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-Omes and -omics
glossary & taxonomy alleome:
A
collection of different allotypes or allelic protein variants, a new type of
protein library. Greg Weiss, Univ. of California, Irvine, personal
communication, Oct. 2005
allergenome: Putative proteinous
allergens. Allergenomics, Div of Medical Devices, National Institute of Health
Sciences, Japan, http://dmd.nihs.go.jp/latex/allergenomics-e.html allergenomics:
Rapid and comprehensive analysis of putative proteinous
allergens (allergenome) by applying such a proteomic strategy … With
allergenomics, we can not only detect and assign the putative allergens
(proteins specifically interacting with IgE antibodies in a patient's blood) in
a short time, but also analyze the quantitative and qualitative change of the
antigens, depending on the surroundings and environmental conditions of an
allergenic causative. Allergenomics, Div of Medical Devices, National Institute
of Health Sciences, Japan, http://dmd.nihs.go.jp/latex/allergenomics-e.html bibliome:
Scientific literature
L. Grivell "Mining the bibliome: searching for a needle in a haystack?: New computing tools are needed to effectively scan the growing amount of scientific literature for useful information."
EMBO Rep 2002 Mar;3(3): 200- 203, Mar. 2002; DB. Searls "Mining the
bibliome: Pharmacogenomics Journal 1 (2): 88- 89, 2001 biome:
This is the oldest of the "-ome" suffix
series. Coined in 1916, It refers to an ecological community of organisms
and environments. The ability of genes or alleles to affect the representation
of the host organism in a biome is an operational definition for the "function"
of the gene (in that context). George Church Lab, Harvard University, US
http://arep.med.harvard.edu/ome.html
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
https://en.wikipedia.org/wiki/Biome
May also be used in the more specialized
sense of the environments for a yeast culture or other model organisms. 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
https://www.wikidoc.org/index.php/Cellome
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 http://www.biochem.northwestern.edu/ibis/morimoto/research/research_chap2.html
Thanks to Heike Aßmus, University of Rostock for alerting me to this
-ome.
chemogenomics: Chemistry
CHOmics:
comprehensive
approaches to biology … for carbohydrates John
N. Weinstein "Pharmacogenomics: Teaching Old Drugs New Tricks" New
England Journal of Medicine 343: 1408-1409, http://discover.nci.nih.gov/host/2000_pharmecogenomics.jsp
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
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 http://www.jnanobiotechnology.com/content/1/1/4
Broader term:
peptidomics
complexome:
It has become evident over the past few years that many complex
cellular processes, including control of the cell cycle and ubiquitin-
dependent proteolysis, are carried out by sophisticated multi- subunit protein
machines that are dynamic in abundance, post- translational modification
state, and composition. To understand better the nature of the macromolecular
assemblages that carry out the cell cycle and ubiquitin- dependent
proteolysis,
we have used mass spectrometry
extensively over the past few years to characterize both the composition of
various protein complexes and the modification states of their subunits.
[Raymond J. Deshaies et. al "Charting the protein 'complexome' in yeast by
mass spectrometry" Molecular and Cellular Proteomics, Nov. 21, 2001] http://www.mcponline.org/cgi/content/abstract/R100001-MCP200v1
computational
RNomics: The first step toward this goal
[Rnomics] is the development of versatile and reliable computational methods
that can detect and classify functional RNAs, preferably within a single genome,
or in case this proves impossible, from a very small set of related genomes. We
propose here to develop a suite of bioinformatics methods that are specifically
geared toward detecting, verifying, and classifying functional RNAs. Our
comprehensive approach to "Computational RNomics" will provide
improved algorithms for RNA secondary structure prediction, improved alignment
algorithms for nucleic acid sequences, novel approaches to compare and align RNA
structures, extensions of existing RNA algorithms to deal with genome- size data
sets, a database system specifically designed for RNA structures. The first step
toward this goal is the development of versatile and reliable computational
methods that can detect and classify functional RNAs, preferably within a single
genome, or in case this proves impossible, from a very small set of related
genomes. Peter F. Stadler, Computational RNomics: The Quest for RNA Genes,
2002 http://www.tbi.univie.ac.at/research/RNomics.html Broader term:
RNomics connectome:
The connection matrix of the human brain
(the human "connectome") represents an indispensable foundation
for basic and applied neurobiological research. However, the network of
anatomical connections linking the neuronal elements of the human brain is still
largely unknown.
Sporns O, Tononi G, Kötter R
(2005) The Human Connectome: A Structural Description of the Human Brain. PLoS
Comput Biol 1(4): e42. doi:10.1371/journal.pcbi.0010042 http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0010042
cross-omics:
In addressing the core technological issue of this endeavor — namely
integration of toxicogenomic data with conventional toxicological
endpoints — researchers face several technological and methodological
limitations .... Kurt Zingler, Cross-Omics and Systems Toxicology, BioIT
World 6 (9): 25, Nov 2007 http://www.bio-itworld.com/issues/2007/nov/cross-omics-and-systems-toxicology/
Related term:
Drug safety & pharmacovigilance systems
toxicology
cryobionomics: Cryopreservation for
the long-term conservation of in vitro germplasm results in the exposure
of tissues to physical, chemical and physiological stresses causing cryoinjury.
Although, the effects of cryoinjury upon the genome are often unknown, any
accumulative DNA polymorphisms may not be induced by cryopreservation per se
but are the result of the whole culture-cryoprotection-regeneration process. It
is desirable to assess the genetic integrity of plants surviving cryogenic
storage to determine if they are 'true to type' after cryopreservation. This can
be done at the phenotypic, histological, cytological, biochemical and molecular
levels. The relevance of these approaches to stability investigations is
discussed with their limitations. This review provides a definition for 'Cryobionomics'
-
a novel term describing the re-modelled concept of genetic stability and the
re-introduction of cryopreserved plants into the environment. Keith Harding,
Genetic integrity of cryopreserved plant cells: A review, CryoLetters 25, 3-22,
2004 http://www.cryoletters.org/Abstracts/vol_25_1_2004.htm crystallomics:
Production of highly purified protein samples
and diffraction quality crystals. [Joint Center for Structural Genomics,
Oct. 2000] http://bioinfo-core.jcsg.org/bic/links/crystallomics.htm
Related terms: NMR & X-ray crystallography.
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 https://en.wikipedia.org/wiki/Cytomics#Cytome
cytomics:
Multiparameter cytometric analysis of the cellular
heterogeneity of cytomes, ... access a maximum of information on the
apparent molecular cell phenotypes, resulting from cell genotypes and exposure.
