitope/antigen profiling is referred to as 'epitomics'. Sorin Draghici, Madhumita Chatterjee & Michael A Tainsky (2005) Epitomics: serum screening for the early detection of cancer on microarrays using complex panels of tumor antigens, Expert Review of Molecular Diagnostics, 5:5, 735-743,DOI: 10.1586/14737159.5.5.735

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"

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

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 

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, wiki   

fieldomics:  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 data to facilitate integration with ‘-omics’ data.”  Field-omics—understanding large-scale molecular data from field crops Erik Alexandersson1*Dan Jacobson2Melané A. Vivier2Wolfram Weckwerth3 and Erik AndreassonPlant Sci., 20 June 2014

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 

In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Environ Microbiol. 2013 Jul;15(7):1901-16. doi: 10.1111/1462-2920.12064. Epub 2013 Jan 1 Fluxomics - connecting 'omics analysis and phenotypes. Winter GKrömer JO.

Functional genomics, proteomics, fluxomics, and physiomics are complementary to pathway engineering, and their successful applications are bound to multiply product turnover per cell, channel carbon efficiently, shrink the size of factories (i.e., reduce steel in the ground), and minimize product development cycle times to bring products to market. G. Chotani et. al. "The commercial production of chemicals using pathway engineering" Biochim Biophys Acta 1543 (2): 434- 455, Dec. 29, 2000

foldome: The 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 DE.

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 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 
Related terms: unfoldome, 
Protein structure, Structural genomics


Low molecular weight metabolite, protein and peptide fragments being explored as potential cancer biomarkers.  

fragmentomics: Natural fragmentation of biological molecules is well known. Fragmentary structural organization is characteristic of both the simplest and most complex biological molecules. Low molecular weight fragments of biological substances can be easily seen on metabolic maps. Therefore, the term “fragmentomics” is grounded and defined, the bases and determination are given for the notion of the “fragmentome” as a set of all fragments of a single substance as well as for global fragmentome of all chemical components of living organisms. Fragments, fragmentome and fragmentomics in proteomics  7th International Conference on Proteomics & Bioinformatics October 24-26, 2016 Rome, Italy Alexander A Zamyatnin    J  Proteomics Bioinform  

fragmentomics cancer:
Background: Cell-free DNA (cfDNA) isolated from plasma consists of DNA fragments surviving clearance of dying cells and bloodstream trafficking. In cancer, these fragments carry the footprint of tumor somatic variation as well as its microenvironment. Since genomic distribution of cell free DNA fragments was shown to reflect nucleosomal occupancy in hematopoietic cells, we hypothesized that (a) heterogeneous patterns of cfDNA positioning would be associated with distinct mutations in patient tumors and (b) integration of fragmentation patterns into analysis would allow increased sensitivity and specificity of somatic mutation detection…. Conclusions: Fragmentomics classification of cancer cfDNA provides independent evidence for observed somatic variation and underlying tumor microenvironment, leading to higher sensitivity and accuracy of variant detection. Diana Abdueva, Helmy Eltoukhy, Darya Chudova, AmirAli Talasaz. Cell-free DNA fragmentation patterns analyzed in over 15000 cancer patients reveal changes associated with tumor somatic mutations and result in improved sensitivity and specificity of somatic variant detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl): Abstract nr 3350. doi:10.1158/1538-7445.AM2017-3350

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
Broader term: lectinomics

functome:  (biochemistry, genetics) The complete set of functional molecular units in biological cells.   

Functome could simply be a repertoire of all functional entities in a genome. A comorbidity of many genes or proteins whose functions are known. The term is widely applicable for diseasome studies. In a nutshell, they are all a complete set of functional units in a cell.

In biology, a Functome is the whole set of functional entities in a cell, tissue, organ, organism, and species....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. Mapping functome leads to gene ontology and the understanding of biological entities.

