CSGene: A literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases

Cell Death and Disease

Volumn 7, Issue , 2016, Pages e2053-

  Zhao, M ^a   Chen, L ^b   Qu, H ^b  

^a UNIVERSITY OF THE SUNSHINE COAST   (Australia)

^b PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA;

ARTICLE; CELL AGING; CHROMATIN; GENE MUTATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC TRANSCRIPTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; NONHUMAN; PRIORITY JOURNAL; VIRUS CARCINOGENESIS; CARCINOGENESIS; CELL TRANSFORMATION; GENETICS; METABOLISM; SIGNAL TRANSDUCTION; UTILIZATION;

CARCINOGENESIS; CELL AGING; CELL TRANSFORMATION, NEOPLASTIC; DATABASES, GENETIC; HUMANS; SIGNAL TRANSDUCTION;

EID: 84955069529     PISSN: None     EISSN: 20414889     Source Type: Journal    
DOI: 10.1038/cddis.2015.414     Document Type: Article

References (68)

1. Campisi J, d'Adda di Fagagna F. Cellular senescence: when bad things happen to good cells. Nat Rev Mol Cell Biol 2007; 8: 729-740.
2. Munoz-Espin D, Serrano M. Cellular senescence: from physiology to pathology. Nat Rev Mol Cell Biol 2014; 15: 482-496.
3. Hayflick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res 1961; 25: 585-621.
4. Collado M, Serrano M. Senescence in tumours: evidence from mice and humans. Nat Rev Cancer 2010; 10: 51-57.
5. Bartkova J, Rezaei N, Liontos M, Karakaidos P, Kletsas D, Issaeva N et al. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature 2006; 444: 633-637.
6. de Magalhaes JP. How ageing processes influence cancer. Nat Rev Cancer 2013; 13: 357-365.
7. Olivieri F, Rippo MR, Monsurro V, Salvioli S, Capri M, Procopio AD et al. MicroRNAs linking inflamm-aging, cellular senescence and cancer. Ageing Res Rev 2013; 12: 1056-1068.
8. Benhamed M, Herbig U, Ye T, Dejean A, Bischof O. Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nat Cell Biol 2012; 14: 266-275.
9. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G et al. The Reactome pathway knowledgebase. Nucleic Acids Res 2014; 42(Database issue): D472-D477.
10. Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ et al. The GOA database: Gene Ontology annotation updates for 2015. Nucleic Acids Res 2015; 43(Database issue): D1057-D1063.
11. Lu Z, Cohen KB, Hunter L. GeneRIF quality assurance as summary revision. Pac Symp Biocomput 2007: 269-280.
12. Hwang JW, Chung S, Sundar IK, Yao H, Arunachalam G, McBurney MW et al. Cigarette smoke-induced autophagy is regulated by SIRT1-PARP-1-dependent mechanism: implication in pathogenesis of COPD. Arch Biochem Biophys 2010; 500: 203-209.
13. Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2015; 43(Database issue): D6-17.
14. Zhao M, Sun J, Zhao Z. TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res 2013; 41(Database issue): D970-D976.
15. Kong L, Cheng L, Fan LY, Zhao M, Qu H. IQdb: an intelligence quotient score-associated gene resource for human intelligence. Database (Oxford) 2013; 2013: bat063.
16. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009; 37: 1-13.
17. Russell J, Zomerdijk JC. The RNA polymerase I transcription machinery. Biochem Soc Symp 2006; 73: 203-216.
18. Kobayashi T. Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast. Cell Mol Life Sci 2011; 68: 1395-1403.
19. Kobayashi T. Ribosomal RNA gene repeats, their stability and cellular senescence. Proc Jpn Acad Ser B Phys Biol Sci 2014; 90: 119-129.
20. Pulawski W, Ghoshdastider U, Andrisano V, Filipek S. Ubiquitous amyloids. Appl Biochem Biotechnol 2012; 166: 1626-1643.
21. Stevenson JS. Alcohol use, misuse, abuse, and dependence in later adulthood. Annu Rev Nurs Res 2005; 23: 245-280.
22. Xueying Chen MZ, Hong Qu. Cellular metabolic network analysis: discovering important reactions in treponema pallidum. BioMed Res Int 2015; 2015: 328568.
23. Zhao M, Qu H. Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors. BMC Genomics 2009; 10(Suppl 3): S31.
24. Zhao M, Qu H. High similarity of phylogenetic profiles of rate-limiting enzymes with inhibitory relation in human, mouse, rat, budding yeast and E. coli. BMC Genomics 2011; 12(Suppl 3): S10.
25. Appay V, Rowland-Jones SL. Premature ageing of the immune system: the cause of AIDS? Trends Immunol 2002; 23: 580-585.
26. Dimauro T, David G. Chromatin modifications: the driving force of senescence and aging? Aging (Albany NY) 2009; 1: 182-190.
27. Shumaker DK, Dechat T, Kohlmaier A, Adam SA, Bozovsky MR, Erdos MR et al. Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc Natl Acad Sci USA 2006; 103: 8703-8708.
