Computational biology for ageing

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 366, Issue 1561, 2011, Pages 51-63

  Wieser, Daniela ^a   Papatheodorou, Irene ^a,b   Ziehm, Matthias ^a   Thornton, Janet M ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Ageing; Bioinformatics; Computational biology; Data analysis; Gene expression; Lifespan

Indexed keywords

AGING; BIOINFORMATICS; DATA ASSIMILATION; DATABASE; GENE EXPRESSION;

EID: 79251529562     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2010.0286     Document Type: Review

References (91)

1. de Magalhães, J. P., Budovsky, A., Lehmann, G., Costa, J., Li, Y., Fraifeld, V. & Church, G. M. 2009 The Human Ageing Genomic Resources: Online databases and tools for biogerontologists. Aging Cell 8, 65-72. (doi:10. 1111/j.1474-9726.2008.00442.x)
2. Pérez, V. I. et al. 2009 Protein stability and resistance to oxidative stress are determinants of longevity in the longest-living rodent, the naked mole-rat. Proc. Natl Acad. Sci. USA 106, 3059-3064. (doi:10.1073/pnas. 0809620106)
3. Kenyon, C., Chang, J., Gensch, E., Rudner, A. & Tabtiang, R. 1993 A C. elegans mutant that lives twice as long as wild type. Nature 366, 461-464. (doi:10. 1038/366461a0)
4. Piper, M. D. W. & Bartke, A. 2008 Diet and aging. Cell Metab. 8, 99-104. (doi:10.1016/j.cmet.2008.06.012)
5. Kenyon, C. J. 2010 The genetics of ageing. Nature 464, 504-512. (doi:10.1038/nature08980)
6. Parkinson, H. et al. 2009 ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 37, D868-D872. (doi:10.1093/nar/gkn889)
7. Barrett, T. et al. 2009 NCBI GEO: Archive for highthroughput functional genomic data. Nucleic Acids Res. 37, D885-D890. (doi:10.1093/nar/gkn764)
8. Letunic, I. & Bork, P. 2007 Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128. (doi:10.1093/ bioinformatics/btl529)
9. Sayers, E. W. et al. 2009 Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37, D5-D15. (doi:10.1093/nar/ gkn741)
10. Pan, F. et al. 2007 Gene Aging Nexus: A web database and data mining platform for microarray data on aging. Nucleic Acids Res. 35, D756-D759. (doi:10.1093/nar/ gkl798)
11. Tacutu, R., Budovsky, A. & Fraifeld, V. E. 2010 The NetAge database: A compendium of networks for longevity, age-related diseases and associated processes. Biogerontology (doi:10.1007/s10522-010-9265-8)
12. Kaeberlein, M., Jegalian, B. & McVey, M. 2002 AGEID: A database of aging genes and interventions. Mech. Ageing Dev. 123, 1115-1119. (doi:10.1016/S0047- 6374(02)00011-8)
13. Olsen, B., Murakami, C. J. & Kaeberlein, M. 2010 YODA: Software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. BMC Bioinform. 11, 141. (doi:10.1186/ 1471-2105-11-141)
14. Gene Ontology Consortium 2010 The Gene Ontology in 2010: Extensions and refinements. Nucleic Acids Res. 38, D331-D335. (doi:10.1093/nar/gkp1018)
15. Zahn, J. M. et al. 2007 AGEMAP: A gene expression database for aging in mice. PLoS Genet. 3, e201. (doi:10.1371/journal.pgen.0030201)
16. Matys, V. et al. 2006 TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108-D110. (doi:10. 1093/nar/gkj143)
17. Reimers, M. & Carey, V. J. 2006 Bioconductor: An open source framework for bioinformatics and computational biology. Methods Enzymol. 411, 119-134. (doi:10.1016/ S0076-6879(06)11008-3)
18. Frith, M. C., Fu, Y., Yu, L., Chen, J.-F., Hansen, U. & Weng, Z. 2004 Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res. 32, 1372-1381. (doi:10.1093/nar/gkh299)
19. Huang, D. W. et al. 2007 DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35, W169-W175. (doi:10.1093/nar/gkm415)
20. Pletcher, S. D., Macdonald, S. J., Marguerie, R., Certa, U., Stearns, S. C., Goldstein, D. B. & Partridge, L. 2002 Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Curr. Biol. 12, 712-723. (doi:10.1016/S0960-9822(02)00808-4)
21. Girardot, F., Lasbleiz, C., Monnier, V. & Tricoire, H. 2006 Specific age-related signatures in Drosophila body parts transcriptome. BMC Genomics 7, 69. (doi:10. 1186/1471-2164-7-69)
22. McElwee, J. J. et al. 2007 Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biol. 8, R132. (doi:10.1186/gb-2007-8-7- r132)
23. Selman, C. et al. 2009 Ribosomal protein S6 kinase 1 signaling regulates mammalian life span. Science 326, 140-144. (doi:10.1126/science.1177221)
24. Gentleman, R., Carey, V., Dudoit, S., Irizarry, R. & Huber, W. (eds.) 2005 Bioinformatics and computational biology solutions using R and bioconductor. New York, NY: Springer.
