List of omics topics in biology

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Inspired by the terms genome and genomics, other words to describe complete biological datasets, mostly sets of biomolecules originating from one organism, have been coined with the suffix -ome and -omics . Some of these terms are related to each other in a hierarchical fashion. For example, the genome contains the ORFeome, which gives rise to the transcriptome, which is translated to the proteome. Other terms are overlapping and refer to the structure and/or function of a subset of proteins (e.g. glycome, kinome).

Contents

An omicist is a scientist who studies omeomics, cataloging all the “omics” subfields. [1]

Omics.org is a Wiki that collects and alphabetically lists all the known "omes" and "omics." [2]

List of topics

-omeField of study
(-omics)		Collection ofParent subjectNotes
Acetylome Acetylomics [3] complete set of proteins and their corresponding lysine residues that undergo acetylation Molecular Biology
Allergenome Allergenomics [4] Proteomics of allergens Genetics
Antibodyome Antibodyomics The complete set of antibodies present in an organism Immunology
Archaeome Archaeomics The collective genetic material of microorganisms in archaeological samples Microbiology
BacteriomeBacteriomicsCommunity of bacteria associated with a particular ecological niche or host organism Microbiology
Bibliome Bibliomics Scientific bibliographic data
Biointeractome Biointeractomics The complete set of molecular interactions within a biological system Molecular Biology
Biome The whole set of ecological community of organisms and environments Ecology
Cellome Cellomics Cellular Biology
Connectome Connectomics Structural and functional brain connectivity at different spatiotemporal scales Neuroscience
Cytome Cytomics Cellular systems of an organism Cytology
Editome RNA editing sites
Embryome Embryomics Cell lineages of embryonic cells, genes expressed and antigens present during development Embryology
Envirome Enviromics Gene related environment factors (envirome)
Environmental DNA Environmental omics Sequencing of ambient DNA
Epigenome Epigenomics Epigenetic modifications Molecular genetics Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, collectively known as the epigenome
Exposome (2005) Exposomics An individual's environmental exposures, including in the prenatal environment Molecular genetics A proposed term and field of study of the disease-causing effects of environmental factors (the "nurture" component of "nature vs. nurture"). [5]
Exposome (2009)Composite occupational exposures and occupational health problems Occupational safety and health The proposers of this term were aware of the previous term as used above but proposed to apply the term to a new field. [6] [7]
Exome Exomics Exons in a genome Molecular Genetics
Foodome Foodomics Food and Nutrition issues related to bioactivity, quality, safety and traceability of foods through the application and integration of advanced omics technologies to improve consumer's well-being, health, and confidence. Nutrition The term was first defined in 2009 [8]
Genome Genomics
(Classical genetics)		 Genes
(DNA sequences/Chromosomes)		 Genetics "Genome" refers to the set of all genes in an organism. However, "genome" was coined decades before it was discovered that most DNA is "non-coding" and not part of a gene; thus, "genome" originally referred to the entire collection of DNA within an organism. Today, both definitions are used, depending on the context. [9]
Glycome Glycomics Glycans Glycobiology
Hologenome Hologenomics Genomes of community members (i.e., holobionts) Metagenomics
Humeome Humeomics The chemical components of soil humus Soil science
Interferome Interferomics Interferons Immunology Also a database of the same name. [10]
Interactome Interactomics All interactionsThe term "interactomics" is generally not used. Instead, interactomes are considered the study of systems biology. [11] [12]
Ionome Ionomics Inorganic biomolecules Molecular Biology
Kinome Kinomics Kinases Molecular Biology Proteins that add a phosphate group
Lipidome Lipidomics [13] Lipids Biochemistry
Mechanome Mechanomics The mechanical systems within an organism
Metabolome Metabolomics Metabolites All products of a biological reaction (including intermediates)
Metagenome Metagenomics Genetic material found in an environmental sample Molecular Biology The genetic material is assumed to contain DNA from multiple organisms and therefore multiple genomes, hence the inclusion of the prefix meta-.
Metallome Metallomics Metals and metalloids
Microbiome microbiomicsCollection of microorganisms in another organism such as an animal Microbiology
Obesidome Obesidomics Obesity related proteins Proteomics Coined by Pardo et al., 2012. [14]
ORFeome ORFeomics Open reading frames (ORFs) Molecular Genetics
Organome Organomics Organ interactions Cellular Signalling / Cell Signaling and Tissue Engineering The study of crosstalk between organs using physiologically relevant in-vitro models
Parvome Parvomics Secondary metabolites Biochemistry Coined by Mark Martin and introduced by Julian Davies in 2008, referring to the Latin parvus for "small", and describing the "humungous microbial world of small (secreted) molecules of great structural diversity". [15] See also [16]
Pharmacogenetics Pharmacogenetics SNPs and their effect on pharmacokinetics and pharmacodynamics Pharmacogenomics
Genomics
Pharmacogenome Pharmacogenomics The effect of changes on the genome on pharmacology Pharmacogenetics
Genomics
Phenome Phenomics Phenotypes Genetics
Physiome Physiomics Physiology of an organism
Phytochemome Phytochemomics Phytochemicals The term has been coined by del Castillo et al., 2013, Food Research International, . Phytochemomics is a comprehensive concept aimed to increase the knowledge of phytochemicals' bioactivity which is of growing importance in agricultural, food, medicine and cosmetic sciences
Proteome Proteomics Proteins Molecular Biology
Regulome Regulomics Transcription factors and other molecules involved in the regulation of gene expression Molecular Biology
Researchsome Research areas covered by an individual researcher or institution Research Coined by Ivan Erill at the 2011 EBM meeting [17]
Secretome Secretomics Secreted proteins Proteomics Subset of the proteome consisting of proteins actively exported from cells. [18]
Speechome Speecheomics Influences on language acquisition Coined by the Human Speechome Project [19]
Synthetome A set of artificial genes in an organism [20] [ circular reference ]
Transcriptome Transcriptomics All RNA molecules including mRNA, rRNA, tRNA and other ncRNAs Molecular Biology
Trialome Medicine Human interventional trials data from clinical trial registries extended with trial results and links to resulting publications
Toponome Toponomics Cell and tissue structure Molecular Biology
Virome Viromicscomplete set of viruses Virology
Volatilome Volatilomics complete collection of volatile metabolites Biomarkers