Related terms: Functional genomics function, gene function,  Gene Ontology;  Proteomics protein function  

functomics: 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   

The scientific discipline of studying the functional entities in biological cells. Functomics encompasses enzyme, cells, and higher level of biological entities and functions. The functome is usually used in the context of enzyme functions. However, the discipline is broadening to encompass other aspects of biological functions.

functionomics:   Sometimes used as a synonym for functional genomics, has been trademarked by Regeneron Pharmaceuticals FunctionomicsTM    

genome, genomics: Genomics  
glycogenomics, glycome, glycomics: Glycosciences 

hemostaseome: 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.   Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders. Fechtel K, Osterbur ML, Kehrer-Sawatzki H, Stenson PD, Cooper DN. Hum Genet. 2011 Jul;130(1):149-66. Epub 2011 May 3.  

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  

ignorome: What 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

The "ignorome" concept  applies across omics "Real knowledge is to know the extent of one's ignorance" Eric Topol, Twitter

immunogenomics: Molecular Medicine  

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 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 today’s 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       

incidentalome:  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.

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

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

interactomics:  a discipline at the intersection of bioinformatics and biology that deals with studying both the interactions and the consequences of those interactions between and among proteins, and other molecules within a cell.[9] Interactomics thus aims to compare such networks of interactions (i.e., interactomes) between and within species in order to find how the traits of such networks are either preserved or varied. Wikipedia accessed 2018 Feb 24

integrome: 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; 2012)

integromics:  [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 

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   

ionome: We introduce the term "ionome" to include all the mineral nutrient and trace elements found in an organism -- extending the metallome to include metals, metalloids and non-metals.  By profiling the mineral ion and trace element compositions of both transgenic and mutant A. thaliana plants, we hope to uncover the gene networks that regulate the ionome and its interactions. Brett Lahner, et. al, Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana, Nature Biotechnology 21 (10): 1215- 1221, Oct. 2003  

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 

Full complement of human protein kinases. 

Protein Kinase Complement of the Human Genome, G Manning et. al. Science 298: 1912-1934, Dec. 6, 2002, Human Kinome supplement, SUGEN 
Related terms: Proteomics categories kinase proteomics Protein categories protein kinases

kinomics: the study of the kinome, a global description of kinases and kinase signaling.  Since kinases drive numerous signaling pathways in biology (both normal and disease), determining the pertinent kinases in a biological system is of high importance. There are several different ways to study the kinome: RNA interference, mass spectrometry, and antibody arrays, just to name a few…. Kinomic profiles can help elucidate cellular signaling pathways driving particular biological processes and phenotypes and be used to identify and develop biomarkers. What is kinomics? Kinome Core

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  
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  Narrower term: functional lectinomics

ligandome;  (biochemistry) All the molecular ligands for proteins in cells and organisms considered as a whole.Wiktionary accessed 2018 Feb 25

ligandomics:  Complete set of organic small molecules. Glen A. Evans "Designer Science and the 'omics revolution" Nature Biotechnology 18 (2): 127, April 2000  

lipidome: refers to the totality of lipids in cells. Lipids are one of the four major molecular components of biological organisms, along with proteinssugars and nucleic acids. Lipidome is a term coined in the context of omics in modern biology, within the field of lipidomics.[2] It can be studied using mass spectrometry and bioinformatics as well as traditional lab-based methods.[3][4] The lipidome of a cell can be subdivided into the membrane-lipidome and mediator-lipidome.[5] The first cell lipidome to be published was that of a mouse macrophage in 2010.[6] The lipidome of the yeast Saccharomyces cerevisiae has been characterised with an estimated 95% coverage;[7] studies of the human lipidome are ongoing.[2][  Wikipedia accessed 2018 Sept 4

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]     

Lipidomics gateway,
Wellcome Trust

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   
Related terms: Gene definitions gene localization, localize, locus; Proteins: protein localization; Proteins: subcellular localization  Narrower terms: localizome maps, yeast localizome

membranome: Wikipedia  gives word origins.
Related term: membrane proteins

metabolome: Total metabolite pool ("metabolome") analysis offers a means of revealing novel aspects of cellular metabolism and global regulation. H. Tweeddale "Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis" Journal of  Bacteriology 180 (19): 5109- 5116, Oct. 1998 
Related terms Cell biology metabolite; Drug discovery informatics: in silico cell, virtual cell

metabolomics: 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 functions.

