- All Genes Related to Senescence from The Human Dataset
- Telomeres Related to Aging from The Human Dataset
- All Genes Related to Ageing from The Human Dataset
- All Genes Related to Aging and Longevity from The Human Dataset
- Genetic Associations Related to Aging from The Human Dataset
- Aging Gene
- Telomeres and Aging
- Reverse Aging
- Genetic Association
All Genes Related to Aging from The Human Dataset
This dataset of All Genes Related to Aging from The Human Dataset is essentially a list of all genes related to aging in humans. It also includes the GenAge ID, symbol, aliases, name, Entrez gene id, SwissProt/UniProt, band, location start, location end, orientation, enzyme acetyl-CoA carboxylase promoter, orf, CDs, references, and orthologs.
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This dataset comes from 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 dataset includes all genes directly related to aging in humans plus the best candidate genes obtained from model organisms. Human genes are thus considerably better annotated and include more information. The dataset is manually curated by experts to ensure high-quality content.
This section of GenAge features genes possibly related to human aging. Briefly, genes were selected for inclusion based on findings in model organisms put in the context of human biology plus the few genes directly related to aging in humans. As such, genes should be seen as candidate human aging-associated genes. All entries are the result of an extensive review of the literature and feature considerable manually-curated annotation; the reason why each gene is featured in GenAge is given in each entry, in addition to other bibliographical references. GenAge also allowed the development of a system-level interpretation of aging which revealed that alterations to DNA are more relevant to aging than other forms of molecular damage.
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, such as a gene’s upregulation with age, in which causality is impossible to determine.
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 are genes commonly differentially expressed during mammalian aging which were identified by performing a meta-analysis of aging microarray data.
Given the above considerations, when using the human dataset, it should not be expected to find genes solely associated with a given age-related pathology but rather genes that can regulate the aging process as a whole or at least multiple aspects of the aging phenotype. As mentioned above, genes in the human dataset are by and large selected based on findings in model organisms, and thus they must be classified as putative, not proven, cases of genes associated with human aging.
Each gene in the human dataset was selected after an extensive review of the literature. Identified genes were associated with aging in model organisms as well as those that may directly modulate aging in mammals, including humans. Of course, genes related to aging in model systems may or may not be related to human aging, and so the literature was reviewed concerning human and mouse homologs of genes identified in lower organisms.
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, an in-depth description of aging in model systems was not provided but rather incorporated in the information gathered from multiple models to gather clues about the genetics of human aging.
Initially, the genes were grouped according to genes associated with organismal aging to obtain functional groups. These are groups of genes that share similar functions or are associated with similar pathways. Identifying the largest groups and those most strongly associated with aging allowed the selection of a number of other genes for inclusion in the human dataset due to their association with other genes or pathways previously linked to aging.
Information from several other databases was also evaluated and, in some cases, integrated into GenAge. Several genes only indirectly linked to aging are featured as a preference for false positives to false negatives; while users can ignore entries they consider irrelevant, false negatives can impact on research conducted using GenAge.
