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Introduction
AgeFactDB is a database aimed at the collection and integration of ageing phenotype data including lifespan information. Currently, we include primarily data on ageing factors. Information related to the effects of ageing factors is called an 'observation' and represents ageing-related evidence. AgeFactDB can be accessed either by browsing through predefined lists or by searching.
The predefined browse lists include a compilation of all ageing factors. Furthermore, there are also separate lists for the three ageing factor types gene, compound and other ageing factors. In addition to the ageing factor lists also observation lists are available.
AgeFactDB offers the two basic search modes Quick Search and Advanced Search. The Quick Search has an input field for search terms and the default search space covers almost all content available on ageing factor and observation pages. The Advanced Search option is still work in progress and offers currently exclusively a number of advanced sequence search options. The Quick Search input field is located in the upper right part oft the AgeFactDB pages. The Advanced Search can be accessed by the corresponding link in the navigation menu at the top.
Ageing Relevance
We distinguish between different types of ageing relevance evidence. Experimental studies on ageing factors result in observations with experimental ageing relevance evidence (1). According to our definition of ageing factors a comparison of two situations, with and without the action of the ageing factor, is required. Almost all data in AgeFactDB is of this type. There are however also a few lifespan data for populations or species included that are certainly relevant to ageing with a slightly different meaning of the term ageing relevance, however. But in this case there is no intervention study and therefore these data cannot be assigned to an ageing factor (2). Furthermore, there are experimental studies where no significant effect of an assumed ageing factor was found (3). And finally there are genes included that are homologous to known ageing-relevant genes for which there is no experimental evidence. They are considered as putative ageing-relevant genes with computational evidence (4).Order of importance:
- yes (Experimental Analysis)
- yes, but no ageing factor assigned (Experimental Analysis)
- no (Experimental Analysis)
- putative (Computational Analysis)
Terminology
Ageing-relevant information is provided in the literature. A document contains ageing-related data that is extracted as one or more observations. Each observation refers to one or more ageing factors that affect the ageing phenotype. For the sake of completeness, AgeFactDB includes population lifespan data which are no intervention studies and therefore they cannot be assigned to an ageing factor. Those observations have always the ageing relevance evidence type (2).Ageing Factor
Ageing factors are genes, chemical compounds or other factors such as dietary restriction or overfeeding, heat shock, low temperature and so on that affect the lifespan or another geing phenotype. The ageing relevance evidence of an ageing factor depends on its observation(s), thus an ageing factor can have several types of ageing relevance evidence at the same time. In case of multiple ageing relevance evidences assigned to one ageing factor the most important color, e.g. the color with lowest number according to the order given above, is chosen as ageing factor ageing relevance evidence color.
Observation
The observations in AgeFactDB can be distinguished in experimental analysis observations and computational analysis observations. Experimental analysis observations are considered as ageing phenotype observations, computational analysis observations might be homology analysis or text mining observations. Currently, the integration of text mining observations is in a test phase and therefore they are not made public.Ageing Phenotype
Due to the different data structures of ageing phenotype observation data integrated from other databases we subdivide these observations into type 1 and 2. Observations of type 1 contain the phenotype data mostly unseparated within a single description. Observations of type 2 contain lifespan data in a more structured form (e.g.: separated into lifespan effect, lifespan change, lifespan value).Homology Analysis
In AgeFactDB an homology analysis is performed for known ageing-relevant genes, e.g. genes with at least one observation with ageing relevance evidence type (1). The homologous genes found for one gene are merged into one homology analysis observation. Thus, an homology analysis observation represents a group of homologous genes, where at least one member in this homology group is a known ageing-relevant gene. Homologous genes without further ageing phenotype observations are considered as candidate or putative ageing-relevant genes in AgeFactDB.Data Tables
With few exceptions, tables can be searched individually by entering a search term in the input field at the top right of the table. The search starts after pressing the 'Enter key'. Table rows that do not match the search term are hidden (temporarily). The search result can be inverted while activating the 'Negate Search'-checkbox.
The rows in each table can be sorted too by clicking on a column header. Multiple columns can be used for sorting by holding the "Shift key" down while clicking on a further header. The sort direction (indicated by a green arrowhead) can be switched by clicking again.
