Common Model Organisms in Aging as Human Homologs

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This dataset of Common Model Organisms in Aging as Human Homologs is essentially a list of genes with a common ancestral DNA sequence with humans. It also includes a brief description of the species, symbol and model organism among others. For a gene to be featured, its association with aging and/or longevity must be unambiguous, and hence most genes were selected based on genetic manipulations and not mere correlations.

Complexity

This dataset is a list of genes related to a second gene by descent from humans that has a common ancestral DNA sequence, which is termed as homolog.

This dataset comes from the GenAge (Genetic Aging) section of the Human Ageing Genomic Resources (HAGR) which is a repository containing information about the genetics of human aging. Information is obtained from modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.

The human dataset in GenAge is a curated database of genes that may regulate human aging or that at least might be considerably associated with the human aging phenotype. It is a functional genomics database designed to provide up-to-date information in the context of aging and molecular genetics. Because the focus is on the fundamental aging process, what some authors call senescence, and not just age-related pathologies, the human dataset features primarily genes related to biological aging rather than genes that only affect longevity by having an impact on overall health.

This is an important point because longevity can be influenced by factors unrelated to aging, and the distinction is crucial, albeit often difficult. (For those interested in genes associated with human longevity, please refer to the LongevityMap). Likewise, a gene is differentially expressed during aging is not by itself proof that this gene is causally involved in the aging process. Nonetheless, for researchers studying transcriptional changes with age, also available is a separate dataset of genes commonly differentially expressed during mammalian aging which were identified by performing a meta-analysis of aging microarray data.

Each gene in the human homolog dataset was selected after an extensive review of the literature. They were identified genes associated with aging in model organisms as well as those that may directly modulate aging in mammals, including humans. Each gene was selected or excluded based on its association with aging in the different model systems, with priority being given to organisms biologically and evolutionary more closely related to humans. Because the focus is on the genetic basis of human aging, there was no in-depth description of aging in model systems but was rather incorporated in the information gathered from multiple models to gather clues about the genetics of human aging.

In each human gene entry, the main reason for inclusion in the database is given. The following criteria are used:

1. Evidence directly linking the gene product to aging in humans (human)
2. Evidence directly linking the gene product to aging in a mammalian model organism (mammal)
3. Evidence directly linking the gene product to aging in a non-mammalian model organism (model)
4. Evidence directly linking the gene product to aging in a cellular model system (cell)
5. Evidence linking the gene or its product to human longevity and/or multiple age-related phenotypes (human link)
6. Evidence directly linking the gene product to the regulation or control of genes previously linked to aging (upstream)
7. Evidence linking the gene product to a pathway or mechanism linked to aging (functional)
8. Evidence showing the gene product to act downstream of a pathway, mechanism, or other gene product linked to aging (downstream)
9. Indirect or inconclusive evidence linking the gene product to aging (putative)

GenAge has its limits but the aim is to include the most relevant information, but not all the data are available. The human dataset in GenAge can be helpful in more classical genetic studies of aging and longevity. For example, if a given chromosomal region is identified, it is possible to look up which genes are present in that region. Although GenAge is not a bibliographic database, the bibliographic references in the human dataset can be a useful resource.

Date Created

2013

Last Modified

2015-10-11

Version

2015-10-11

Update Frequency

Irregular

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs; Human Ageing Genomic Resources;

Source License URL

Source License Requirements

N/A

Source Citation

Tacutu, R., Craig, T., Budovsky, A., Wuttke, D., Lehmann, G., Taranukha, D., Costa, J., Fraifeld, V. E., de Magalhaes, J. P. (2013) "Human Ageing Genomic Resources Integrated databases and tools for the biology and genetics of ageing." Nucleic Acids Research 41(D1)D1027-D1033. PubMed

Keywords

Model Organism, Organism Examples, Genetic Model, Genome Database, Gene Database, Genomics, Gene, Genetic Association, Aging, Longevity

Other Titles

Model Organisms in Aging as Human Homologs, Organism Samples in Aging as Human Homologs, Genetic Model Organisms in Aging as Human Homologs, Genome Database of Aging In Model Organisms, Gene Database of Aging In Human Homologs, Genetic Association in Longevity or Aging In Human Homologs

NameDescriptionTypeConstraints
Type_of_SpeciesType of the model organism species.stringrequired : 1
SymbolSymbol assigned to the model organism speciesstringrequired : 1
Entrez_IdEntrez ID is a unique identifier that is assigned to a gene record in Entrez Gene. Entry number with individual genes starting with single integer digits.integerlevel : Nominal
Model_OrganismType of model organism where the human homolog was taken.stringrequired : 1
Model_Organism_SymbolSymbol assigned to the model organismstringrequired : 1
Model_Organism_Entrez_IDA gene ID for a model organism is a unique identifier that is assigned to a gene record in Entrez Gene. Entry number with individual genes starting with single integer digits.integerrequired : 1 level : Nominal
Type_of_SpeciesSymbolEntrez_IdModel_OrganismModel_Organism_SymbolModel_Organism_Entrez_ID
Homo sapiensKL9365Mus musculusKl16591
Homo sapiensATM472Mus musculusAtm11920
Homo sapiensBAX581Mus musculusBax12028
Homo sapiensCAT847Mus musculusCat12359
Homo sapiensGH12688Mus musculusGh14599
Homo sapiensATR545Mus musculusAtr245000
Homo sapiensFXN2395Mus musculusFxn14297
Homo sapiensCSH21443Mus musculusGh14599
Homo sapiensGHR2690Mus musculusGhr14600
Homo sapiensXPA7507Mus musculusXpa22590