About this Dataset
John Snow Labs; Human Ageing Genomic Resources;
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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
Aging Gene, Senescence, Telomeres, Telomerase, Telomeres and Aging, Reverse Aging, Genetic Association, Longevity, Ageing
All Genes Related to Senescence from The Human Dataset, Telomeres Related to Aging from The Human Dataset, All Genes Related to Ageing from The Human Dataset, All Genes Related to Aging and Longevity from The Human Dataset, Genetic Associations Related to Aging from The Human Dataset
|GenAge_ID||Entry number or GenAge ID given to the genes related to aging in human in this dataset.||integer||level : Nominalrequired : 1unique : 1|
|Gene_Symbol||Short form of the gene related to aging in Humans.||string||required : 1|
|Gene_Aliases||Another short name form of the gene related to aging in Humans.||string||-|
|Gene_Full_Name||Complete name of the gene related to aging in Humans.||string||required : 1|
|Reason_for_Inclusion||Reason Why This Gene Is Included In The Dataset? In each human gene entry, the main reason for inclusion in the database is given. The following criteria are used:||string||required : 1|
|Entrez_Gene_Id||Entrez Gene generates unique integers (GeneID) as stable identifiers for genes.||integer||level : Nominalrequired : 1unique : 1|
|Swissprot_Uniprot_ID||UniProt/Swiss-Prot entry name of the gene. It is a unique entry name upon integration into UniProtKB/Swiss-Prot||string||-|
|Chromosomal_Band_Position||Cytogenetic location or position of a gene related to aging on the human chromosome.||string||-|
|Starting_Point||The location of the start position in base pairs of the human aging-related gene on the chromosome.||integer||level : Ratiorequired : 1|
|Ending_Point||The location of the end position in base pairs of the human aging-related gene on the chromosome.||integer||level : Ratiorequired : 1|
|Orientation||DNA strand orientation: The DNA strand orientation is by convention 5' → 3'. This concept allows determining, for a given gene, the gene orientation relative to the 5' → 3' DNA strand. Sense: same direction (+1 or no sign); antisense: opposite direction (-1)||string||required : 1|
|Accession_Number_For_Promoter_Sequence||Eucaryotic promoter sequence identifier number.||string||-|
|Open_Reading_Frame_Accession_Number||Identifier number given by HGNC to the region of the nucleotide sequences from the start codon (ATG) to the stop codon also called as the Open Reading frame - ACC ORF.||string||required : 1|
|Coding_DNA_Sequence_Accession_Number||Identifier number given by HGNC to Coding Sequence (CDS) which is the actual region of DNA that is translated to form proteins - ACC CDS.||string||-|
|References||Pubmed ID numbers from the NCBI website for referring the article.||string||required : 1|
|Ortholog_Genes||Genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Gene symbol and the species are described under this heading.||string||-|
|GenAge ID||Gene Symbol||Gene Aliases||Gene Full Name||Reason for Inclusion||Entrez Gene Id||Swissprot Uniprot ID||Chromosomal Band Position||Starting Point||Ending Point||Orientation||Accession Number For Promoter Sequence||Open Reading Frame Accession Number||Coding DNA Sequence Accession Number||References||Ortholog Genes|
|1||GHR||GHBP||growth hormone receptor||mammal||2690||GHR_HUMAN||5p13-p12||42423775||42721878||1||NM_000163||NP_000154||9371826,12933651,10875265,11213276,2233903,10895047,12392795,14698816,15295107,15308771,15342923,8612101,15466429,15536017,15582293,15621211,15919742,16129095,15985475,16339324,16524678,16682650,16799137,16939484,17183314,17173483,21325617,19286975,19234595,7664676,16282554||ghra;Danio rerio,Ghr;Mus musculus,Ghr;Rattus norvegicus|