25. Smyth, G. K. 2005 Limma: Linear models for microarray data. In Bioinformatics and computational biology solutions using R and bioconductor, ch. 23, pp. 397-420. New York, NY: Springer.
26. Amador-Noguez, D., Yagi, K., Venable, S. & Darlington, G. 2004 Gene expression profile of long-lived Ames dwarf mice and Little mice. Aging Cell 3, 423-441. (doi:10.1111/j.1474-9728.2004.00125.x)
27. Breslin, T., Edn, P. & Krogh, M. 2004 Comparing functional annotation analyses with Catmap. BMC Bioinform. 5, 193. (doi:10.1186/1471-2105-5-193)
28. Huang, D. W., Sherman, B. T. & Lempicki, R. A. 2009 Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57. (doi:10.1038/nprot.2008.211)
29. Smith, E. D. et al. 2008 Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. Genome Res. 18, 564-570. (doi:10.1101/gr. 074724.107)
30. de Magalhães, J. P., Curado, J. & Church, G. M. 2009 Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 25, 875-881. (doi:10.1093/bioinformatics/ btp073)
31. Dogruel, M., Down, T. A. & Hubbard, T. J. 2008 NestedMICA as an ab initio protein motif discovery tool. BMC Bioinform. 9, 19. (doi:10.1186/1471- 2105-9-19)
32. Portales-Casamar, E. et al. 2010 JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105-D110. (doi:10.1093/nar/gkp950)
33. Cheng, C., Fabrizio, P., Ge, H., Longo, V. D. & Li, L. M. 2007 Inference of transcription modification in long-live yeast strains from their expression profiles. BMC Genomics 8, 219. (doi:10.1186/1471-2164-8-219)
34. Wheeler, H. E. et al. 2009 Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. PLoS Genet. 5, e1000685. (doi:10.1371/ journal.pgen.1000685)
35. Southworth, L. K., Owen, A. B. & Kim, S. K. 2009 Aging mice show a decreasing correlation of gene expression within genetic modules. PLoS Genet. 5, pe1000776. (doi:10.1371/journal.pgen.1000776)
36. Sharov, V. S. & Schöneich, C. 2007 Proteomic approach to aging research. Expert Rev. Proteomics 4, 309-321. (doi:10.1586/14789450.4.2.309)
37. Schiffer, E., Mischak, H. & Zimmerli, L. U. 2009 Proteomics in gerontology: Current applications and future aspects-a mini-review. Gerontology 55, 123-137. (doi:10.1159/000191653)
38. Jones, L. M., Staffa, K., Perally, S., Lacourse, E. J., Brophy, P. M. & Hamilton, J. V. 2010 Proteomic analyses of Caenorhabditis elegans dauer larvae and long-lived daf-2 mutants implicates a shared detoxification system in longevity assurance. J. Proteome Res. 9, 2871-2881 (doi:10.1021/pr9009639)
39. Murphy, C. T., McCarroll, S. A., Bargmann, C. I., Fraser, A., Kamath, R. S., Ahringer, J., Li, H. & Kenyon, C. 2003 Genes that act downstream of DAF- 16 to influence the lifespan of Caenorhabditis elegans. Nature 424, 277-283. (doi:10.1038/nature01789)
40. Dong, M.-Q., Venable, J. D., Au, N., Xu, T., Park, S. K., Cociorva, D., Johnson, J. R., Dillin, A. & Yates, J. R. 2007 Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science 317, 660-663. (doi:10.1126/science.1139952)