Example Table
| # | Name | Type | NCBI Gene ID | Species | Synonyms | Ageing Relevance Analysis | Ageing Factor Stable ID | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1, 1-Dimethylbiguanide hydrochloride | compound | Mus musculus |
|
AF_009127 | ||||||||
| 2 | 14-3-3epsilon | gene | 42186 | Drosophila melanogaster | Gene Synonyms: 14-3-3 | 14-3-3 epsilon | 14-3-3&epsilon | 14-3-3-e | 14-3-3-epsilon | 14-3-30epsilon | 14-3-3e | 14-3-3EPSILON | 14-3-3epsilon | 14-3-3epsilon-PA | 14-3-3epsilon-PB | 14-3-3epsilon-PC | 14-3-3epsilon-PD | 14-3-3omicron | 1433epsilon | 143E_DROME | CG31196 | CG31196 gene product from transcript CG31196-RB | CG31196-PA | CG31196-PB | CG31196-PC | CG31196-PD | CT24092 | D14-3-3e | D14-3-3epsilon | d14-3-3epsilon | Dmel_CG31196 | DmelCG31196 | EK3-5 | eps | Epsilon | epsilon | l(3)j2B10 | PAR-5 | Par-5 | par-5 | PAR5 | SR3-9 | Su(Raf)3B | Suppressor of Ras85D 3-9 | suppressor of Ras85D 3-9 | Tyrosine-3-monooxygenase Source: ![[GPSDB icon]](assets/images/general/db_gpsdb.gif) GPSDB |
|
AF_000903 | ||||||
| 3 | 2,4-dinitrophenol | compound | Mus musculus |
|
AF_009101 | ||||||||
| 4 | 2-Cys Prx B | gene | 830517 | Arabidopsis thaliana | Gene Synonyms: 2-CYS PEROXIREDOXIN B | 2-Cys peroxiredoxin BAS1-like protein | 2-CYS PRX B | 2-Cys Prx B | 2-CYSTEINE PEROXIREDOXIN B | 2-cysteine peroxiredoxin B | 2CPB | AT5G06290 | At5g06290 | AT5G06290.1 | MHF15.19 Source: GPSDB |
|
AF_003034 | ||||||
| 5 | 25-azacoprostane | compound | Caenorhabditis elegans |
|
AF_009131 |
![[Lifespan Observations Database icon]](assets/images/general/db_lodb.gif)
Lifespan Observations Database![[AgeFactDB Homology Analysis icon]](assets/images/general/db_agefactdb.gif)
AgeFactDB Homology Analysis![[GenAge icon]](assets/images/general/db_genage.gif)
GenAgeSearch
Quick Search
Search terms and also terms defining search options are generally case-insensitive. The minimum length for a term is three non-wildcard characters. The search can be performed for one or more search terms. In case of more than one term the default combination is the logical AND. Combining terms by a logical OR is possible too. In addition, one can search for specific phrases consisting of more than one term. Two wildcard characters can be used. The question mark (?) represents any single character. It can also be used in a consecutive manner as ?? or ??? ... The asterisk (*) represents zero or more characters.
The Quick Search covers all content that is related to an ageing factor page or an observation page except sequences. The search space can be reduced, e.g. to search in the Medical Subject Headings, the PubMed IDs or PubMed Central IDs and the ageing factor names in the header of the ageing factor pages (not in the descriptions). This includes synonyms too. These extended search options are specified in square brackets and can be combined in any order, see examples. Furthermore the extended search options [pattern] and [blast] will perform a search for sequences (or a part) using default options. The pattern search accepts the wildcards but the BLAST search not. Thus the BLAST search can be performed with a raw sequence only. If you want to use FASTA format, PROSITE pattern or regular expression or change other defaults of pattern and BLAST search, please use the Advanced Search.
The Quick Search menu provides two filters, regarding Ageing-related Sources and Ageing Relevance Evidence. The Ageing-related Sources filters can be used to restrict the search space to the content of the respective sources. The Ageing Relevance Evidence filter provides four options, whereas "both" is availabe for ageing factors only. An observation has either experimental or computational evidence but never both.
If no search term (or a wildcard only) is entered, the result will be the respective ageing factor or observation browse list. Both lists can be modified too while using the Ageing-related Sources and/or Ageing Relevance Evidence filter in the Quick Search menu.
There are two options for the display of the search output. The default output shows ageing factor pages but one can change the output format to observation pages. These different output options have implications for multi-term searches. If one combines two terms by a logical AND, for example, then for the observation option hits are found if both terms occur within one and the same observation. On the other hand, for the ageing factor output both terms must occur in the complete information related to a particular ageing factor. So, it may well be that the two terms come from different observations or papers.
Further information is provided on additional pages:
Advanced Search
Sequence Search
The advanced sequence search can also be performed as pattern or BLAST search.
In addition to the Quick Search option the pattern search accepts as input PROSITE patterns and regular expressions and or a raw sequence with the wildcards question mark (?) and asterisk (*). In that case, the question mark (?) represents any single character. It can also be used in a consecutive manner as ?? or ??? ... The asterisk (*) represents zero or more characters. The search output can be grouped by the detected UniProt sequences or the matching sequence motifs.
The advanced BLAST search is performed with NCBI Blast+. The search accepts input sequences in FASTA format or a raw format. The sequences must be represented in the standard IUPAC amino acid or nucleic acid codes. Nucleic acid sequences will be translated into protein sequences. The sequences can be entered directly or uploaded in a file.
Further information is provided on additional pages: