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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).

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

[edit]
-ome Field of study
(-omics)		 Collection of Parent subject Notes
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
Bacteriome Bacteriomics Community 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 interactions The 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 microbiomics Collection 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, [1]. 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 Viromics complete set of viruses Virology
Volatilome Volatilomics complete collection of volatile metabolites Biomarkers

Hierarchy of topics

[edit]

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

References

[edit]
  1. ^ Yadav SP. (2007). "The Wholeness in Suffix -omics, -omes, and the Word Om". J Biomol Tech. 18 (5): 277. PMC 2392988. PMID 18166670.
  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)
  5. ^ Wild CP (2005). "Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology". Cancer Epidemiol. Biomarkers Prev. 14 (8): 1847–50. doi:10.1158/1055-9965.EPI-05-0456. PMID 16103423.
  6. ^ Faisandier, Laurie; De Gaudemaris, Régis; Bicout, Dominique J. (2009). "Occupational Health Problem Network : the Exposome". arXiv:0907.3410 [stat.ME].
  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.
  9. ^ "genome, n". Oxford English Dictionary. March 2008.[dead link‍]
  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
  13. ^ Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR (2011). "Bioinformatics and Systems Biology of the Lipidome". Chemical Reviews. 111 (10): 6452–6490. doi:10.1021/cr200295k. PMC 3383319. PMID 21939287.
  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.
  15. ^ Schaechter M (2014-05-15). "Of Terms in Biology: The Parvome". Small Things Considered. Retrieved 2020-04-21.
  16. ^ Davies J, Ryan KS (2012). "Introducing the parvome: bioactive compounds in the microbial world". ACS Chemical Biology. 7 (2): 252–259. doi:10.1021/cb200337h. PMID 22074935.
  17. ^ (2011) "15th EBM PROGRAM" Archived 2016-01-26 at the Wayback Machine Evolutionary Biology Meeting at Marseilles. Retrieved December 14, 2011.
  18. ^ Dov Greenbaum; Nicholas M. Luscombe; Ronald Jansen; et al. (2001). "Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function". Genome Research. 11 (9): 1463–1468. doi:10.1101/gr.207401. PMID 11544189.
  19. ^ BBC article on the Speechome Project
  20. ^ Synthetome
  21. ^ Carlson, Scott M.; Gozani, Or (2014-10-09). "Emerging technologies to map the protein methylome". Journal of Molecular Biology. 426 (20): 3350–3362. doi:10.1016/j.jmb.2014.04.024. ISSN 1089-8638. PMC 4177301. PMID 24805349.
  22. ^ Huser, V.; Cimino, J. J. (2012). "Precision and Negative Predictive Value of Links between ClinicalTrials.gov and PubMed". AMIA Annual Symposium Proceedings. 2012: 400–408. PMC 3540528. PMID 23304310.
  23. ^ Bouhifd, Mounir; Andersen, Melvin E.; Baghdikian, Christina; Boekelheide, Kim; Crofton, Kevin M.; Fornace, Albert J.; Kleensang, Andre; Li, Henghong; Livi, Carolina (2015-01-01). "The human toxome project". ALTEX. 32 (2): 112–124. doi:10.14573/altex.1502091. ISSN 1868-596X. PMC 4778566. PMID 25742299.
  24. ^ DeFelipe, Javier (2010-11-26). "From the Connectome to the Synaptome: An Epic Love Story". Science. 330 (6008): 1198–1201. Bibcode:2010Sci...330.1198D. doi:10.1126/science.1193378. ISSN 0036-8075. PMID 21109663. S2CID 33348231.
  25. ^ Kopell, Nancy J.; Gritton, Howard J.; Whittington, Miles A.; Kramer, Mark A. (2014-09-17). "Beyond the connectome: the dynome". Neuron. 83 (6): 1319–1328. doi:10.1016/j.neuron.2014.08.016. ISSN 1097-4199. PMC 4169213. PMID 25233314.
  26. ^ Dimitrov, DS (May–Jun 2010). "Therapeutic antibodies, vaccines and antibodyomes". mAbs. 2 (3): 347–56. doi:10.4161/mabs.2.3.11779. PMC 2881260. PMID 20400863.
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