All Genes Related to Aging from The Human Dataset

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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.

Complexity

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.

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

John Snow Labs Standard License

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

Aging Gene, Senescence, Telomeres, Telomerase, Telomeres and Aging, Reverse Aging, Genetic Association, Longevity, Ageing

Other Titles

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

Name Description Type Constraints
GenAge_IDEntry number or GenAge ID given to the genes related to aging in human in this dataset.integerunique : 1 required : 1 level : Nominal
Gene_SymbolShort form of the gene related to aging in Humans.stringrequired : 1
Gene_AliasesAnother short name form of the gene related to aging in Humans.string-
Gene_Full_NameComplete name of the gene related to aging in Humans.stringrequired : 1
Reason_for_InclusionReason 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:stringrequired : 1
Entrez_Gene_IdEntrez Gene generates unique integers (GeneID) as stable identifiers for genes.integerunique : 1 required : 1 level : Nominal
Swissprot_Uniprot_IDUniProt/Swiss-Prot entry name of the gene. It is a unique entry name upon integration into UniProtKB/Swiss-Protstring-
Chromosomal_Band_PositionCytogenetic location or position of a gene related to aging on the human chromosome.string-
Starting_PointThe location of the start position in base pairs of the human aging-related gene on the chromosome.integerrequired : 1 level : Ratio
Ending_PointThe location of the end position in base pairs of the human aging-related gene on the chromosome.integerrequired : 1 level : Ratio
OrientationDNA 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)stringrequired : 1
Accession_Number_For_Promoter_SequenceEucaryotic promoter sequence identifier number.string-
Open_Reading_Frame_Accession_NumberIdentifier 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.stringrequired : 1
Coding_DNA_Sequence_Accession_NumberIdentifier number given by HGNC to Coding Sequence (CDS) which is the actual region of DNA that is translated to form proteins - ACC CDS.string-
ReferencesPubmed ID numbers from the NCBI website for referring the article.stringrequired : 1
Ortholog_GenesGenes 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_IDGene_SymbolGene_AliasesGene_Full_NameReason_for_InclusionEntrez_Gene_IdSwissprot_Uniprot_IDChromosomal_Band_PositionStarting_PointEnding_PointOrientationAccession_Number_For_Promoter_SequenceOpen_Reading_Frame_Accession_NumberCoding_DNA_Sequence_Accession_NumberReferencesOrtholog_Genes
292MT1EMTD MT1metallothionein 1Eputative4493MT1E_HUMAN16q1356625673566271131NM_175617NP_78331616585059
304CTF1CT-1 CT1cardiotrophin 1putative1489CTF1_HUMAN16p11.230896607309035601NM_001330NP_00132123172930,23541490Ctf1;Mus musculus,Ctf1;Rattus norvegicus
184HESX1RPX ANFHESX homeobox 1upstream8820HESX1_HUMAN3p14.35719791657200252-1NM_003865NP_0038569620767,12173688,11136712,11283314Hesx1;Mus musculus,Hesx1;Rattus norvegicus
100SSTR3somatostatin receptor 3downstream6753SSR3_HUMAN22q13.13720423737212376-1NM_001051NP_00104210499533,12601018sstr3;Danio rerio,Sstr3;Mus musculus,Sstr3;Rattus norvegicus
167IL7IL-7interleukin 7putative3574IL7_HUMAN8q12-q137873277278805523-1NM_000880NP_00087111772533,11160192,9414271,7680962,11602642,9630227Il7;Mus musculus,Il7;Rattus norvegicus
156GSTA4glutathione S-transferase alpha 4functional2941GSTA4_HUMAN6p12.15297794852995380-1NM_001512NP_00150312956415,12742531,12600725,12470840,15664625,15664737,16164425,16260109
255ADCY5AC5adenylate cyclase 5mammal111ADCY5_HUMAN3q21.1123282296123448545-1NM_183357NP_89920017662940,23020244,20372150adcy5;Danio rerio,Adcy5;Mus musculus,Adcy5;Rattus norvegicus
280PYCR1P5Cpyrroline-5-carboxylate reductase 1putative5831B4DMU0_HUMAN17q25.38193238681937257-1NM_153824NP_72254619648921,19576563,21567914Pycr1;Mus musculus,Pycr1;Rattus norvegicus
111GTF2H2BTF2 TFIIH BTF2P44 T-BTF2P44 p44general transcription factor IIH, polypeptide 2, 44kDadownstream2966TF2H2_HUMAN5q13.270415374704479061NM_001515NP_00150611341993,14550632,10416615
181LMNB1lamin B1functional4001LMNB1_HUMAN5q23.21267766231268370201NM_005573NP_0055648838815,15331638,15688064,16543417,15232008lmnb1;Danio rerio,Lmnb1;Mus musculus,Lmnb1;Rattus norvegicus