41. Fuchs, S., Bundy, J. G., Davies, S. K., Viney, J. M., Swire, J. S. & Leroi, A. M. 2010 A metabolic signature of long life in Caenorhabditis elegans. BMC Biol. 8, 14. (doi:10.1186/1741-7007-8-14)
42. Prasad, T. S. K., Kandasamy, K. & Pandey, A. 2009 Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol. Biol. 577, 67-79. (doi:10.1007/978-1-60761-232-2-6)
43. Aranda, B. et al. 2010 The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38, D525-D531. (doi:10.1093/nar/gkp878)
44. de Magalhães, J. P. & Toussaint, O. 2004 GenAge: A genomic and proteomic network map of human ageing. FEBS Lett. 571, 243-247. (doi:10.1016/j.febslet.2004. 07.006)
45. Bell, R. et al. 2009 A human protein interaction network shows conservation of aging processes between human and invertebrate species. PLoS Genet. 5, e1000414. (doi:10.1371/journal.pgen.1000414)
46. Promislow, D. E. L. 2004 Protein networks, pleiotropy and the evolution of senescence. Proc. Biol. Sci. 271, 1225-1234. (doi:10.1098/rspb.2004.2732)
47. Ferrarini, L., Bertelli, L., Feala, J., McCulloch, A. D. & Paternostro, G. 2005 A more efficient search strategy for aging genes based on connectivity. Bioinformatics 21, 338-348. (doi:10.1093/bioinformatics/bti004)
48. Budovsky, A., Abramovich, A., Cohen, R., Chalifa- Caspi, V. & Fraifeld, V. 2007 Longevity network: Construction and implications. Mech. Ageing Dev. 128, 117-124. (doi:10.1016/j.mad.2006.11.018)
49. Williams, G. C. 1957 Pleiotropy, natural selection, and the evolution of senescence. Evolution 11, 398-411. (doi:10.2307/2406060)
50. Lorenz,D. R.,Cantor, C.R.&Collins, J. J. 2009Anetwork biology approach to aging in yeast. Proc.NatlAcad. Sci.USA 106, 1145-1150. (doi:10.1073/pnas.0812551106)
51. Hucka, M. et al. 2003 The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (doi:10.1093/bioinformatics/btg015)
52. Chen, Y., Lawless, C., Gillespie, C. S.,Wu, J., Boys, R. J. & Wilkinson, D. J. 2010 CaliBayes and BASIS: Integrated tools for the calibration, simulation and storage of biological simulation models. Brief Bioinform. 11, 278-289. (doi:10.1093/bib/bbp072)
53. McAuley, M. T., Kenny, R. A., Kirkwood, T. B. L., Wilkinson, D. J., Jones, J. J. L. & Miller, V. M. 2009 A mathematical model of aging-related and cortisol induced hippocampal dysfunction. BMC Neurosci. 10, 26. (doi:10.1186/1471-2202-10-26)
54. Johnston, J., Iser, W. B., Chow, D. K., Goldberg, I. G. & Wolkow, C. A. 2008 Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues. PLoS ONE, 3, e2821. (doi:10.1371/ journal.pone.0002821)
55. Shamir, L., Wolkow, C. A. & Goldberg, I. G. 2009 Quantitative measurement of aging using image texture entropy. Bioinformatics 25, 3060-3063. (doi:10.1093/ bioinformatics/btp571)
56. Selman, C. et al. 2006 Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice. Physiol. Genomics 27, 187-200. (doi:10.1152/physiolgenomics.00084.2006)
57. Swindell, W. R., Harper, J. M. & Miller, R. A. 2008 How long will my mouse live? Machine learning approaches for prediction of mouse life span. J. Gerontol. A Biol. Sci. Med. Sci. 63, 895-906.