Molecular cell phenotypes in the naturally existing cellular and cell population
heterogeneity of disease affected body cytomes contain the information on
the future development (prediction) as well as on the present status (diagnosis)
of a disease. [G. K. Valet, Predictive Medicine by Cytomics"
Max- Planck- Institut für Biochemie, Martinsreid, Germany, 2008 http://www.classimed.de/cytomics.html
The bulk of our knowledge concerning the plant cytoskeleton has come
primarily from the use of techniques and probes derived from animal research.
However, in comparison with animal tissues, relatively few plant cytoskeleton
proteins have been identified. We presume this is not because the plant
cytoskeleton is really made up of such few proteins, but rather that only rarely
have attempts been made to identify plant- specific cytoskeleton proteins, using
plant- specific methods. Here we outline methods that we have developed both for
the isolation and identification of novel cytoskeleton proteins as well as for
the visualization of novel filamentous structures in plant cells, and we
describe several novel cytoskeleton proteins and two novel cytoskeleton
structures, 'nanofilaments' and 'nanotubules'. We postulate that use of such
approaches will lead to a rapid expansion of our knowledge of the plant
cytoskeleton. E. Davies et. al. "Novel components of the plant
cytoskeleton: a beginning to plant 'cytomics'"
Plant Science 160(2): 185- 196, Jan. 5, 2001 Related/narrower? term:
nucleome
degradome:
The entire protease
complement of human cells and tissues. Santiago Cal, Víctor
Quesada, Cecilia Garabaya and Carlos López-Otín, Polyserase-I, a human
polyprotease with the ability to generate independent serine protease domains
from a single translation product PNAS | August 5, 2003 | vol. 100 | no.
16 | 9185- 9190 http://www.pnas.org/cgi/content/full/100/16/9185
degradomics:
The application of genomic and proteomic
approaches to identify the protease and protease- substrate repertoires, or 'degradomes',
on an organism-wide scale — promises to uncover new roles for proteases in
vivo. This knowledge will facilitate the identification of new pharmaceutical
targets to treat disease. Here, we review emerging degradomic techniques and
concepts. Protease Degradomics: A New Challenge for Proteomics, Carlos Lopez-
Otin & Christopher M. Overall, Nature Reviews Molecular Cell Biology 3, 509
-519, 2002
http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrm/journal/v3/n7/abs/nrm858_r.html
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 differential
transcriptome:
The differential transcriptome represents the set of
genes that are differentially expressed during a cellular transition. The static
transcriptome is the set of genes that does not change expression under that
particular condition. Koen J. Dechering, The transcriptome's drugable frequenters,
Drug Discovery Today 10:12/24, 857- 864, June 15, 2005 and cites Mark Gerstein's
http://bioinfo.mbb.yale.edu/what-is-it/omes/
as the originator of this phrase.
economics:
An important aspect of the
"omics" family as well. Business
of biopharmaceuticals
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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785062/
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
https://en.wikipedia.org/wiki/Envirome
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
https://www.ncbi.nlm.nih.gov/pubmed/16149876
exome:
The exome is the 1% of the genome most easily interpreted and most likely to
cause noticeable phenotypes. George Church, Nature Genetics "Question of
the year"
http://colinfarrelly.blogspot.com/2007/01/ng-question-of-year.html
exposome:
the full catalogue of a person's environmental exposures throughout their life. Epidemiology:
Every bite you take "how to measure everything" Nature News Published
online 16 February 2011
| Nature 470,
320-322 (2011) | doi:10.1038/470320a http://www.nature.com/news/2011/110216/full/470320a/box/1.html
expressome: Expressome is a slightly larger concept than
transcriptome.
Transcriptome is the set of transcripts, while expressome includes transcripts, proteins
and other ligands
(how much concentration). Wikipedia accessed Aug. 15, 2005 http://en.wikipedia.org/wiki/Expressome
Refers
to the whole set of gene
expression in a cell,
tissue, organ, organisms, and species.
expressomics: Expressomics
has two major branches. One is RNA expression represented by transcriptomics and
protein expression by proteomics (or translatomics if you insist). Expressomics,
omics.org wiki http://omics.org/index.php/Expressomics
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 Jacobson2, Melané A. Vivier2, Wolfram Weckwerth3 and Erik Andreasson1
Plant Sci., 20 June 2014 https://doi.org/10.3389/fpls.2014.00286
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
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.
http://www.ncbi.nlm.nih.gov/pubmed/19964073 The population of gene products classified through their
tertiary structure. Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of
Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome
Research 11 (9): 1484- 1502, Sept. 2001 A number of projects are currently being launched to determine the three-
dimensional structure of most protein folds or "foldome" of several
proteomes. Marc Vidal "A Biological Atlas of Functional Maps" Cell
104: 333-339, Feb. 9, 2001 A comprehensive set of protein folds.
Marc Vidal, personal communication,
Dec. 2001 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
https://www.omicsonline.org/proceedings/fragments-fragmentome-and-fragmentomics-in-proteomics-56777.h
fragonomics:
The use of smaller molecules (fragments) in the drug discovery process has led
to success in delivering novel leads for many different targets. ER Zartler, MJ
Shapiro, Fragonomics:
fragment-based drug discovery, Current opinion in chemical biology, 9 (4):
366- 370, Aug 9, 2005
functional lectinomics: Encompasses,
among other activities, intra- and intercellular transport processes, sensor
branches of innate immunity, regulation of cell-cell (matrix) adhesion or
migration and positive/negative growth control with implications for
differentiation and malignancy. HJ Gabius, S Andre, H Kaltner, HC Siebert, The
sugar code: functional lectinomics. Biochim Biophys Acta. 1572(2-3): 165- 177,
Sept 19, 2002 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12223267&dopt=Abstract functome:
(biochemistry, genetics) The
complete set of functional molecular units in biological cells.
https://en.wiktionary.org/wiki/functome
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.
Bioinformatics.org
https://bioinformatics.org/wiki/Functome
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
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
The "ignorome" concept http://bit.ly/1oCa3aE
applies across omics "Real knowledge is to know the extent of one's ignorance"
Eric Topol, Twitter
https://twitter.com/EricTopol/status/435065444139925504
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.
http://jama.jamanetwork.com/article.aspx?articleid=211038
inflammasome:
The adapter molecules ASC, Ipaf and Cryopyrin/Nalp3 have each been proposed to
regulate caspase-1 within a multi-protein complex called the
"inflammasome". Activation of caspase-1 leads to the cleavage and
activation of pro-inflammatory cytokines such as interleukin (IL)-1beta and
IL-18. The analysis of mice deficient in ASC, Ipaf and Cryopyrin/Nalp3 has
revealed that the inflammasome is a dynamic entity that is assembled from
different adapters in a stimulus-dependent manner. ASC, Ipaf and
Cryopyrin/Nalp3: bona fide intracellular adapters of the caspase-1 inflammasome.
