Research Centre Information Centre AgeFactDB
Release 1 - Aug 15, 2013

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AgeFactDB - Release Info

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Remarks

Ageing factors from different sources are merged, if possible. Genes are merged by their NCBI gene ID, if assigned, and otherwise by the combination of gene symbol and species name. For genes with NCBI gene IDs gene symbol and species name are also available, of course. They are, however, not merged with genes for which the NCBI gene ID is not assigned, because it cannot be excluded that the same gene symbol/species combination is used for different genes. Compounds and other factors are merged by their name. Currently, the normalization for compounds and other factors is done manually, so the current release may be partially redundant for compounds and ageing factors.

The lifespan effect values from the Lifespan Observations Database are harmonized according to the lifespan change values reported (positive change = increased, negative change = decreased).

Lifespan observations, independent from the input source (currently: Lifespan Observations Database and GenAge), are significant, if the difference between observed value and base value is at least 5%. If this difference can not be determined, the significance information from the source is taken, if provided.

A homology analysis is applied for genes with experimental evidence for ageing relevance. If only lifespan data are available, the lifespan change must be greater than 5% for at least one observation to take the gene into account. For homology groups with only one experimentally known ageing-relevant gene, computational evidence for ageing relevance is assigned to all other genes but not to the experimentally known one. For homology groups with more than one experimentally known ageing relevant gene, formally computational ageing relevance is assigned to all genes including the ones with experimentally known ageing relevance.

Release Statistics

Release Number : 1
Release Date : Aug 15, 2013
Ageing Factors : 16599
Genes : 16450
Compounds : 91
Other Ageing Factors : 58
Observations : 9611
Ageing Phenotype : 8159
Data Type 1 : 940
Data Type 2 : 7219
Homology Analysis : 1452

Data Source Version Info

Source Name Released Downloaded Comment
GenAge Build 16 Sep 15, 2012 Jul 23, 2013 major update with structural changes; downloadable release files very incomplete therefore downloaded newer HTML pages
GenDR Build 1 Jun 29, 2012 Jun 11, 2012
GPSDB Feb 01, 2013 Aug 07, 2013 no defined releases; usually updated twice a year; not completely downloadable; downloaded AgeFactDB related search results individually;
HomoloGene Release 67 Dec 12, 2012 Aug 07, 2013
Lifespan Observations Database Aug 14, 2013 no defined releases; might be updated daily
NCBI Gene Jul 24, 2013 no defined releases; might be updated daily
UniProtKB Release 2013_08 Jul 24, 2013 Jul 24, 2013

Unification of Ageing Factor Names

AgeFactDB offers information on effects of ageing factors on lifespan and/or ageing phenotype. Ageing factors include genes, chemical compounds and other factors such as dietary restriction or overfeeding, heat shock, low temperature and so on. The information is taken from other source databases such as the GenAge Database and the Lifespan Observations Database, for example. In addition, new entries will be added by either manual or automatic text mining or by still other methods.

AgeFactDB makes an attempt to unify ageing factor names. Thus far, unification is only done for gene symbols and the (unified) AgeFactDB name is taken from a name source database. Currently, the AgeFactDB name is identical to the shortest preferred name suggested by the Gene/Protein Synonym Database - GPSDB. In GPSDB information from other databases such as UniProt/SwissProt or Wormbase, for example, is collected. Detailed information can be found by clicking on the GPSDB link. The table shown below lists all ageing factor names for which the AgeFactDB names differ from the original names used in the source databases. In addition to the unified name AgeFactDB provides information on many synonym names. Therefore, when searching for a gene in AgeFactDB it is not necessary to know the unified gene name in advance. The search will succeed for any of the synonym names including the name used in the source databases.

Ageing Factor Name Changes

Modification of Source Input Data

AgeFactDB is a curated database. This table contains a listing of modifications that were applied to the data of the original sources. Not annotated in this table are general modifications to unify the data representation. This includes the spelling of compounds and other ageing factors. In AgeFactDB compounds and other factors are spelled in lowercase except the first letter. Exceptions for abbreviations (e.g. CCCP) and proper names (Coenzyme Q10) are allowed. Furthermore, to become independent from the variability of input sources, the lifespan effects and the significance values are derived from an own rule system. AgeFactDB provides the following qualitative significant lifespan effects: increased, decreased and none. An observed lifespan changed is significant, if the difference between observed value and base value is at least 5%. If this difference can not be determined, the significance information from the source is taken, if provided.

