Genetic Dietary Restriction Gene Manipulations Database

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Genetic Dietary Restriction (GenDR) Gene Manipulations Database is an informational resource on genes related to dietary restriction (DR), the most powerful non-genetic intervention shown to extend lifespan in a wide range of model organisms. Specifically, this dataset includes a manually curated list of DR-essential genes (“Gene manipulations”).

Complexity

DR-essential genes are genes that when genetically manipulated (e.g. by loss-of-functions such as mutation, transposition, or knockdown, or by gain-of-function like overexpression of additional transgenes) interfere with the ability of DR to extend the lifespan. In the ideal case, a genetic alteration of a DR-essential gene does not change the lifespan on ad libitum (AL) but totally cancels out lifespan-extension by a restricted diet.

In such cases, their selection criteria follow the same logic behind GenAge but focus specifically on those genes which are necessary for the modulation of the aging process by diet (which are by definition not necessary also aging genes).

A focus on genes from gene manipulation experiments means that the selection procedure for including genes related to DR will be more objective and unbiased, just like for GenAge. Nonetheless, as there are multiple different forms of DR regimens, most of which can be applied at several different levels of severity, genes were included if there is evidence that they interfere with at least one kind of DR regimen or strength of restriction. This includes by definition a shift in the response to the food concentration at which lifespan is extended (e.g. chico).

Each record in GenDR on a DR-essential gene contains comments (i.e. observations) about literature-based evidence and the reason(s) for inferring an association with DR. References are also cited. In the case of conflicting reports for a given gene, the policy is to still include this gene in GenDR but mention all the conflicting studies.

Specific for yeast, genes which are DR-essential in either a replicative or a chronological lifespan assay were included. Both the specific DR regimen and the aging model in which a gene was found to be essential for DR-lifespan extension is annotated in GenDR. The intention for using a broad definition of DR-essential genes, rather than a more specific one, is that this will make it possible to focus on mechanisms universal to DR and therefore more likely relevant to human aging.

Understanding the genetic basis of DR is of great importance not only to the biology of aging but to understand how diet can influence aging, longevity, health and age-related diseases. Pharmaceutical interventions that target DR-associated genes are also an emerging area with huge potential.

Date Created

2012

Last Modified

2017-06-24

Version

2017-06-24

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

Wuttke, D., Connor, R., Vora, C., Craig, T., Li, Y., Wood, S., Vasieva, O., Shmookler Reis, R., Tang, F., de Magalhaes, J. P. (2012) "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes." PLoS Genetics 8(8)e1002834. PubMed

Keywords

Senescence, Reverse Aging, Dietary Restrictions, Human Genomics, Dietary Guidelines, Caloric Restriction Aging, Genetic Association, Longevity, Aging

Other Titles

Dietary Guidelines Restriction Gene Manipulations Database, Dietary Restrictions Gene Manipulations Database, Caloric Restriction Aging Gene Manipulations Database

NameDescriptionTypeConstraints
Gene_IdGene ID number given to the genes related to aging in human in this dataset.integerunique : 1 required : 1 level : Nominal
Gene_SymbolGene symbol of the gene associated with aging or gene studied. The official gene symbol approved by the HAGR.stringunique : 1 required : 1
Species_NameName of the species associated with aging in this study.stringrequired : 1
Entrez_Gene_IdGeneID 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
Gene_NameThe recommended name used to officially represent a gene.stringrequired : 1
Gene IdGene SymbolSpecies NameEntrez Gene IdGene Name
1SIR2Saccharomyces cerevisiae851520Silent Information Regulator 2
2CDC25Saccharomyces cerevisiae851019Cell Division Cycle 25
3HAP4Saccharomyces cerevisiae853751Heme Activator Protein 4
4PNC1Saccharomyces cerevisiae852846Pyrazinamidase/NiCotinamidase 1
5CYT1Saccharomyces cerevisiae854231Cyt1p
6SCH9Saccharomyces cerevisiae856612serine/threonine protein kinase SCH9
196Mdh2Drosophila melanogaster42185Malate dehydrogenase 2
7NPT1Saccharomyces cerevisiae854384Nicotinate PhosphoribosylTransferase 1
9RPD3Saccharomyces cerevisiae855386Reduced Potassium Dependency 3
10HST2Saccharomyces cerevisiae856092Homolog of SIR Two (SIR2) 2