S Mariathasan, Microbes Infect 2007 Apr 9 (5): 664- 671. Epub 2007 Jan 27
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
https://en.wikipedia.org/wiki/Interactome#Interactomics 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
http://doi.org/hrq; 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
http://discover.nci.nih.gov/weinstein.jsp
http://www.ncbi.nlm.nih.gov/pubmed/15687693 invariome:
the complement of genes in an organism whose level of expression does not change
significantly from condition to another, i.e. they are invariantly expressed.
Ben Sidders personal communication Jan 12, 2008 and Sidders et. al
Quantification of global transcription patterns in prokaryotes using spotted
microarrays, Genome Biology 2007, 8:R265doi:10.1186/gb-2007-8-12-r265
http://genomebiology.com/2007/8/12/R265 Full complement of human protein
kinases. http://kinase.com/human/kinome/ Protein Kinase Complement of the Human Genome,
G Manning et. al. Science 298: 1912-1934, Dec. 6, 2002, Human Kinome supplement,
SUGEN http://www.kinase.com/human/kinome/ kinomics:
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
http://www.kinomecore.com/what-is-kinomics/ In this review, we describe and
evaluate modern techniques for studying the protein kinases, or, in other words,
state-of-the-art kinomics. Sam A Johnson & Tony Hunter, Kinomics:
methods for deciphering the kinome, Nature Methods 2, 17 - 25, 2005
Published online: 21 December 2004; | doi:10.1038/nmeth731 http://www.nature.com/nmeth/journal/v2/n1/full/nmeth731.html
lectinomics: Carbohydrate-binding
proteins, excluding sugar-specific antibodies, receptors of free mono- or
disaccharides for transport or chemotaxis and enzymes modifying the bound
carbohydrate. HJ Gabius, S Andre, H Kaltner, HC Siebert, The sugar code:
functional lectinomics. Biochim Biophys Acta. 1572(2-3): 165- 177, Sept 19, 2002
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12223267&dopt=Abstract
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
https://en.wiktionary.org/wiki/ligandome 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 proteins, sugars 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
https://en.wikipedia.org/wiki/Lipidome
lipidomics:
Mass
spectrometry-based analysis of lipids, called lipidomics, presents a number of
opportunities not only for understanding the cellular processes in health and
disease but also in enabling personalized medicine. Lipidomics in its most
advanced form is able to quantify hundreds of different molecular lipid species
with various structural and functional roles. Unraveling this complexity will
improve our understanding of diseases such as atherosclerosis at a level of
detail not attainable with classical analytical methods.
Lipidomics: A Tool for Studies
of Atherosclerosis, Ekroos K, Jänis M, Tarasov K, Hurme R, Laaksonen R., Zora
Biosciences Oy, Curr Atheroscler Rep. 2010 Apr 28. [Epub ahead of print]
http://www.ncbi.nlm.nih.gov/pubmed/20425241 In recent years large-scale
determination of protein localization, localizome analysis, has been
investigated in yeast and certain organella in higher Eukaryotic cells. This
information augments the long accumulation of small- scale experiments which
have determined the localization of various proteins under specific conditions.
Together these findings have begun to reveal the complexity of protein
localization. A Knowledge base for the Protein Localizome, Mitsuteru Nakao et.
al, poster Intelligent Systems for Molecular Biology, 2004
http://www.iscb.org/ismb2004/posters/nakao-mitsuteruATaist.go.jp_879.html
membranome: Wikipedia http://en.wikipedia.org/wiki/Membranome
gives word origins. 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. For functional genomic or plant breeding programmes, as well as for diagnostic usage
in industrial or clinical routines, it might not be necessary to determine the levels of all
metabolites individually. Instead, a rapid classification of samples according to their origin
or their biological relevance might be more
adequate in order to maintain a high through- put. This process can be called
metabolic finger- printing. Such approaches have occasionally been termed metabonomics, which on the one
hand could be mixed up with the completely different goal of metabolomics, and on the
other hand with the earlier defined concept of the metabolon, the coordinated channelling of
substrates through tightly connected enzyme
complexes. Oliver Fiehn, "Combining genomics, metabolome analysis
and biochemical modelling to understand metabolic networks" Comparative and
Functional Genomics 2:155-168 April, 2001 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447208/
The presented data illustrate the potential of the
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 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] 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 https://en.wikipedia.org/wiki/Metallome
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
https://en.wikipedia.org/wiki/Metallome
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
https://en.wiktionary.org/wiki/methylome
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, https://doi.org/10.1093/hmg/ddt356
https://academic.oup.com/hmg/article/22/24/5065/569877
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 http://microbe.net/2015/04/08/
Related terms:
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 http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&dopt=AbstractPlus&list_uids=15475115 morphome:
The quantitative description
of anatomical structure, chemical and biochemical composition, and material
properties of an intact organism, including its genome, proteome, cell,
tissue and organ structures up to those of the whole intact being. JB
Bassingthwaighte, National Simulation Resource, Univ. of Washington, personal
communication, May 2000 See also JB Bassingthwaighte
"Strategies for the physiome project" Annals of Biomedical Engineering
28 (8): 1043- 1058, Aug. 2000 Google = about 227 July 11, 2002;
about 340 July 14, 2003; about 667 June 7, 2004, about 877 Aug. 15, 2005, about
21,200 Oct. 25, 2006 Related terms:
Cell biology morphometry;
Functional
genomics; Pharmacogenomics
morphomics:
(biology)
The identification of the totality
of the morphological
features of species
Wiktionary http://en.wiktionary.org/wiki/morphomics
Google = about 78 Oct.
25, 2006, about 752 Feb 16 2011
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 nucleome:
Over the last decade, a variety of technological
innovations have accelerated the acquisition of knowledge concerning the
regulation of gene expression. In particular, techniques have been devised that
permit analysis of the behavior of essentially all genes contained within the
genome. Nonetheless, we still confront the problem of dissecting the different
patterns of gene expression that occur within the frequently complex
interspersions of individual cell types within the tissues and organs of higher
eukaryotes. This lecture will outline recent progress in the global analysis of
cell- specific gene expression within complex
tissues, drawing on developments in analytical cytology, particularly microarray
technologies, Fluorescent Protein targeting to the nucleus, and flow cytometry.
David Galbraith, Univ. of Arizona Cancer Center, International Society for
Analytical Cytology, May 6-9, 2002, San Diego US http://www.isac-net.org/congresses/ISACFA/PlenarySessions.html
Google = about 12 July 11, 2002;
about 31 July 14, 2003; about 24, June 7, 2004, about 53 Aug. 15, 2005, about
253 Oct. 25, 2006
-ome:
According to Merriam-Webster
Online from the Latin for "mass". http://www.m-w.com/cgi-bin/dictionary?book=Dictionary&va=ome
In physics, probably starting with Faraday's ion, cation, anion, the -on
suffix has tended to signify an elementary particle, later materially focused on
the photon, electron, proton, meson, etc., whereas -ome in biology
has the opposite intellectual function, of directing attention to a holistic
abstraction, an eventual goal, of which only a few parts may be initially at
hand. Joshua Lederberg and Alexa T. McCray "'Ome Sweet 'Omics: A
Genealogical Treasury of Words" Scientist 15 (7): 8 April 2, 2001
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
Genome
Transcriptome
Proteome
Physiome
Biome/Phenome A key approach in genomic research is to divide the cellular contents into distinct
sub- population, each given an -omic term.