|2||GHRH||GHRF||growth hormone releasing hormone||mammal||2691||SLIB_HUMAN||20q11.2||37251086||37256896||-1||HS_GHRH||NM_021081||NP_066567||11443181,11213276,12392795,14751587,15342923,15579798,8670892,10522985,8421089,15464751,10654626,11283314,11742825,24175087,7904758||ghrh;Danio rerio,Ghrh;Mus musculus,Ghrh;Rattus norvegicus|
|3||SHC1||p66 ShcA SHC||SHC (Src homology 2 domain containing) transforming protein 1||mammal||6464||SHC1_HUMAN||1q21||154962298||154974483||-1||NM_003029||NP_003020||10580504,11884717,12032825,12571362,12483226,14530863,14501182,12763525,7564569,14698816,15078873,15036421,15295107,15308771,15466429,15582293,15339240,15992607,15930121,16439820,16763167,18413607,18838380,19327338,19892704,20085805,20624962,16026332||si:dkey-246i14.4;Danio rerio,Shc1;Mus musculus,Shc1;Rattus norvegicus|
|4||POU1F1||GHF-1 POU1F1a PIT1||POU class 1 homeobox 1||mammal||5449||PIT1_HUMAN||3p11||87259633||87276587||-1||NM_000306||NP_000297||11371619,1509263,1509262,11718806,10549301,8612966,14698816,12173688,15295107,15342923,15147972,15466429,15582293,15699523,15888324,15621211,15919742,16449798,11283314,15459176||pou1f1;Danio rerio,Pou1f1;Mus musculus,Pou1f1;Rattus norvegicus|
|5||PROP1||PROP paired-like homeobox 1||mammal||5626||PROP1_HUMAN||5q35.3||177992235||177996242||-1||NM_006261||NP_006252||8900272,11487592,12915652,9920061,11213270,11927387,8612966,12663691,14698816,12173688,15295107,15342923,15466429,15569359,15664625,15664737,15718052,15860463,15621211,15919742,11283314,11719795,16611697,15459176,20679996,19286975,20720157,8934515||Prop1;Mus musculus,Prop1;Rattus norvegicus|
|7||TERC||TR hTR TRC3 DKCA1 PFBMFT2 SCARNA19||telomerase RNA component||mammal,cell||7012||3q26||169764609||169765060||-1||NR_001566||12540856,7544491,9454332,1582420,9335332,10089885,2655926,1689810,10973262,9849895,9742964,9560153,11850781,10568811,15974869,11574891,11081503,15098033,15235603,15189140,15312299,15367665,14746617,15466429,15556289,15545322,15326392,12174094,20139977,23159929,23535734,12426399,16284252,19915151|
|8||TERT||TRT TP2 TCS1 hEST2 EST2||telomerase reverse transcriptase||cell,functional||7015||TERT_HUMAN||5p15.33||1253147||1295069||-1||NM_003219||NP_003210||8978029,9110970,9454332,9288757,1582420,11387197,12034875,2655926,12917625,9849895,9742964,7761406,11850781,10568811,12764382,8692840,8618017,7727765,8808676,15974869,9600234,11081503,12527915,12827497,9988278,11452025,11277998,12717449,12729798,9328464,12089551,15079066,15189140,10440377,15247011,15312299,14726476,10606235,15556289,15574496,15326392,15688016,15814878,15905204,16477310,18073191,19571879,19013273,21307849,21113150,20643931,18184747,15184392,18843043,15843522,19580824,23349637,23159929,23535731,23535734,16107853,23744274,9973199,20605919,19915151||tert;Danio rerio,Tert;Mus musculus,Tert;Rattus norvegicus,EST2;Saccharomyces cerevisiae,trt1;Schizosaccharomyces pombe|
|9||ATM||TEL1 TELO1 ATA ATDC ATC ATD||ATM serine/threonine kinase||mammal||472||ATM_HUMAN||11q22-q23||108222832||108369099||1||NM_000051||NP_000042||12540856,9733514,9733515,12142523,9363685,10037601,12919958,2005780,9117983,12215213,9312059,9353177,2836804,10783165,10802669,10839545,10567403,14712078,14707289,15073328,15059890,11331603,15122331,12526788,15353794,14745549,7777860,15466429,15655364,15345673,15905204,15733840,8843194,11172010,10691732,12629512,16675955,10435585,21459046,20966255,21186350,19524511,17522062,18804090,20453858,20194434,23019125,23277187,18931659,12447382,9405657,23408054||tefu;Drosophila melanogaster,atm;Danio rerio,Atm;Mus musculus,Atm;Rattus norvegicus|
|10||PLAU||URK UPA||plasminogen activator, urokinase||mammal||5328||UROK_HUMAN||10q22.2||73911104||73917500||1||HS_PLAU||NM_002658||NP_002649||12898287,12149463,12954482,15247062,10638529,15621205,16139868,16787960,9060969||plaua;Danio rerio,Plau;Mus musculus,Plau;Rattus norvegicus|