Hierarchy of topics

For the sake of clarity, some topics are listed more than once.

Related Research Articles

<span class="mw-page-title-main">Proteome</span> Set of proteins that can be expressed by a genome, cell, tissue, or organism

The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.

<span class="mw-page-title-main">Genomics</span> Discipline in genetics

Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

Glycomics is the comprehensive study of glycomes, including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the omics naming convention established by genomics and proteomics.

<span class="mw-page-title-main">Glycome</span> Complete set of all sugars, free or bound, in an organism.

A glycome is the entire complement or complete set of all sugars, whether free or chemically bound in more complex molecules, of an organism. An alternative definition is the entirety of carbohydrates in a cell. The glycome may in fact be one of the most complex entities in nature. "Glycomics, analogous to genomics and proteomics, is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology.

<span class="mw-page-title-main">Omics</span> Suffix in biology

The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.

The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term transcriptome is a portmanteau of the words transcript and genome; it is associated with the process of transcript production during the biological process of transcription.

Regulome refers to the whole set of regulatory components in a cell. Those components can be regulatory elements, genes, mRNAs, proteins, and metabolites. The description includes the interplay of regulatory effects between these components, and their dependence on variables such as subcellular localization, tissue, developmental stage, and pathological state.

<span class="mw-page-title-main">Lipidome</span> Totality of lipids in cells

The 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. It can be studied using mass spectrometry and bioinformatics as well as traditional lab-based methods. The lipidome of a cell can be subdivided into the membrane-lipidome and mediator-lipidome.

In, molecular genetics, an ORFeome refers to the complete set of open reading frames (ORFs) in a genome. The term may also be used to describe a set of cloned ORFs. ORFs correspond to the protein coding sequences (CDS) of genes. ORFs can be found in genome sequences by computer programs such as GENSCAN and then amplified by PCR. While this is relatively trivial in bacteria the problem is non-trivial in eukaryotic genomes because of the presence of introns and exons as well as splice variants.

Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. While metabolomics can provide instantaneous information on the metabolites in a biological sample, metabolism is a dynamic process. The significance of fluxomics is that metabolic fluxes determine the cellular phenotype. It has the added advantage of being based on the metabolome which has fewer components than the genome or proteome.

<span class="mw-page-title-main">60S ribosomal protein L36</span> Protein found in humans

60S ribosomal protein L36 is a protein that in humans is encoded by the RPL36 gene.

<span class="mw-page-title-main">Peroxisomal membrane protein PMP34</span> Protein found in humans

Peroxisomal membrane protein PMP34 is a protein that in humans is encoded by the SLC25A17 gene.

<span class="mw-page-title-main">L3MBTL2</span> Protein-coding gene in the species Homo sapiens

Lethal(3)malignant brain tumor-like 2 protein is a protein that in humans is encoded by the L3MBTL2 gene.

<span class="mw-page-title-main">ZNF471</span> Protein-coding gene in the species Homo sapiens

Zinc finger protein 471 is a protein that in humans is encoded by the ZNF471 gene.

<span class="mw-page-title-main">Exposome</span>

The exposome is a concept used to describe environmental exposures that an individual encounters throughout life, and how these exposures impact biology and health. It encompasses both external and internal factors, including chemical, physical, biological, and social factors that may influence human health.