Broadly, these 'omes can be divided into those that represent a population of molecules, and those that define their actions.
... Once the individual sub- populations are defined and analyzed, we can then try to reconstruct the full organism by interrelating them, eventually allowing for a full and
dynamic view of the cell. ... A problem in comparing the different 'omes' is
that each represents a different set of genes. Mark Gerstein "What is
Bioinformatics?" Molecular Biology & Biochemistry 474b3, Yale Univ.
2001 http://bioinfo.mbb.yale.edu/what-is-it.html
See also Dov Greenbaum, Mark Gerstein et. al. "Interrelating
Different Types of Genomic Data" Dept. of Biochemistry and Molecular
Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
-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 http://en.wikipedia.org/wiki/-omics
oncogenomics: Cancer
Google = about 333 July 11, 2002;
about 1,070 July 14, 2003; about 3,080 June 7, 2004, about 10,600 Aug. 15, 2005,
about 50,300 Oct. 25, 2006 operome:
The characterization of proteins with unknown biological function.
Gerstein Lab, Bioinformatics, Omes Table, Molecular
Biology & Biochemistry, Yale Univ. http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html operomics:
Our group has embarked on a major effort to integrate genomics transcriptomics and proteomics for the profiling of cancer tissue,
an approach we refer to as Operomics. Our major goals are the molecular classification of tumors and the identification of markers for the early detection of cancer.
S.M. Hanash, University of Michigan Medical Center
"Integrating Genomics and Proteomics in the Post- Genome Era" Michigan
State Univ. May 4, 2001 http://www.pa.msu.edu/seminars/ctss/abstracts/20010504.txt
The profiling of tissues and cell populations at the
genomic, transcriptomic and proteomic levels. The molecular analysis of tissues
at all three levels. SM Hanash "Operomics: molecular
analysis of tissues from DNA to RNA to protein" Clin Chem Lab Med 38 (9):
805- 813 Sep. 2000
The whole operation of
molecular analysis of a cell, extending from DNA to
RNA to protein. [“Proteomics,
transcriptomics: what's in a name?” Nature 402:715 Dec 16, 1999] ORFeome:
The sum total of open reading frames in the genome, without regard to whether or not they code; a subset of
this is the proteome. Gerstein Lab, Molecular Biology &
Biochemistry, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/figures.pdf.
Complete sets of open reading frames (ORFs), or
"ORFeomes," need to be cloned into various expression vectors.
J. Reboul et. al Open- reading- frame sequence tags (OSTs) support
the existence of at least 17,300 genes in C. elegans. Nature Genetics
27 (3): 332- 336 Mar. 2001
Complete set of
protein-encoding open reading frames (Reboul et al, Nature Genetics,
2003) Marc Vidal, Harvard Medical School faculty
ORFeomics:
C. Boone, B. Andrews, ORFeomics: correcting the wiggle in worm genes, Nature
Genetics 34 (1): 8- 9, May 2003 Google = about 155 Oct.
25, 2006
paleogenomics: Genomics
categories Google = about 234 Nov 6, 2005, about 576 Oct. 25, 2006 parasitome:
A subset of the secretome of a
parasite that mediates parasitism. Richard S. Hussey et. al,, Brazilian Journal of
Plant Physiology 14:183-194, 2002 Google = about 7, Feb. 4, 2003;
about 23 July 14, 2003; about 46 June 7, 2004, about 117 Aug. 15, 2005, about
318 Oct. 25, 2006 Narrower term: secretome; Related term: Gene
categories parasitism genes pathogenomics, pathome:
Molecular
Medicine Google = pathogenomics about 271 July 11, 2002;
about 1,240 July 14, 2003; about 1,880 June 7, 2004, about 9,580 Aug. 15, 2005,
about 52,400 Oct. 25, 2006
pathome: It had become increasingly clear with the completion of
the human genome project that genotyping alone will have little impact on the
medical treatment of chronic diseases. To accomplish this, a better
understanding of the pathophysiology of the subsets that underline many of these
conditions is required. For example, subdividing hypertensive patients by
intermediate phenotypes - traits that are found to be present in some but not
all hypertensive subjects - has the potential to substantially increase the
power of such genetic approaches. We have termed the collection of these
intermediate phenotypes, a Human Hypertension Pathome Project. Gordon
Harold Williams, Brigham & Women's Hospital, Boston, US "Endocrine
Renal and Genetic Factors in Human and Experimental Hypertension, 2001
http://research.bwh.harvard.edu/rdbook/en18.htm
pathomics:
the study of the molecular basis of infectious disease. It focuses on the changes in protein levels and other molecules that occur when a body has been exposed to a pathogen.
Science & Technology Lawrence Livermore Lab, 2004 https://www.llnl.gov/str/June04/NewsJune04.html
peptaibiomics:
Isolates were screened for the production of a group of polypeptide antibiotics
named peptaibiotics, including its subgroups peptaibols and lipopeptaibols.
Fully-grown fungal cultures on potato-dextrose agar were extracted with
CH(2)Cl(2)/MeOH, and these extracts were subjected to SPE using C(18)
cartridges. The methanolic eluates were analyzed by on-line LC/ESI-MS(n)
coupling--a method which is referred to as 'peptaibiomics. Peptaibiomics:
screening for polypeptide antibiotics (peptaibiotics) from plant-protective
Trichoderma species. T. Degenkolb, et al. Chem Biodivers. 2006 Jun;3(6):
593- 610 Thanks to Willibald Schliemann for telling me about this
omics.
peptidome:
Biologically active peptides are one of the most important
substances that transmit and regulate bio- information in the circulatory and
neuronal systems. In order to elucidate and identify the mechanism in the
pathogenesis and development of cardiovascular and related diseases, we are
trying to identify new biologically active peptides and analyze their molecular mechanism in the
regulation of circulation system. ... We have also developed the highly
sensitive techniques for the measurement of biological activity of peptides and
for the separation and sequence determination of peptides with ultra- low
abundance. Indeed, we have applied these methods to the screening of
unidentified peptides. We have also started the "Peptidome" project
that is aimed to construct fact- databases of all peptides that exist in the
tissue or body. These databases are expected to be utilized for developing new
drugs and therapy as an intellectual infrastructure. Naoto Minamino, Takeshi
Katafuchi and postdocs, Laboratory of Development and Evaluation of Biomedical
Instruments and Systems (LDEBIS), National CardioVascular Center NCVC, Japan
http://www.ncvc.go.jp/english/res/LDEBIS.html
N. Minamino [Peptidome: the fact- database for endogenous
peptides Article in Japanese] Tanpakushitsu Kakusan Koso 46 (11 Suppl): 1510-
1517 Aug. 2001
Peptides and small proteins of a
whole organism or a subsystem (peptidome). M Schrader et. al. Peptidomics
technologies for human body fluids, Trends in
Biotechnology 19 (10 Suppl): S55- 60, Oct. 2001 peptidomics:
Peptide profiles of the pars intercerebralis and the
corpora cardiaca [of insects, the endocrinological equivalent of the
hypothalamus- pituitary system of vertebrates] were characterized using simple sampling protocols in combination with
MALDI- TOF and electrospray ionization double quadrupole time of flight
(ESI-Qq-TOF) mass spectrometric technologies. The results were compared with earlier results of conventional
sequencing methods and immunocytochemical methods. In addition to many known
peptides, several m/z signals corresponding to putative novel peptides were observed in the
corpora cardiaca and/or pars intercerebralis. Furthermore, for a number of peptides evidence was provided about their localization and
MALDI- TOF analysis of the released material from the corpora cardiaca yielded information on the hormonal status of particular brain peptides.
E. Clynen "Peptidomics of the pars intercerebralis- corpus cardiacum complex of the migratory locust, Locusta
migratoria" European Journal of Biochemistry 268 (7): 1929- 1939,
Apr. 2001 Google = about 174 July 11, 2002;
about 404 July 14, 2003; about 700 June 7, 2004, about 4,790 Aug. 15, 2005,
about 28,100 Oct. 25, 2006 Related terms: Chemistry peptidomimetic; Proteins
peptides
pharmacoepigenomics:
Pharmacogenomics
Google = about 19 Nov
5, 2005, about 38 Oct. 25, 2006
pharmacogenome:
custom chips or alternative multiplexed genotyping technologies will
undoubtedly be developed for specific diagnostic needs and updated as novel
pharmacogenetic variants are discovered. These types of highly multiplexed
assays for individual variants provide a view into the `pharmacogenome'
of an individual, Pharmacogenetics and personal genomes,
Michael Wagner
Per Med. 2009 November 1; 6(6): 643–652.doi:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826717/
Google = about 4 July 11, 2002;
about 10 July 14, 2003; about 11 June 7, 2004, about 18 Aug. 15, 2005, about 66
Oct. 25, 2006
Related terms: Pharmacogenomics
pharmacometabonomics
Google
pharmacogenomics = about 22,400 July 19, 2002;
about 37,100 July 14, 2003; about 107,000 June 7, 2004, about 414,000 Aug. 15,
2005, about 1,670,000 Oct. 25, 2006
pharmacomethylomics:
John N. Weinstein "Pharmacogenomics:
Teaching Old Drugs New Tricks" New England Journal of Medicine 343:
1408-1409, 2000 Google = about 13 July 11, 2002;
about 91 July 14, 2003; about 131 June 7, 2004, about 106 Aug. 15, 2005, about
125 Oct. 25, 2006
pharmacophylogenomics:
David B. Searls, Pharmacophylogenomics: genes, evolution and drug targets,
Pharmacophylogenomics: genes, evolution and drug targets, Nature Reviews Drug
Discovery 2(8) : 613- 623 Aug. 2003
Google = about
21 Mar. 3, 2004, about 70 Aug.
15, 2005 ,about 181 Oct. 25, 2006
pharmanome:
The pharmaceutically important set of the human genome comprising whole sets of
protein families, including secreted factors, all cancer cell surface antigens
and small molecule targets. Five Prime Therapeutics press release, 2003 http://www.atvcapital.com/news.php?id=103
Google = about 20, June
22, 2005, about 54 Oct. 25, 2006
phenome:
The digital system depicted for the phenome refers to the
presence or absence of particular phenotypes conferred by gene knockout. Marc Vidal
"Biological Atlas of Functional Maps" Cell 104: 333 339, February 9,
2001
Perhaps the "phenome" or
phenotype lies between morphome and physiome, in recognition of the importance
of the qualitative identification of form and function derived from the
gene, though lacking in the quantitative, integrative definition. JB Bassingthwaighte,
National Simulation Resource, Univ. of Washington
http://www.physiome.org/Models/xsim_modeldocs/OLD/Documents/pdf/7.1jun98.pdf
The phenotype of a
comprehensive set of mutants (ideally measuring a comprehensive set
environmental and internal states). A play on the word "phenomenon"
too. George Church Lab,
Harvard Molecular Technology Group & Lipper
Center for Computational Genetics, Harvard http://arep.med.harvard.edu/ome.html
Qualitative identification
of the form and function derived from genes, but lacking a quantitative,
integrative definition Omes Table,
Gerstein Lab, Yale
http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html
See also note on variant meanings for genome, genotype and phenotype
in Genomics under genome
citing M. Mahner, M. Kary "What exactly are genomes, genotypes and phenotypes? And what about
phenomes?" Journal of Theoretical Biology 186 (1): 55- 63, May 1997 phenomics:
the systematic cataloging of phenotype terms
on a genome-wide 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 http://www.bioontology.org/node/525
Study of phenotypes with knowledge of the genotypes ... will have an
important theoretical component through mathematical model building and
computer simulation. B. Palsson "The challenges of in silico biology"
Nature Biotechnology 18:1147-1150, Nov. 2000
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]
http://www.ciphergen.com/tech_doc5.html
Phenomics ® is also an automated technology trademarked by Proteus SA. http://www.proteus.fr
and a linguistics term.
Google = about 544 July 11, 2002;
about 1,110 July 14, 2003; about 2,840 June 7, 2004, about 9,220 Aug. 15,
2005, about 46,400 Oct. 25, 2006, about 35,200 Oct 5, 2009 Narrower term: metabolic phenomics Related terms Functional genomics function; Genomics complex
diseases; Drug discovery informatics
phenotypic screening
phosphatome:
Phosphatome gene families. Arena S, Benvenuti S,
Bardelli A, Genetic
analysis of the kinome and phosphatome in cancer, Cell Mol Life Sci. 62(18):
2092- 2099, Sept. 2005
phosphatomics:
totality of phosphatases
http://www.argosbiotech.de/info/omics/Xomics/P.htm
phosphoproteome,
phosphoproteomics : Proteomics
categories
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
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 physiomics: Knowledge
of the complete physiology of an organism, including all interacting metabolic pathways, structural and biochemical scaffolding, the proteins and accessories
that make them up, and the gene interactions and cues that control them. Mark
Lesney "Finding New Targets" Modern Drug Discovery 4(9): 34- 36 Sept.