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 

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 

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 "19 F NMR metabolomics for the elucidation of microbial degradation pathways of fluorophenols"  Journal of  Industrial  Microbiol Biotechnol 26 (1/2): 22- 34 Jan 2001  
Related terms metabonomics; Functional genomics metabolic profiling; Mass spectrometryNMR  See also Pharmacogenomics 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] 

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]  
Related terms Functional genomics; Pharmacogenomics Metabolic engineering  metabonomics  Narrower term: pharmacometabonomics: Metabolic engineering See under metabonomics

metallome: In biochemistry, the metallome distribution of free metal ions in every one of cellular compartments. The term was defined in analogy with proteome as[1] metallomicsis the study of metallome: the "comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type".[2] Therefore, metallomics can be considered a branch of metabolomics,[citation needed] even though the metals are not typically considered as metabolites. …An alternative definition of "metallomes" as metalloproteins or any other metal-containing biomolecules, and "metallomics" as a study of such biomolecules.[3]    In the study of metallomes the transcriptome, proteome and the metabolome constitutes the whole metallome. A study of the metallome is done to arrive at the metallointeractome. …  In the study of metallomes the transcriptome, proteome and the  metabolome constitutes the whole metallome. A study of the metallome is done to arrive at the metallointeractome.  Wikipedia accessed 2018 Feb 25 

metallomics: the study of metallome: the "comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type".[2]Therefore, metallomics can be considered a branch of metabolomics,[citation needed] even though the metals are not typically considered as metabolites. An alternative definition of "metallomes" as metalloproteins or any other metal-containing biomolecules, and "metallomics" as a study of such biomolecules.[3] Wikipedia accessed 2018 Sept 4

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

(genetics) The set of nucleic acid methylation modifications in an organism's genome or in a particular cell  Wiktionary

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 AP Feinberg, Methylation meets genomics,  Nature Genetics, 27, 9-10, 2001

DNA methylation is one of several epigenetic mechanisms that contribute to the regulation of gene expression; however, the extent to which methylation of CpG dinucleotides correlates with gene expression at the genome-wide level is still largely unknown. ongmei Liu, Jingzhong Ding, Lindsay M. Reynolds, Kurt Lohman, Thomas C. Register, Alberto De La Fuente, Timothy D. Howard, Greg A. Hawkins, Wei Cui, Jessica Morris, Shelly G. Smith, R. Graham Barr, Joel D. Kaufman, Gregory L. Burke, Wendy Post, Steven Shea, Charles E. Mccall, David Siscovick, David R. Jacobs, Russell P. Tracy, David M. Herrington, Ina Hoeschele; Methylomics of gene expression in human monocytes, Human Molecular Genetics, Volume 22, Issue 24, 15 December 2013, Pages 5065–5074,

microbiome:  ” as the “characteristic microbial community occupying a reasonably well defined habitat which has distinct physico-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatres of activity.”   Jonathan Eisen 2015    While often attributed to Joshua Lederberg, a search of Google Books showed an earlier definition.  

Related terms: See related Molecular Medicine Human Microbiome -Omes Human Microbiome, microbiota, metagenomics, Pharmacogenomics  Microbiome based precision medicine,  Cancer   Microbiome in Cancer Immunotherapy, Microbiome in Immuno-oncology

The ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space and have been all but ignored as determinants of health and disease. Joshua Lederberg and Alexa T. McCray "'Ome Sweet 'Omics: A Genealogical Treasury of Words" Scientist 15 (7): 8 April 2, 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

mitochondriomics: Mitochondria perform several fundamental cellular processes in higher eukaryotes including oxidative phosphorylation, Fe/S cluster formation and apoptosis. Dysfunction of the organelle is associated with a wide range of human diseases. To gain a better understanding of mitochondrial function, several recent proteomic, genetic, transcriptomic and bioinformatic approaches have set out to determine the complete set of mitochondrially located proteins in yeast, plants and mammals. AS Reichert, W Neupert, Mitochondriomics: or what makes us breathe, Trends in Genetics 20 (11): 555-562, 2004, Nov  

(genetics) The study of the complete genome of the mitochondrion of an organism. Wiktionary accessed August 10, 2018

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    Google = about 78 Oct. 25, 2006, about 752 Feb 16 2011

neurogenome, neurogenomics: Molecular 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
neurogenomics about 547 July 11, 2002; about 1,130 July 11, 2003; about 2,190 June 7, 2004, about 14,100 Aug. 15, 2005, about 72,400 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

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".

