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).

List of topics[edit]

-ome Field of study
(-omics)
Collection of Parent subject Notes
Allergenome Allergenomics[1] Proteomics of allergens
Bibliome Bibliomics Scientific bibliographic data
Trialome Medicine Human interventional trials data from clinical trial registries extended with trial results and links to resulting publications
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
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").[2]
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.[3][4]
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 [5]
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.[6]
Glycome Glycomics Glycans Glycobiology
Interferome Interferomics Interferons Immunology Also a database of the same name.[1]
Interactome Interactomics All interactions The term "interactomics" is generally not used. Instead, interactomes are considered the study of systems biology.[7][8]
Ionome Ionomics Inorganic biomolecules Molecular Biology
Kinome Kinomics Kinases Molecular Biology Proteins that add a phosphate group
Lipidome Lipidomics[9] 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
Obesidome Obesidomics Obesity related proteins Proteomics Coined by Pardo et al., 2012.[2]
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
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
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 [10]
Secretome Secretomics Secreted proteins Proteomics Subset of the proteome consisting of proteins actively exported from cells.[11]
Speechome Speecheomics Influences on language acquisition Coined by the Human Speechome Project[12]
Transcriptome Transcriptomics mRNA transcripts Molecular Biology
Toponome Toponomics Cell and tissue structure Molecular Biology
Phytochemome Phytochemomics Phytochemicals The term has been coined by del Castillo et al., 2013, Food Research International, [3]. 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

Hierarchy of topics[edit]

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

References[edit]

  1. ^ Yagami T, Haishima Y, Tsuchiya T, Tomitaka-Yagami A, Kano H, Matsunaga K. (2004). "Proteomic analysis of putative latex allergens". Int Arch Allergy Immunol 135 (1): 3–11. doi:10.1159/000080036. 
  2. ^ 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. 
  3. ^ Faisandier, Laurie; De Gaudemaris, Régis; Bicout, Dominique J. (2009). "Occupational Health Problem Network : the Exposome". arXiv:0907.3410 [stat.ME].
  4. ^ 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].
  5. ^ Cifuentes, A. (2009). "Food analysis and Foodomics". Journal of Chromatography A 1216 (43): 7109–7109. doi:10.1016/j.chroma.2009.09.018. 
  6. ^ "genome, n.". Oxford English Dictionary. March 2008. 
  7. ^ http://www.the-scientist.com/article/display/14769/
  8. ^ Main Page - Interactomics
  9. ^ Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes R.W, Cotter D, Dinasarapu A.R and Maurya M.R (2011). "Bioinformatics and Systems Biology of the Lipidome". Chemical Reviews 111 (10): 6452–6490. doi:10.1021/cr200295k. PMC 3383319. PMID 21939287. 
  10. ^ (2011) "15th EBM PROGRAM" Evolutionary Biology Meeting at Marseilles'.' Retrieved December 14, 2011.
  11. ^ 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. 
  12. ^ BBC article on the Speechome Project
  13. ^ Huser, V.; Cimino, J. J. (2012). "Precision and Negative Predictive Value of Links between ClinicalTrials.gov and PubMed". AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2012: 400–408. PMC 3540528. PMID 23304310.  edit
  14. ^ Dimitrov, DS (May–Jun 2010). "Therapeutic antibodies, vaccines and antibodyomes.". mAbs 2 (3): 347–56. doi:10.4161/mabs.2.3.11779. PMID 20400863. 

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