Tacutu, R.1, Craig, T.1, Budovsky, A. 2,3, Wuttke, D. 1, Lehmann, G. 2, Taranukha, D2, Costa, J. 4, Fraifeld, V.E. 2 and de MagalhÃes J.P.1,*
1 Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
2 The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
3 Judea Regional Research & Development Center, Carmel 90404, Israel
4 Department of Genetics, Liverpool Women's Hospital, Liverpool L8 7SS, UK
The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available, online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality, manually-curated data: 1) GenAge, a database of genes associated with ageing in humans and model organisms; 2) AnAge, an extensive collection of longevity records and complementary traits for over 4,000 vertebrate species; and 3) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation (1), major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. Altogether, we hope that through its improvements the current version of HAGR will continue to provide users with the most-comprehensive and accessible resources available today in the field of biogerontology.
Since our last update in 2009 (2), we have made numerous improvements in terms of both the quantity and the quality of the content in HAGR. The dataset of human genes in GenAge has been continually improved in terms of data quality, while it has also grown slightly. The set of genes associated with longevity in model organisms has seen an increase of more than 2 fold, while the structure of the database has also been updated to accommodate new features. Now, this section hosts for each longevity-associated gene multiple observations from the same or different studies, and more quantitative data on the impact (relative change) that a certain genetic intervention has on lifespan. Genes have also been classified as pro-longevity, anti-longevity or necessary to fitness. The GenDR database, which has been previously described elsewhere (3), is now fully integrated in HAGR with abundant cross-links to the other HAGR resources. Although in terms of content AnAge has grown only slightly, we have consistently continued to curate its data and enhance its quality, in line with defined standards and procedures (4). Additionally, new information and references have also been added to some of the AnAge entries. The HAGR interface has been completely redesigned to be more intuitive and user-friendly, with an improved cross-integration of our different databases and tools.
The authors would like to thank the numerous contributors and experts who have provided valuable advice and suggestions concerning our resources, and in particular Steve Austad for helping curate AnAge. This work was funded by a Wellcome Trust grant (ME050495MES) to JPM. JPM is also grateful for support from the Ellison Medical Foundation. VEF was partly funded by the European Commission FP7 Health Research Grant number HEALTH-F4-2008-202047.
1. de MagalhÃ£es, J.P., Costa, J. and Toussaint, O. (2005) HAGR: the Human Ageing Genomic Resources. Nucleic Acids Res., 33, Database issue, D537-D543.
2. de MagalhÃ£es, J.P., Budovsky, A., Lehmann, G., Costa, J., Li, Y., Fraifeld, V. and Church, G.M. (2009) The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell, 8, 65-72.
3. Wuttke, D., Connor, R., Vora, C., Craig, T., Li, Y., Wood, S., Vasieva, O., Reis, R.S., Tang, F. and de MagalhÃ£es, J.P. (2012) Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes. PLoS Genetics, 8, e1002834.
4. de MagalhÃ£es, J.P. and Costa, J. (2009) A database of vertebrate longevity records and their relation to other life-history traits. J Evol Biol., 22, 1770-1774.