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  

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



Protein interactions

Bio-System models


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

See also Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of  Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001
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 

-omics:  Joshua Lederberg and Alexa T. McCray "'Ome Sweet 'Omics: A Genealogical Treasury of Words" Scientist 15 (7): 8 April 2, 2001] 

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 

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

operome: The characterization of proteins with unknown biological function. Gerstein Lab, Bioinformatics, Omes Table, Molecular Biology & Biochemistry, Yale Univ.   
Google = about 10 July 11, 2002; about 21 July 14, 2003; about 34 June 7, 2004, about 38 Aug. 10, 2005, about 99 Oct. 25, 2006  Related terms: Proteomics.

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

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]

A correspondent has suggested that this term is linked to operons (Gene definitions) but I have not been able to find any evidence for (or against). Any insights would be welcomed.  
Related terms: Cell biologyExpression
,  Functional genomics,   Proteomics  Google = about 40 July 11, 2002; about 125 July 14, 2003; about 134 June 7, 2004, about 156 Aug. 15, 2005, about 308 Oct. 25, 2006

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

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  
ORFeome Project 

Google = about 458 July 11, 2002; about 758 July 14, 2003; about 9,470 June 7, 2004, about 14,000 Aug. 15, 2005, about 308,000 Oct. 25, 2006  Narrower term: proteome  Related terms  translatome; Gene definitions ORF, ORESTES

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

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

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 

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

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 
Google = about 20 July 11, 2002; about 56 July 14, 2003; about 293 June 7, 2004, about 520 Aug. 15, 2005, about 14,400 Oct. 25, 2006

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): 643–652.doi:   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  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  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 knockoutMarc 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

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 

Qualitative identification of the form and function derived from genes, but lacking a quantitative, integrative definition  Omes Table, Gerstein Lab, Yale

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

Mouse Phenome Project
, Jackson Labs, US

phenomics:  the systematic cataloging of phenotype terms on a genome-wide scale—is 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 

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  

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 system’s applications for protein research and biomarker discovery when a single, integrated biochip platform can be used for protein discovery through functional analysis. [Ciphergen’s FAQ, US]

Phenomics ® is also an automated technology trademarked by Proteus SA. 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: 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  
Google = about 235 Aug. 15, 2005, about 1,070 Oct. 25, 2006

phosphatomics:  totality of phosphatases
Google = about 16, Oct. 25, 2006, about 37 Feb 16 2011 

phosphoproteome, phosphoproteomics : Proteomics categories  
phosphoproteome Google = about 88 Sept. 19, 2002; about 773 June 18, 2004; about 3,600 Feb. 14, 2005, about 1,070 Oct. 25, 2006  phosphoproteomics Google = about 6,030 Aug. 15, 2005, about 39,400 Oct. 25, 2006

phylogenome, 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
phylome about 21 July 11, 2002; about 43 July 14,2003; about 47 June 7, 2004, about 103 Aug. 15, 2005, about 308 Oct. 25, 2006

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

Google = about 9,190 July 11, 2002; about 10,900 June 7, 2004, about 27,500 Aug. 15, 2005, about 82, 500 Oct. 25, 2006  

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  Google = about 156 July 11, 2002; about 793 June 7, 2004, about 3,420 Aug. 15, 2005, about 14,200 Oct. 25, 2006

physionomics:  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  

post-translatomics:  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  
Google = about 62, Nov 5, 2005, about 47 Oct. 25, 2006

promoterome: A complete set of promoters. Marc Vidal, personal communication, Dec. 2001  
Google = about 146 Aug. 15, 2005, about 599 Oct. 25, 2006

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   Related term: small molecules Drug discovery & development 