The secretome is the set of proteins expressed by an organism and secreted into the extracellular space. In humans, this subset of the proteome encompasses 13-20% of all proteins, including cytokines, growth factors, extracellular matrix proteins and regulators, and shed receptors. The secretome of a specific tissue can be measured by mass spectrometry and its analysis constitutes a type of proteomics known as secretomics.

<span class="mw-page-title-main">Multiomics</span> Biological analysis approach

Multiomics, multi-omics, integrative omics, "panomics" or "pan-omics" is a biological analysis approach in which the data sets are multiple "omes", such as the genome, proteome, transcriptome, epigenome, metabolome, and microbiome ; in other words, the use of multiple omics technologies to study life in a concerted way. By combining these "omes", scientists can analyze complex biological big data to find novel associations between biological entities, pinpoint relevant biomarkers and build elaborate markers of disease and physiology. In doing so, multiomics integrates diverse omics data to find a coherently matching geno-pheno-envirotype relationship or association. The OmicTools service lists more than 99 softwares related to multiomic data analysis, as well as more than 99 databases on the topic.

Michael P. Snyder is an American genomicist and the Stanford B. Ascherman Professor, and since 2009, chair of genetics and director of genomics and personalized medicine at Stanford University. He is the former director of the Yale Center for Genomics and Proteomics. He was elected to the American Academy of Arts and Sciences in 2015. During his tenure as chair of the department at Stanford, U.S. News & World Report has ranked Stanford University first or tied for first in genetics, genomics and bioinformatics under his leadership.

<span class="mw-page-title-main">Translatomics</span>

Translatomics is the study of all open reading frames (ORFs) that are being actively translated in a cell or organism. This collection of ORFs is called the translatome. Characterizing a cell's translatome can give insight into the array of biological pathways that are active in the cell. According to the central dogma of molecular biology, the DNA in a cell is transcribed to produce RNA, which is then translated to produce a protein. Thousands of proteins are encoded in an organism's genome, and the proteins present in a cell cooperatively carry out many functions to support the life of the cell. Under various conditions, such as during stress or specific timepoints in development, the cell may require different biological pathways to be active, and therefore require a different collection of proteins. Depending on intrinsic and environmental conditions, the collection of proteins being made at one time varies. Translatomic techniques can be used to take a "snapshot" of this collection of actively translating ORFs, which can give information about which biological pathways the cell is activating under the present conditions.

<span class="mw-page-title-main">Tohoku Medical Megabank Project</span>

The Tohoku Medical Megabank Project is a national project in Japan, which started in 2012. The mission of the Tohoku Medical Megabank (TMM) project is to carry out a long-term health survey in the Miyagi and Iwate prefectures, which were affected by the Great East Japan Earthquake, and provide the research infrastructure for the development of personalized medicine by establishing a biobank and conducting cohort studies.

References

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  2. ↑ "Error 403(Invalid User)".
  3. ↑ Wen, Siqi; Li, Jiajia; Yang, Jingru; Li, Biao; Li, Na; Zhan, Xianquan (2021). "Quantitative Acetylomics Revealed Acetylation-Mediated Molecular Pathway Network Changes in Human Nonfunctional Pituitary Neuroendocrine Tumors". Frontiers in Endocrinology. 12. doi: 10.3389/fendo.2021.753606 . ISSN   1664-2392. PMC   8546192 . PMID   34712204.
  4. ↑ Yagami T, Haishima Y, Tsuchiya T, Tomitaka-Yagami A, Kano H, Matsunaga K.; Haishima; Tsuchiya; Tomitaka-Yagami; Kano; Matsunaga (2004). "Proteomic analysis of putative latex allergens". Int Arch Allergy Immunol. 135 (1): 3–11. doi:10.1159/000080036. PMID   15286439. S2CID   35112557.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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  7. ↑ Faisandier, Laurie; Bonneterre, Vincent; De Gaudemaris, Régis; Bicout, Dominique J. (2009). "A network-based approach for surveillance of occupational health exposures". arXiv: 0907.3355 [stat.ME].
  8. ↑ Cifuentes, A. (2009). "Food analysis and Foodomics". Journal of Chromatography A. 1216 (43): 7109. doi:10.1016/j.chroma.2009.09.018. hdl: 10261/154212 . PMID   19765718.
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  10. ↑ "Home". interferome.org.
  11. ↑ "Protein Snapshots". www.the-scientist.com. Archived from the original on December 2, 2008.
  12. ↑ Main Page – Interactomics Archived July 6, 2008, at the Wayback Machine
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  14. ↑ Pardo, Maria; Roca-Rivada, Arturo; Seoane, Luisa Maria; Casanueva, Felipe F. (2012). "Obesidomics: Contribution of adipose tissue secretome analysis to obesity research". Endocrine. 41 (3): 374–383. doi:10.1007/s12020-012-9617-z. PMID   22434412. S2CID   20503653.
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  19. ↑ BBC article on the Speechome Project
  20. ↑ Synthetome
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