28. Sarg B, Koutzamani E, Helliger W, Rundquist I, Lindner HH. Postsynthetic trimethylation of histone H4 at lysine 20 in mammalian tissues is associated with aging. J Biol Chem 2002; 277: 39195-39201.
29. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-615.
30. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2011; 39(Database issue): D685-D690.
31. Zhao M, Li X, Qu H. EDdb: a web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder. Sci China Life Sci 2013; 56: 1086-1096.
32. Jin Y, Turaev D, Weinmaier T, Rattei T, Makse HA. The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PLoS One 2013; 8: e58134.
33. Karia PS, Han J, Schmults CD. Cutaneous squamous cell carcinoma: estimated incidence of disease, nodal metastasis, and deaths from disease in the United States, 2012. J Am Acad Dermatol 2013; 68: 957-966.
34. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011; 39(Database issue): D38-D51.
35. Magrane M, Consortium U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011; 2011: bar009.
36. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y et al. Ensembl 2011. Nucleic Acids Res 2011; 39(Database issue): D800-D806.
37. Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 2010; 38(Database issue): D331-D335.
38. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004; 101: 6062-6067.
39. Zhao M, Chen Y, Qu D, Qu H. TSdb: a database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates. Sci China Life Sci 2011; 54: 60-64.
40. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005; 33: 6083-6089.
41. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008; 36(Database issue): D480-D484.
42. Zhao M, Chen X, Gao G, Tao L, Wei L. RLEdb: a database of rate-limiting enzymes and their regulation in human, rat, mouse, yeast and E. coli. Cell Res 2009; 19: 793-795.
43. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 2003; 13: 2129-2141.
44. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T et al. PID: the pathway interaction database. Nucleic Acids Res 2009; 37(Database issue): D674-D679.
45. Zhao M, Qu H. PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. BMC Genomics 2010; 11(Suppl 4): S13.
46. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011; 39(Database issue): D691-D697.
47. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B et al. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2009; 37(Database issue): D619-D622.
48. Becker KG, Barnes KC, Bright TJ, Wang SA. The genetic association database. Nat Genet 2004; 36: 431-432.
49. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010; 38(Database issue): D355-D360.
50. Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ et al. Annotating the human genome with Disease Ontology. BMC Genomics 2009; 10(Suppl 1): S6.
51. Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA et al. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of geneontology associations. Bioinformatics 2009; 25: i63-i68.
52. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009; 106: 9362-9367.
53. Hermjakob H, Fleischmann W, Apweiler R. Swissknife - 'lazy parsing' of SWISS-PROT entries. Bioinformatics 1999; 15: 771-772.
54. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2011; 39: D52-D57.
55. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 2009; 37: D767-D772.
56. Willis RC, Hogue CW. Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND). Curr Protoc Bioinformatics 2006; Chapter 8: Unit 8.9.
57. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2011; 39: D698-D704.
58. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006; 34: D354-D357.
59. Nishimura D. BioCarta. Biotech Software & Internet Report 2001; 2: 117-120.
60. Feramisco JD, Sadreyev RI, Murray ML, Grishin NV, Tsao H. Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database. J Invest Dermatol 2009; 129: 2628-2636.
61. Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 2009; 37: W305-W311.
62. Supek F, Bosnjak M, Skunca N, Smuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 2011; 6: e21800.
63. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013; 6: pl1.
64. Zhao M, Sun J, Zhao Z. Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One 2012; 7: e44175.
65. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004; 5: 101-113.
66. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011; 27: 431-432.
67. Zhao M, Kong L, Liu Y, Qu H. dbEMT: an epithelial-mesenchymal transition associated gene resource. Sci Rep 2015; 5: 11459.
68. Zhao M, Li Z, Qu H. An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. Sci Rep 2015; 5: 15478.