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

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   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

Surveying "dead" parts. Mark Gerstein, MB&B Bioinformatics Group, Yale Univ, 2001   
Google = about 7 July 11, 2002; about 9 Sept. 10, 2003, about 17 Aug. 15, 2005, about 57 Oct. 25, 2006

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 content/8/1/4 
Google - about 1,070 Dec 2 2013

regulome:   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 
International Regulome Consortium 
Related terms: ExpressionFunctional genomics
Google = about 33 July 11, 2002; about 406 June 7, 2004; about 778 Feb. 17, 2005, about 652 Aug. 15, 2005, about 965 Oct. 25, 2006

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

regulomics: 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  
Google = about 71 March 3, 2005, about 115 Aug. 15, 2005, about 615 Oct. 25, 2006
Related terms: Expression
, Functional genomics; Molecular Medicine regulatory therapies; Proteomics regulatory homology

relevantome: See under ridiculome  Google = about 1 Oct. 25, 2006

resistome:  a proposed expression by Gerard D. Wright[1] for the collection of all the antibiotic resistance genes and their precursors in both pathogenic and non-pathogenic bacteria.  This complete set of antibiotic resistance genes is composed of four different types of genes:  1.    Resistance genes found on pathogenic bacteria. These are the fewest but also the most problematic ones at present.  2.    Resistance genes found on antibiotic producers. The microorganisms such as soil-dwelling bacteria and fungi that naturally produce antibiotics have their own protection mechanisms[2] to avoid the adverse effects of the antibiotics on themselves. The genes which code for these resistances are a strong source[3] for the pathogenic bacteria.  3.    Cryptic resistance genes. These genes are embedded in the bacterial chromosome but do not obviously confer resistance, because their level of expression is usually low or they are not expressed.[4]  4.    Precursor genes. These genes do not confer antibiotic resistance. However they encode proteins that confer to some kind of basal level activity against the antibiotic molecule or have affinity to the molecule. In both cases this interaction may evolve to a full resistance gene given the appropriate selection pressure.  Note that these groups are not independent, and some overlapping is expected between them. Wikipedia accessed 2018 Feb 25

Google = about 6 July 11, 2002; about 22 June 7, 2004, about 43 Aug. 15, 2005, about 757 Oct. 25, 2006 
Related terms: Expression

resourceome:  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 resources—the “resourceome”—should 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

Google = about 24, Jan 12, 2006. about 359 Oct. 25, 2006  Many thanks to Nicola Cannata for calling this term to my attention.

ribosomics: 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.

Google = about 12 Nov 5, 2005, about 17 Oct. 25, 2006, about 103 2018 Oct 23

ridiculome: What does it take to turn a ridiculome into a relevantome? 
Quality control metrics (recall/precision)
Context specificity 
   Cellular: Is the interaction specific to a cellular phenotype
   Molecular: Is the interaction dependent on the availability of other molecular species
Links to data (and literature) Links to analysis of biomedical problems
Focus on specific features (e.g. mechanisms)
MAGNet Center: Andrea Califano, NCIBI: Brian Athey, Simbios: Russ Altman, Creating a DBP Community to Enhance the NCBC Biomedical Impact, NCBC Work Group Report, 18 July 2006
Google = about 3 Oct. 25, 2006  Thanks to Gustavo Stolovitsky for calling my attention to this -ome. 

RNome: The complement of non-coding RNAs   
Google = about 42 Aug. 29, 2003 (in the context of RNA), about 48 Aug. 15, 2005, about 76 Oct. 25, 2006

RNomics: The understanding of functional RNAs and their interactions at a genomic level. Peter F. Stadler,  Computational RNomics: The Quest for RNA Genes, 2002
Google = about 26 July 17, 2003 (in the context of RNA), about 995 Aug. 15, 2005, about 694 Oct. 25, 2006
Narrower term: computational RNomics

robogenomics: At what biological levels are data from single-celled organisms akin to a Rosetta stone for multicellular ones? … Gene order is not evolutionarily conserved … 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  
Google = about 12 Nov 5, 2005, about 34 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]  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
Google = about 131 July 11, 2002; about 754 June 7, 2004, about 15,300 Aug. 15, 2005, about 79,700 Oct. 25, 2006  Broader term: transportome; Related terms: Proteomics  secreted proteins