2001 http://pubs.acs.org/subscribe/journals/mdd/v04/i09/html/09lesney.html
Google = about 156 July 11, 2002;
about 793 June 7, 2004, about 3,420 Aug. 15, 2005, about 14,200 Oct. 25, 2006
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 promoterome:
A complete set of promoters.
Marc Vidal, personal
communication, Dec. 2001 proteogenomics:
The study of gene expression during the infectious cycle, in
mutants or after environmental or chemical stimuli, is a powerful approach
towards understanding parasite virulence and the development of control
measures. Like other trypanosomatids ... With the impending completion of
the Leishmania genome, global approaches surveying mRNA and protein expression
are now feasible. Our laboratory has developed the Drosophila transposon mariner
as a tool for trapping Leishmania genes and studying their regulation in the
form of protein fusions; a classic approach in other microbes that can be termed
'proteogenomics'. SM Beverley et. al., Putting
the Leishmania genome to work: functional genomics by transposon trapping and
expression profiling, Mitsubishi Kagaku Institute of Life Sciences (MITILS)
Japan, Annual Report, 2001, Philos Trans R Soc Lond B Biol Sci. 357 (1417): 47-
53, Jan. 29, 2002 Related term: small molecules Drug
discovery & development
pseudogenome:
The complement of pseudogenes in the proteome.
Dov Greenbaum "Interrelating Different Types of
Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001
http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome
Research 11 (9): 1484- 1502, Sept. 2001 See also Goro Terai1, 2, Toshihisa Takagi1, Kenta Nakai "Prediction
of co- regulated genes in Bacillus subtilis on the basis of upstream
elements conserved across three closely related species" Genome Biology
2(11): research0048.1-0048.12,
2001 Google = about 8 July 11, 2002;
about 28 Jan. 6, 2004, about 58 Aug. 15, 2005, about 235 Oct. 25, 2006
pseudogenomics:
Five years after completion of the yeast
genome sequence, I will give examples of truly "genomic" (global) achievements as well as of other
"pseudogenomic" approaches abusively called
"postgenomics" or "functional
genomics" which use gene sequence information to study specific traits.
André Goffeau (ENS) "Yeast Genomics, Pseudogenomics and Postgenomics"
Structures macromoléculaires dans le cadre biologique, mathématique et algorithmique,
6 décembre 2001
http://www.ihes.fr/IHES/Scientifique/Seminaires/Sgenomique2001.html Surveying "dead" parts.
Mark Gerstein, MB&B Bioinformatics
Group, Yale Univ, 2001 http://bioinfo.mbb.yale.edu/lectures/woodshole/talk.pdf
psychiatome: Herein,
we investigate the putative relationships among and between biological and
environmental factors in psychiatric diseases, in what we call “psychiatome”,
inspired by the concept of “diseasome”. Our approach is to assess
the shared genes (via mining through genetic databanks), shared networks (using
inferred proteomics data) and shared networks of anatomical regions (i.e.
toponomics, exploiting the PubBrain tool) in such a way as to develop a unique
picture of salient inter-relationships that may subserve or be reflected by
psychiatric disorders. … Perhaps the “psychiatome” will provide an
adequate translational framework for both psychiatric research and practice,
being holistic and broad, rather than narrow and simplistic, even though this
promising paradigm at present is still at an early stage of its development and
implementation. Rethinking psychiatry with OMICS science in the age of
personalized P5 medicine: ready for psychiatome? Nicola Luigi
Bragazzi Philosophy, Ethics, and Humanities in Medicine 2013, 8:4 doi:10.1186/1747-5341-8-4 http://www.peh-med.com/ 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 http://en.wikipedia.org/wiki/Regulome
regulome maps:
Will
be established for health and disease, namely, data bases for networks of
regulatory gene and protein interactions, with quantitative features and
alternative routes incorporated. Such maps will have many uses and will need to
be extensive if scientists and physicians; are to be able to chose the best
targets for an intervention. Regulomics after Genomics: A Challenge for the 21st
Century, Emile Zuckerkandl, Institute of Molecular Medical Sciences,
International Union of Biological Sciences http://www.iubs.org/test/bioint/41/16.htm
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 http://www.iubs.org/test/bioint/41/16.htm
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. Google = about 6 July 11, 2002;
about 22 June 7, 2004, about 43 Aug. 15, 2005, about 757 Oct. 25, 2006
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
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0010076
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.
http://omics.org/index.php/Ribosomics
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?
RNome:
The complement of non-coding RNAs
RNomics: The
understanding of functional RNAs and their interactions at a genomic level.
Peter F. Stadler, Computational RNomics: The Quest for RNA Genes,
2002 http://www.tbi.univie.ac.at/research/RNomics.htm 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 http://www.pnas.org/cgi/content/abstract/95/7/3731 secretome:
A subset of the proteome that is defined by its action,
i.e. it is actively exported from the cell. [Dov Greenbaum "Interrelating
Different Types of Genomic Data" Dept. of Biochemistry and Molecular
Biology, Yale Univ. 2001] http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome
Research 11 (9): 1484- 1502, Sept. 2001
The recent sequencing of the genome of
B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported
Tjalsma et al., "Signal peptide-
dependent protein transport in Bacillus subtilis:" Microbiol Mol Biol Rev.64: (3) 515-
547 Sept. 2000 secretomics:
We present a "differential secretomics analysis" as the most direct
approach to identify the underlying alterations. MW Volmer et. al, Tumor
suppressor Smad4 mediates downregulation of the anti-adhesive invasion-promoting
matricellular protein SPARC: Landscaping activity of Smad4 as revealed by a
"secretome" analysis, Proteomics. 4(5): 1324- 1334, May 2004
Google = about 12, Aug. 15, 2005, about 172 Oct. 25, 2006
separomics:
Protein purification is one of the most fundamental, yet most challenging, operations in life science research and the biotech industry. Depending on the complexity of the sample, the scale of the process and the characteristics of the target protein, vastly different starting conditions can be encountered. This "universe" of starting conditions can be viewed as the working ground for
Separomics: the challenge to provide a simple solution to every purification situation.
... Affinity capture is one of the most attractive procedures for isolating biomolecules from complex mixtures because it offers an efficient purification and concentration of the target in a single step.
