A Table of 'omes, Together with their Occurrence in the Literature and on the World Wide Web
| Term | Description | PubMed | Year of first PubMed citation | |
| Genome | The full complement of genetic information both coding and non coding in the organism | ∼1880000 | 66171 | 1932** |
| Proteome | The protein-coding regions of the genome | ∼63,000 | 703 | 1995 |
| Transcriptome | The population of mRNA transcripts in the cell, weighted by their expression levels | 3520 | 72 | 1997 |
| Physiome | Quantitative description of the physiological dynamics or functions of the whole organism | 2980 | 15 | 1997 |
| Metabolome | The quantitative complement of all the small molecules present in a cell in a specific physiological state | 349 | 12 | 1998 |
| Phenome | Qualitative identification of the form and function derived from genes, but lacking a quantitative, integrative definition | 4980 | 6 | 1995 |
| Morphome | The quantitative description of anatomical structure, biochemical and chemical composition of an intact organism, including its genome, proteome, cell, tissue and organ structures | 238 | 2 | 1996 |
| Interactome | List of interactions between all macromolecules in a cell | 56 | 2 | 1999 |
| Glycome | The population of carbohydrate molecules in the cell | 46 | 1 | 2000 |
| Secretome | The population of gene products that are secreted from the cell | 21 | 1 | 2000 |
| Ribonome | The population of RNA-coding regions of the genome | 1 | 1 | 2000 |
| 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 | 42 | – | – |
| Regulome | Genome-wide regulatory network of the cell | 18 | – | – |
| Cellome | The entire complement of molecules and their interactions within a cell | 17 | – | – |
| Operome | The characterization of proteins with unknown biological function | 8 | – | – |
| Transportome | The population of the gene products that are transported; this includes the secretome | 1 | – | – |
| Pseudome | The complement of pseudogenes in the proteome | – | – | – |
| Functome | The population of gene products classified by their functions | 1 | – | – |
| Translatome | The population of proteins in the cell, weighted by their expression levels | – | – | – |
| Foldome | The population of gene products classified through their tertiary structure | – | – | – |
| Unknome | Genes of unknown function | – | – | – |
-
Updated versions of this table will be available through our Web site at http://bioinfo.mbb.yale.edu/what-is-it. Note that we define five new 'omes: the translatome, the foldome, the pseudome, the functome, and the unknome. Our definition of the translatome is motivated partially by the ambiguities in term proteome, which has two competing definitions. First, broadly favored by computational biologists, it is a list of all the proteins encoded in the genome (Gaasterland 1999; Doolittle 2000). In this context, it is equivalent to what some refer to as the orfeome, (i.e., the set of genes excluding noncoding regions). Experimentalists, especially those involved in large-scale experiments such as expression analysis and 2D electrophoresis, favor a second definition. 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 latter. See http://www.genomic_glossaries.com/content/omes.asp for a listing of other 'omes and their definitions.
-
↵This term is also used in other fields with different meanings. **First citation according to the Oxford English Dictionary.