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  Google = about 56, Aug 15, 2005, about 92 Oct. 25, 2006 Related terms: ProteinsProteomics

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]

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 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
Google = about 4 Nov 5, 2005, about 19 Oct. 25, 2006

targetomics: 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  
Google = about 12 Nov 5, 2005, about 11 Oct. 25, 2006

toponomics: See Proteomics categories topological proteomics, toponomics  
Google  toponomics = about 1,090 Oct. 25, 2006

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

toxicomics: An omics field to study the totality of toxic chemicals in cells.
Google, as of Mar. 19, 2002 turned up references, but no definitions, July 11, 2002 = about 10; Sept. 10, 2003 about 14 (but not definitions); about 20 [and no definitions June 7, 2004 [though several toxicomics domains are for sale.], about 40 Aug. 15, 2005, about 149 Oct. 25, 2006

toxome, human: The project will comprehensively map pathways of endocrine disruption (ED), representing a first step towards mapping the human toxome
Human Toxome Project

transcriptome: The population of mRNA transcripts in the cell, weighted by their expression levels.  Gerstein Lab, Molecular Biology & Biochemistry, Yale Univ. 2001

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

The set of genes expressed from the yeast genome, VE Velculescu et al. “Characterization of the yeast transcriptome” Cell 88: 243-251, 1997    

Narrower terms: cancer transcriptomes- human, differential transcriptome, static transcriptome; in silico transcriptomics Related terms interactome, translatome; ExpressionMicroarraysProteomics reverse proteomics

Google = about 7330 July 11, 2002; about 53,400 Sept. 10, 2003; about 74,300 June 7, 2004, about 291,000 Aug. 15, 2005, about 1,800,000 Oct. 25, 2006 

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. 
Google = about 1530 July 11, 2002; about 6,050 Sept. 10, 2003; about 9,270 June 7, 2004, about 47,800 Aug. 15, 2005, about 525,000 Oct. 25, 2006 
Related terms: Expression; Sequences, DNA & beyond transcript; protein transcription
. See also Pharmacogenomics  transcriptomics for toxicology specific definition

transductome:  We call this superset of signalling pathways the transductome.  Institute of Biotechnology, University of Helsinki, Finland, 2005    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  
Google = about 176 Aug. 15, 2005, about 631 Oct. 25, 2006

translatome: The cellular population of proteins expressed in the organism at a given time, explicitly weighted by their abundance. ... Our definition of the translatome is partially motivated by the ambiguities in term proteome, which has two competing definitions. First, broadly 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   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 109 July 11, 2002; about 129 June 7, 2004, about 277 Aug. 15, 2005, about 364 Oct. 25, 2006 
Related terms: ORFeome, transcriptome; Proteins translation; Proteomics proteome

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  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   Related terms: foldome, Protein structures:  intrinsically disodered proteins, protein folding

unfoldomics: Unfoldomics 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.

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 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]   
Google = about 24 July 11, 2002; about 81 June 7, 2004, about 123 Aug. 15, 2005, about 400 Oct. 25, 2006  Related terms: Pharmaceutical biology antibody, antigen, DNA vaccine, vaccine

vaccinomics: Using bioinformatics and genomics for vaccine development.  Tom Hollow "Clad against all cades" Scientist 14 (18): 1 Sep. 18, 2000  

variome: Wikipedia  Variome TM: is/was a structural pharmacogenomics database.
Human Variome Project  
Google = about 198 Aug. 15, 2005, about 13,700 Oct. 25, 2006

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

viromics: 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  
Google = about 168 Nov 5, 2005, about 822 Oct. 25, 2006

-Omes Resources
Omics Gateway   Current content, Alphabetical list of -omes and -omics Wiki 

Big biology: The ’omes puzzle, Monya Baker  Nature 494, 416–419, (28 February 2013) doi:10.1038/494416a 27 February 2013

How to look for other unfamiliar  terms

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