"Business Areas: Separomics" Affibody AB, Sweden http://www.affibody.se/
Google = about 56, Aug
15, 2005, about 92 Oct. 25, 2006 Related terms: Proteins, Proteomics
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
http://www.google.com
did not retrieve any websites but this article (and this glossary) when
searching for somatonome or somatonomics. Google = about 11,
June 7, 2004 including several which seem to be unattributed copies of this
glossary, about 9 Aug.. 15, 2005
static transcriptome: See under differential transcriptome
strainomics: Unbiased analyses of a
total subset of strains isolated from specific soybean-cropping areas (an
approach which could be called "strainomics") can be used to
answer various biological questions. J. Thomas-Oates, et al, A catalogue of
molecular, physiological and symbiotic properties of soybean- nodulating
rhizobial strains from different soybean cropping areas of China, Syst Appl
Microbiol. 26(3): 453- 465, Sept 2003 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14529189&query_hl=40
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 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14559105&dopt=Abstract
toponomics: See Proteomics
categories topological proteomics, toponomics
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. http://omics.org/index.php/Toxicomics. toxome,
human:
The project will comprehensively map pathways of endocrine disruption (ED),
representing a first step towards mapping the human toxome transcriptome:
The population of mRNA transcripts in the cell, weighted by their expression levels.
Gerstein Lab, Molecular Biology & Biochemistry, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/figures.pdf.
Complement of mRNAs
transcribed from a 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 transcriptomics:
Generation of messenger
RNA expression profiles. “Proteomics, transcriptomics: what's in a name?”
Nature 402:715 Dec 16, 1999
The study of genome- wide mRNA levels. transductome:
We call this superset of signalling pathways the
transductome. Institute of Biotechnology, University of Helsinki, Finland,
2005 http://ekhidna.biocenter.helsinki.fi:9801/research Google = about 18, Oct.
25, 2006
Transgenome: Our
new resource, TRANSGenomeTM provides an overall annotation of the human genome
with emphasis on its regulatory characteristics. We show that the occurrence of
sequence patterns with regulatory potential may be supported by, but cannot be
fully explained by either the GC content of a whole chromosome or its putative
promoter regions, nor by the information content of the patterns. Composition-
sensitive analysis of the human genome for regulatory signals, O.V. Kel-
Margoulis, D. Tchekmenev et. al., In Silico Biol. 2003;3 (1-2):145- 171
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 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
See also D. Greenbaum et. al. Interrelating different types of genomic
data, from proteome to secretome: 'oming in on function" Genome
Research 11 (9): 1484- 1502, Sept. 2001 transportome:
The population of the gene products that are
transported; this includes the secretome. Mark Gerstein "What is
Bioinformatics? Omes Table" Molecular Biology & Biochemistry 474b3, Yale Univ.
2001 http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html
Google = about 14 July 11, 2002;
about 40 June 7, 2004, about 140 Aug. 15, 2005, about 367 Oct. 25, 2006 Narrower term: secretome
unfoldome: a set
of unstructured proteins in a proteome. Intrinsically Disordered Proteins Gordon
Research Conferences 2010 http://www.grc.org/programs.aspx?year=2010&program=intrinsic
Related terms: foldome, Protein
structures: intrinsically disodered proteins, protein folding
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.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709268/ unknome:
At present, a large proportion of genes can only be described
as members of the unnamed - those with currently no functional
information! Dov Greenbaum "Interrelating Different Types of
Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf
See also D. Greenbaum et. al. "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function" Genome
Research 11 (9): 1484- 1502, Sept. 2001 Google = about 81 Aug.
15, 2005, about 164 Oct. 25, 2006 vaccinome:
Genomics could provide a new way to develop DNA vaccines
for malaria, which, if successful, could be applied toward other diseases.
"DNA vaccines would offer this flexibility because of the ease of
production, stability, and versatility of use," reported Stephen L.
Hoffman of the Naval Medical Research Institute. DNA vaccines are
fundamentally different from traditional ones, Hoffman notes. "The
difference in this approach is that we would be receiving DNA that encodes a
substance and asking our bodies to make a protein in response to it. However,
this approach, while potentially flexible, is also more complex. It requires
assessing potential antigen proteins encoded by the malaria genome, using
that "vaccinate" to induce antibodies, judging the accuracy of
expression, immunizing mice with each plasmid, and ultimately, developing a cultigens
DNA vaccine. [Ilene Schneider and Paul Shavlik "Harnessing the
Microbial World: Big Info in Small Packages" Scientist 13 (4): 1 Feb. 15,
1999] vaccinomics:
Using bioinformatics
and genomics for vaccine
development. Tom Hollow "Clad against all cades" Scientist 14
(18): 1 Sep. 18, 2000
variome:
Wikipedia
http://en.wikipedia.org/wiki/Variome
Variome TM:
is/was a structural pharmacogenomics database. variomics:
Study of variants of DNA, RNA and proteins. How/ does this
relate to population genomics? Related terms: SNPs
& other genetic
variations Google = about 20, Aug.
15, 2005, about 110 Oct. 25, 2006 VeloceGenomics:
The
aim of this study is to test the predictive power of in vivo multigrain RNA expression profiling in identifying the biologic activity of molecules...
a strategy of coupling in vivo compound testing with genomic
technologies. The process enables prediction of the mechanism of action and,
coupled with other relevant data, prediction of the suitability of compounds for
advancement in the drug development process. R. Papuan et. al,
"VeloceGenomics:
An Accelerated in Vivo Drug Discovery Approach to Rapidly Predict the
Biologic, Drug- Like Activity of Compounds, Proteins, or Genes" Pharma Res. 2005 Aug 13; [Epub ahead of print] Google = about 96 Oct.
25, 2006 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 -Omes Resources
Big
biology: The ’omes puzzle, Monya Baker
Nature
494, 416–419, (28 February 2013) doi:10.1038/494416a
27
February 2013
http://www.nature.com/news/big-biology-the-omes-puzzle-1.12484
How
to look for other unfamiliar terms
I have tried to determine the status
of all words known to be, or are suspected of being, proprietary names
or trademarks and to include this information. No judgment concerning the
legal status of such words is claimed.
Evolving terminology for emerging
technologies
Comments? Revisions? Suggestions?
