The NetAge database: A compendium of networks for longevity, age-related diseases and associated processes

Biogerontology

Volumn 11, Issue 4, 2010, Pages 513-522

  Tacutu, Robi ^a   Budovsky, Arie ^a   Fraifeld, Vadim E ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

Age related diseases; Longevity genes; Micro RNAs; Networks; Protein protein interactions

Indexed keywords

MICRORNA;

AGING; DATA BASE; DNA POLYMORPHISM; GENE INTERACTION; GENE MUTATION; GENE SILENCING; GENETIC ANALYSIS; LONGEVITY; ONLINE SYSTEM; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW; RNA INTERFERENCE; SACCHAROMYCES CEREVISIAE; ANIMAL; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; FACTUAL DATABASE; GENE REGULATORY NETWORK; GENETICS; HUMAN; INTERNET; PROCEDURES; PROTEIN ANALYSIS;

AGING; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GENE REGULATORY NETWORKS; HUMANS; INTERNET; LONGEVITY; MICRORNAS; PROTEIN INTERACTION MAPPING; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77954951646     PISSN: 13895729     EISSN: 15736768     Source Type: Journal    
DOI: 10.1007/s10522-010-9265-8     Document Type: Review

References (50)

1. Agrawal S, Dimitrova N, Nathan P, Udayakumar K, Lakshmi SS, Sriram S, Manjusha N, Sengupta U (2008) T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics 9:320
2. Ashford JW, Atwood CS, Blass JP, Bowen RL, Finch CE, Iqbal K, Joseph JA, Perry G (2005) What is aging? What is its role in Alzheimer's disease? What can we do about it? J Alzheimers Dis 7:247-253
3. Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL (2008) InParanoid 6: eukaryotic ortholog clusters with in paralogs. Nucleic Acids Res 36:D263-D266
4. Bertram L, McQueen MB, Mullin K, Blacker D, Tanzi RE (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet 39:17-23
5. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bahler J, Wood V, Dolinski K, Tyers M (2008) The BioGRID interaction database: 2008 update. Nucleic Acids Res 36:D637-D640
6. Budovsky A, Muradian KK, Fraifeld VE (2006) From diseaseoriented to aging/longevity-oriented studies. Rejuvenation Res 9:207-210
7. Budovsky A, Abramovich A, Cohen R, Chalifa-Caspi V, Fraifeld V (2007) Longevity network: construction and implications. Mech Ageing Dev 128:117-124
8. 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
9. Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S (2009) MatrixDB, a database focused on extracellular protein- protein and protein-carbohydrate interactions. Bioinformatics 25:690-691
10. Chautard E, Thierry-Mieg N, Ricard-Blum S (2010) Interaction networks as tools to investigate the mechanisms of aging. Biogerontology. doi:10.1007/s10522-010-9268-5
11. Csermely P, Soti C (2006) Cellular networks and the aging process. Arch Physiol Biochem 112:60-64
12. Curran SP, Ruvkun G (2007) Lifespan regulation by evolutionarily conserved genes essential for viability. PLoS Genet 3:e56
13. de Magalhaes JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, Church GM (2009) The human ageing genomic resources: online databases and tools for biogerontologists. Aging Cell 8:65-72
14. Eyre TA, Ducluzeau F, Sneddon TP, Povey S, Bruford EA, Lush MJ (2006) The HUGO gene nomenclature database, 2006 updates. Nucleic Acids Res 34:D319-D321
15. Feinberg AP (2008) Epigenetics at the epicenter of modern medicine. JAMA 299:1345-1350
16. Ferrarini L, Bertelli L, Feala J, McCulloch AD, Paternostro G (2005) A more efficient search strategy for aging genes based on connectivity. Bioinformatics 21:338-348
17. Finch CE, Marchalonis JJ (1996) Evolutionary perspectives on amyloid and inflammatory features of Alzheimer disease. Neurobiol Aging 17:809-815
18. Finch CE, Ruvkun G (2001) The genetics of aging. Annu Rev Genomics Hum Genet 2:435-462
19. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811 (Pubitemid 28099681)
20. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL (2007) The human disease network. Proc Natl Acad Sci USA 104:8685-8690
21. Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM (2008) Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res 36:D577-D581
22. Hsu CW, Juan HF, Huang HC (2008) Characterization of microRNA-regulated protein-protein interaction network. Proteomics 8:1975-1979
23. Ideker T, Sharan R (2008) Protein networks in disease. Genome Res 18:644-652
24. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A (2009) Human protein reference database-2009 update. Nucleic Acids Res 37:D767-D772
25. Lee SS (2006) Whole genome RNAi screens for increased longevity: important new insights but not the whole story. Exp Gerontol 41:968-973
26. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787-798
27. Liang H, Li WH (2007) MicroRNA regulation of human protein protein interaction network. RNA 13:1402-1408
28. Liang R, Bates DJ, Wang E (2009) Epigenetic control of microRNA expression and aging. Curr Genomics 10: 184-193
29. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10:295
30. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343-349.
31. Miller JA, Oldham MC, Geschwind DH (2008) A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci 28:1410-1420
32. Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ (2007) Gene aging nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res 35:D756-D759
33. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 37:D155-D158
34. Promislow DE (2004) Protein networks, pleiotropy and the evolution of senescence. Proc Biol Sci 271:1225-1234
35. Rattan SI, Singh R (2009) Progress & prospects: gene therapy in aging. Gene Ther 16:3-9
36. Reddy VP, Zhu X, Perry G, Smith MA (2009) Oxidative stress in diabetes and Alzheimer's disease. J Alzheimers Dis 16:763-774
37. Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P, Chan J, Chen WJ, Davis P, Fernandes J, Fiedler TJ, Han M, Harris TW, Kishore R, Lee R, McKay S, Muller HM, Nakamura C, Ozersky P, Petcherski A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW (2008) WormBase 2007. Nucleic Acids Res 36:D612-D617
38. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 37: D5-D15
39. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504
40. Simko GI, Gyurko D, Veres DV, Nanasi T, Csermely P (2009) Network strategies to understand the aging process and help age-related drug design. Genome Med 1:90
41. Strausberg RL, Buetow KH, Greenhut SF, Grouse LH, Schaefer CF (2002) The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer. Cancer Investig 20:1038-1050
42. Tacutu R, Budovsky A, Wolfson M, Fraifeld V (2010) MicroRNA- regulated protein-protein interaction networks: how could they help in searching for pro-longevity targets? Rejuvenation Res 13(2). doi:10.1089/rej.2009.0980
43. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H (2009) FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res 37:D555-D559
44. Wang E (2007) MicroRNA, the putative molecular control for mid-life decline. Ageing Res Rev 6:1-11
45. Wang J, Zhang S, Wang Y, Chen L, Zhang XS (2009) Diseaseaging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Comput Biol 5: e1000521
46. Wolfson M, Tacutu R, Budovsky A, Aizenberg N, Fraifeld V (2008) MicroRNAs: relevance to aging and age-related diseases. Open Longev Sci 2:66-75. doi:10.2174/1876326 X00802010066
47. Wolfson M, Budovsky A, Tacutu R, Fraifeld V (2009) The signaling hubs at the crossroad of longevity and age-related disease networks. Int J Biochem Cell Biol 41:516-520
48. Xue H, Xian B, Dong D, Xia K, Zhu S, Zhang Z, Hou L, Zhang Q, Zhang Y, Han JD (2007) A modular network model of aging. Mol Syst Biol 3:147
49. Yang Y, Fu LM (2003) TSGDB: a database system for tumor suppressor genes. Bioinformatics 19:2311-2312
50. Zhang Q, Lu M, Shi L, Rui W, Zhu X, Chen G, Shang T, Tang J (2004) Cardio: a web-based knowledge resource of genes and proteins related to cardiovascular disease. Int J Cardiol 97:245-249