58. Park, S.-K. & Prolla, T. A. 2005 Gene expression profiling studies of aging in cardiac and skeletal muscles. Cardiovasc. Res. 66, 205-212. (doi:10.1016/j.cardiores. 2005.01.005)
59. Lee, C. K., Weindruch, R. & Prolla, T. A. 2000 Geneexpression profile of the ageing brain in mice. Nat. Genet. 25, 294-297. (doi:10.1038/77046)
60. Rodwell, G. E. J. et al. 2004 A transcriptional profile of aging in the human kidney. PLoS Biol. 2, e427. (doi:10.1371/journal.pbio.0020427)
61. Zhan, M., Yamaza, H., Sun, Y., Sinclair, J., Li, H. & Zou, S. 2007 Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster. Genome Res. 17, 1236-1243. (doi:10.1101/gr.6216607)
62. Zahn, J. M. et al. 2006 Transcriptional profiling of aging in human muscle reveals a common aging signature. PLoS Genet. 2, e115. (doi:10.1371/journal. pgen.0020115.eor)
63. Hong, M.-G., Myers, A. J., Magnusson, P. K. E. & Prince, J. A. 2008 Transcriptome-wide assessment of human brain and lymphocyte senescence. PLoS ONE 3, e3024. (doi:10.1371/journal.pone.0003024)
64. Pletcher, S. D., Libert, S. & Skorupa, D. 2005 Flies and their golden apples: The effect of dietary restriction on Drosophila aging and age-dependent gene expression. Ageing. Res. Rev. 4, 451-480. (doi:10.1016/j.arr.2005. 06.007)
65. Landis, G. N., Abdueva, D., Skvortsov, D., Yang, J., Rabin, B. E., Carrick, J., Tavaré, S. & Tower, J. 2004 Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 101, 7663-7668. (doi:10.1073/pnas. 0307605101)
66. Kim, S. N. et al. 2005 Age-dependent changes of gene expression in the Drosophila head. Neurobiol. Aging 26, 1083-1091. (doi:10.1016/j.neurobiolaging. 2004.06. 017)
67. Chintapalli, V. R., Wang, J. & Dow, J. A. T. 2007 Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat. Genet. 39, 715-720. (doi:10. 1038/ng2049)
68. Bergman, A., Atzmon, G., Ye, K., MacCarthy, T. & Barzilai, N. 2007 Buffering mechanisms in aging: A systems approach toward uncovering the genetic component of aging. PLoS Comput. Biol. 3, e170. (doi:10.1371/journal.pcbi. 0030170)
69. Willcox, D. C., Willcox, B. J., Wang, N.-C., He, Q., Rosenbaum, M. & Suzuki, M. 2008 Life at the extreme limit: Phenotypic characteristics of supercentenarians in Okinawa. J. Gerontol. A Biol. Sci. Med. Sci. 63, 1201-1208.
70. Bessenyei, B., Márka, M., Urbán, L., Zeher, M. & Semsei, I. 2004 Single nucleotide polymorphisms: Aging and diseases. Biogerontology 5, 291-303. (doi:10. 1007/s10522-004-2567-y)
71. Sebastiani, P. et al. In press. Genetic signatures of exceptional longevity in humans. Science. (doi:10.1126/ science.1190532)
72. McCarroll, S. A., Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C.-S., Jan, Y. N., Kenyon, C., Bargmann, C. I. & Li, H. 2004 Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat. Genet. 36, 197-204. (doi:10. 1038/ng1291)
73. Mair, W. & Dillin, A. 2008 Aging and survival: The genetics of life span extension by dietary restriction. Annu. Rev. Biochem. 77, 727-754. (doi:10.1146/ annurev.biochem.77.061206.171059)
74. Partridge, L., Piper, M. D. W. & Mair, W. 2005 Dietary restriction in Drosophila. Mech. Ageing Dev. 126, 938-950. (doi:10.1016/j.mad.2005.03.023)
75. Selman, C. et al. 2006 Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice. Physiol. Genomics 27, 187-200. (doi:10.1152/physiolgenomics. 00084.2006)