Mary Chitty MSLS mchitty@healthtech.com
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
bibliomics:
A subset of high
quality and rare information, retrieved and organized by systematic literature-
searching tools from existing databases, and related to a subset of genes
functioning together in '-omic' sciences. Rihn BH, Vidal S, Nemurat C, Vachenc
S, Mohr S, Mazur F, Houdry P, Grandjean F, Visvikis S, Ducloy J., From
transcriptomics to bibliomics, Medical Science Monitor. 2003 Aug; 9(8): MT89- 95
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
Related terms: Cell biology;
Functional genomics
chemoproteomics:
Chemistry
chromatinomics:
The field of stem cell biology is currently being redefined. Stem cell
(hematopoietic and non-hematopoietic) differentiation has been considered
hierarchical in nature, but recent data suggest that there is no progenitor/stem
cell hierarchy, but rather a reversible continuum. The stem cell (hematopoietic
and non-hematopoietic) phenotype, the total differentiation capacity
(hematopoietic and non-hematopoietic), gene expression as well as other stem
cell functional characteristics (homing, receptor and adhesion molecule
expression) vary throughout a cell-cycle transit widely. This seems to be
dependent on shifting chromatin and gene expression with cell-cycle transit. The
published data on DNA methylation, histone acetylation, and also RNAi, the major
regulators of gene expression, conjoins very well and provides an explanation
for the major issues of stem cell biology. … We are entering a new era of stem
cell biology the era of 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 http://onlinelibrary.wiley.com/doi/10.1002/jcp.20071/abstract
chromonomics:
The
Genome Project will give us the genetic sequence, but understanding how that raw
data is used in the body will require a better understanding of chromosomes,
said speaker Huntington Willard of Case Western Reserve University. Willard
spoke of his attempts to build artificial human chromosomes, emphasizing how
much is left to learn about how chromosomes work. Only
half- joking, Willard suggested the most exciting field in genetics is not
genomics, but "chromonomics." Institute of Genetic Medicine Symposium,
Health Sciences Campus, Univ. of Southern California, 1998 http://www.usc.edu/hsc/info/pr/1vol4/403/igm.html
http://www.blackwell-synergy.com/doi/pdf/10.1046/j.1365-2796.1998.00277.x
Related term:
Imaging flow cytometry
Related term: Microarrays
categories substrate chips
impact
https://www.frontiersin.org/articles/10.3389/fpls.2014.00286/full
fluxomics:
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
G, Krömer
JO.
http://www.ncbi.nlm.nih.gov/pubmed/23279205
Related terms: unfoldome,
Protein structure, Structural genomics
foldomics:
fragmentome:
Low molecular weight metabolite, protein and peptide fragments being explored as
potential cancer biomarkers.
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
http://cancerres.aacrjournals.org/content/77/13_Supplement/3350
Broader term: lectinomics
glycogenomics,
glycome, glycomics: Glycosciences
Glycome
Wikipedia http://en.wikipedia.org/wiki/Glycome
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.
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
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088889
immunogenomics:
Molecular Medicine
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 http://www.nature.com/nmeth/journal/v2/n1/full/nmeth731.html
Related terms: Proteomics
categories kinase proteomics Protein categories
protein kinases
Related term: Protein categories protein
kinases
Wikipedia http://en.wikipedia.org/wiki/Lipidomics
Lipidomics gateway,
Wellcome Trust
https://www.lipidmaps.org/
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
Related terms: Gene definitions gene
localization, localize, locus; Proteins: protein
localization; Proteins: subcellular localization Narrower terms: localizome maps, yeast localizome
Related term: membrane proteins
Related terms Cell biology metabolite;
Drug discovery informatics:
in
silico cell, virtual cell
Due to pleiotropic
effects, the effect of a single
mutation may lead to the alteration of metabolite levels of seemingly unrelated
biochemical pathways. This is especially liable to happen if genes are
constitutively overexpressed or anti- sense inhibited. A comprehensive and
quantitative analysis of all metabolites could help researchers understand such
systems. Since such an analysis reveals the metabolome of the biological
system under study, this approach should be called metabolomics. Analogous to
proteins and proteomics, metabolomics, or metabonomics, is the
study of all the metabolites of a cell or organism. Identifying and quantifying
these components helps to reveal cellular regulation, pathways, activity, and
response under normal and other conditions. Brush up on
your 'omics, Chemical & Engineering News, 81(49): 20, Dec. 2003 http://pubs.acs.org/cen/coverstory/8149/8149genomics1.html
Related
terms metabonomics; Functional
genomics metabolic profiling; Mass
spectrometry, NMR See also Pharmacogenomics metabonomics/metabolomics
Wikipedia
http://en.wikipedia.org/wiki/Metabonomics
Related terms Functional
genomics; Pharmacogenomics Metabolic
engineering metabonomics Narrower term:
pharmacometabonomics: Metabolic engineering See under metabonomics
mitogenomics:
(genetics) The
study of the complete genome of
the mitochondrion of
an organism. Wiktionary accessed August 10, 2018
https://en.wiktionary.org/wiki/mitogenomics
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
http://arep.med.harvard.edu/labgc/
DNAs
RNAs
Protein interactions
Bio-System models
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 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.
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 biology, Expression,
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 Project http://worfdb.dfci.harvard.edu/
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
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
Wikipedia http://en.wikipedia.org/wiki/Phenome
Mouse Phenome Project, Jackson Labs, US
Google = about 235
Aug. 15, 2005, about 1,070 Oct. 25, 2006
Google
= about 16, Oct. 25, 2006, about 37 Feb 16 2011
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
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 Project:
http://physiome.org/
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
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
Google = about 146 Aug.
15, 2005, about 599 Oct. 25, 2006
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
Google = about 7 July 11, 2002;
about 9 Sept. 10, 2003, about 17 Aug. 15, 2005, about 57 Oct. 25, 2006
Google
- about 1,070 Dec 2 2013
International
Regulome Consortium http://www.internationalregulomeconsortium.ca/
Related terms: Expression, Functional 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
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
Related terms:
Expression
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 http://www.na-mic.org/Wiki/images/5/52/Systems_WG7.ppt.
Google = about 3 Oct.
25, 2006 Thanks to Gustavo Stolovitsky for calling my attention to this -ome.
Google
= about 42 Aug. 29, 2003 (in the context of RNA), about 48 Aug. 15, 2005,
about 76 Oct. 25, 2006
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
Google = about 12 Nov 5, 2005,
about 34 Oct. 25, 2006
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
Google = about 4 Nov 5, 2005,
about 19 Oct. 25, 2006
Google = about 12 Nov 5, 2005,
about 11 Oct. 25, 2006
Google toponomics
= about 1,090 Oct. 25, 2006
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
Human Toxome Project
https://www.ewg.org/sites/humantoxome/
http://caat.jhsph.edu/programs/HumanToxome/index.html
Narrower terms: cancer transcriptomes- human,
differential transcriptome, static transcriptome; in silico transcriptomics Related terms
interactome, translatome; Expression;
Microarrays; Proteomics
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
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
Google = about 176 Aug.
15, 2005, about 631 Oct. 25, 2006
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
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
Human Variome
Project http://www.humanvariomeproject.org/
Google = about 198 Aug.
15, 2005, about 13,700 Oct. 25, 2006
Google = about 168 Nov
5, 2005, about 822 Oct. 25, 2006
Omics Gateway http://www.nature.com/omics/index.html
Current content http://www.nature.com/omics/current/subject/index.html
omics.org, Alphabetical list of -omes and
-omics
http://omics.org/index.php/Alphabetically_ordered_list_of_omes_and_omics
omics.org Wiki http://omics.org/index.php/Main_Page
Wikipedia http://en.wikipedia.org/wiki/List_of_omics_topics_in_biology
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