# AgeFactDB Stable ID Original Source Original Value Modified Value Modification Description Modification Comment
1 OB_000302 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 131) Skip import of an observation from the Lifespan Observations Database.
2 OB_000334 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 160) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
3 OB_004200 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 889) Anopheles stephensi Correct the species of an observation from the Lifespan Observations Database.
4 OB_004202 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 890) Anopheles stephensi Correct the species of an observation from the Lifespan Observations Database.
5 OB_004203 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 891) Anopheles stephensi Correct the species of an observation from the Lifespan Observations Database.
6 OB_004204 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 892) Anopheles stephensi Correct the species of an observation from the Lifespan Observations Database.
7 OB_004205 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 893) Anopheles stephensi Correct the species of an observation from the Lifespan Observations Database.
8 OB_004206 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 894) Anopheles stephensi Correct the species of an observation from the Lifespan Observations Database.
9 OB_004345 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2272) N-acetyl-1-cysteine N-acetyl-cysteine Rename compound from Lifespan Observations database.
10 OB_004346 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2273) N-acetyl-1-cysteine N-acetyl-cysteine Rename compound from Lifespan Observations database.
11 OB_004347 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2274) N-acetyl-1-cysteine N-acetyl-cysteine Rename compound from Lifespan Observations database.
12 OB_004348 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2275) N-acetyl-1-cysteine N-acetyl-cysteine Rename compound from Lifespan Observations database.
13 OB_001232 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2560) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
14 OB_001543 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2885) 0 20 Correct the lifespan change of an observation from the Lifespan Observations Database.
15 OB_001543 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 2885) decreased increased Correct the lifespan effect of an observation from the Lifespan Observations Database.
16 OB_002388 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 3656) 0 75 Correct the lifespan change of an observation from the Lifespan Observations Database.
17 OB_002399 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 3666) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
18 OB_002662 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 3953) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
19 OB_003059 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4401) Saccharomyces cerevisiae Correct the species of an observation from the Lifespan Observations Database.
20 OB_003108 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4488) rho0 RAS2 Rename gene symbol from Lifespan Observations database.
21 OB_003153 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4547) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
22 OB_003167 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4563) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
23 OB_004945 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4578) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
24 OB_004955 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4641) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
25 OB_004496 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4648) N-acetyl-cystein N-acetyl-cysteine Rename compound from Lifespan Observations database. In the publication it is written with 'e' at the end, so it is not N-acetyl-cystein.
26 OB_004497 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4649) N-acetyl-cystein N-acetyl-cysteine Rename compound from Lifespan Observations database. In the publication it is written with 'e' at the end, so it is not N-acetyl-cystein.
27 OB_004498 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4650) N-acetyl-cystein N-acetyl-cysteine Rename compound from Lifespan Observations database. In the publication it is written with 'e' at the end, so it is not N-acetyl-cystein.
28 OB_004499 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4651) N-acetyl-cystein N-acetyl-cysteine Rename compound from Lifespan Observations database. In the publication it is written with 'e' at the end, so it is not N-acetyl-cystein.
29 OB_004500 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4652) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
30 OB_004504 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4656) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
31 OB_004508 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4660) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
32 OB_003240 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4667) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
33 OB_003279 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4701) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
34 OB_003280 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4702) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
35 OB_003281 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4703) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
36 OB_003480 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4906) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
37 OB_004543 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4981) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
38 OB_003572 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5007) 0 -13 Correct the lifespan change of an observation from the Lifespan Observations Database.
39 OB_003591 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5027) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
40 OB_003603 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5038) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
41 OB_003607 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5041) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
42 OB_004976 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5050) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
43 OB_004977 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5051) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
44 OB_003615 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5055) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
45 OB_003617 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5057) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
46 OB_004978 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5061) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
47 OB_004565 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5092) increased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
48 OB_004567 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5100) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
49 OB_004568 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5101) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
50 OB_004569 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5102) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
51 OB_004570 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5103) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
52 OB_004571 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5104) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
53 OB_004572 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5105) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
54 OB_004573 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5106) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
55 OB_004574 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5107) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
56 OB_004575 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5108) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
57 OB_004576 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5109) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
58 OB_004577 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5110) NAC N-acetyl-cysteine Rename compound from Lifespan Observations database.
59 OB_003665 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5185) 0 25 Correct the lifespan change of an observation from the Lifespan Observations Database.
60 OB_003667 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5187) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
61 OB_003668 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5188) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
62 OB_003777 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5358) decreased none Correct the lifespan effect of an observation from the Lifespan Observations Database.
63 OB_005006 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5372) N2 Caenorhabditis elegans Correct the species of an observation from the Lifespan Observations Database.
64 OB_005006 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5372) N2 Correct the strain of an observation from the Lifespan Observations Database.
65 OB_004942 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4575) paraquat Oxidative stress Rename other factor from Lifespan Observations database.
66 OB_004943 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 4576) paraquat Oxidative stress Rename other factor from Lifespan Observations database.
67 OB_004975 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 5049) Paraquat Oxidative stress Rename other factor from Lifespan Observations database.
68 OB_000518 [Lifespan Observations Database icon]Lifespan Observations Database (ID: 177) 854598 802462 Correct NCBI Gene ID of a gene from the Lifespan Observations Database. NCBI Gene ID 854598 belongs to gene COX1 from Saccharomyces cerevisiae (wrong species).