76. Tsuchiya, T., Dhahbi, J. M., Cui, X., Mote, P. L., Bartke, A. & Spindler, S. R. 2004 Additive regulation of hepatic gene expression by dwarfism and caloric restriction. Physiol. Genomics 17, 307-315. (doi:10. 1152/physiolgenomics.00039.2004)
77. Spindler, S. R. & Mote, P. L. 2007 Screening candidate longevity therapeutics using gene-expression arrays. Gerontology 53, 306-321. (doi:10.1159/000103924)
78. Selman, C. et al. 2008 Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice. FASEB J. 22, 807-818. (doi:10. 1096/fj.07-9261com)
79. Redman, L. M., Veldhuis, J. D., Rood, J., Smith, S. R., Williamson, D., Ravussin, E. & Team, P. C. 2010 The effect of caloric restriction interventions on growth hormone secretion in nonobese men and women. Aging Cell 9, 32-39. (doi:10.1111/j.1474-9726.2009. 00530.x)
80. Holloszy, J. O. & Fontana, L. 2007 Caloric restriction in humans. Exp. Gerontol. 42, 709-712. (doi:10.1016/j. exger.2007.03.009)
81. Colman, R. J. et al. 2009 Caloric restriction delays disease onset and mortality in rhesus monkeys. Science 325, 201-204. (doi:10.1126/science.1173635)
82. Bodkin, N. L., Alexander, T. M., Ortmeyer, H. K., Johnson, E. & Hansen, B. C. 2003 Mortality and morbidity in laboratory-maintained rhesus monkeys and effects of long-term dietary restriction. J. Gerontol. A Biol. Sci. Med. Sci. 58, 212-219.
83. Salmon, A. B., Richardson, A. & Pérez, V. I. 2010 Update on the oxidative stress theory of aging: Does oxidative stress play a role in aging or healthy aging? Free. Radic. Biol. Med. 48, 642-655. (doi:10.1016/j. freeradbiomed.2009.12.015)
84. Curtis, C. et al. 2007 Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes. Genome Biol. 8, R262. (doi:10.1186/gb-2007-8- 12-r262)
85. Pérez, V. I., Remmen, H. V., Bokov, A., Epstein, C. J., Vijg, J. & Richardson, A. 2009 The overexpression of major antioxidant enzymes does not extend the lifespan of mice. Aging Cell 8, 73-75. (doi:10.1111/j.1474- 9726.2008.00449.x)
86. Doonan, R., McElwee, J. J., Matthijssens, F., Walker, G. A., Houthoofd, K., Back, P., Matscheski, A., Vanfleteren, J. R. & Gems, D. 2008 Against the oxidative damage theory of aging: Superoxide dismutases protect against oxidative stress but have little or no effect on life span in Caenorhabditis elegans. Genes Dev. 22, 3236-3241. (doi:10.1101/gad.504808)
87. Salmon, A. B., Leonard, S., Masamsetti, V., Pierce, A., Podlutsky, A. J., Podlutskaya, N., Richardson, A., Austad, S. N. & Chaudhuri, A. R. 2009 The long lifespan of two bat species is correlated with resistance to protein oxidation and enhanced protein homeostasis. FASEB J. 23, 2317-2326. (doi:10.1096/fj.08-122523)
88. Mitchell, T. W., Buffenstein, R. & Hulbert, A. J. 2007 Membrane phospholipid composition may contribute to exceptional longevity of the naked mole-rat (Heterocephalus glaber): A comparative study using shotgun lipidomics. Exp. Gerontol. 42, 1053-1062. (doi:10.1016/j.exger.2007.09.004)
89. Wang, J., Zhang, S., Wang, Y., Chen, L. & Zhang, X.-S. 2009 Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Comput. Biol. 5, e1000521. (doi:10.1371/journal.pcbi. 1000521)
90. Budovsky, A., Tacutu, R., Yanai, H., Abramovich, A., Wolfson, M. & Fraifeld, V. 2009 Common gene signature of cancer and longevity. Mech. Ageing Dev. 130, 33-39. (doi:10.1016/j.mad.2008.04.002)
91. Li, S., Shi, F., Pu, F., Li, X., Jiang, T., Xie, S. &Wang, Y. 2007 Hippocampal shape analysis of Alzheimer disease based on machine learning methods. Am. J. Neuroradiol. 28, 1339-1345. (doi:10.3174/ajnr.A0620)