메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

Author keywords

Ageing; Gene expression; Model fish species; Nothobranchius furzeri; RNA seq; Transcript catalogue; Transcriptome assembly

Indexed keywords

COMPLEMENTARY DNA; FISH PROTEIN; MESSENGER RNA; TRANSCRIPTOME;

EID: 84874939976     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-185     Document Type: Article
Times cited : (52)

References (55)
  • 1
    • 33646863656 scopus 로고    scopus 로고
    • The quest for genetic determinants of human longevity: challenges and insights
    • 10.1038/nrg1871, 2726954, 16708071
    • Christensen K, Johnson TE, Vaupel JW. The quest for genetic determinants of human longevity: challenges and insights. Nat Rev Genet 2006, 7:436-448. 10.1038/nrg1871, 2726954, 16708071.
    • (2006) Nat Rev Genet , vol.7 , pp. 436-448
    • Christensen, K.1    Johnson, T.E.2    Vaupel, J.W.3
  • 2
    • 34247569105 scopus 로고    scopus 로고
    • Lifespan Regulation by Evolutionarily Conserved Genes Essential for Viability
    • 10.1371/journal.pgen.0030056, 1847696, 17411345
    • Curran SP, Ruvkun G. Lifespan Regulation by Evolutionarily Conserved Genes Essential for Viability. PLoS Genet 2007, 3:e56. 10.1371/journal.pgen.0030056, 1847696, 17411345.
    • (2007) PLoS Genet , vol.3
    • Curran, S.P.1    Ruvkun, G.2
  • 4
    • 38349103636 scopus 로고    scopus 로고
    • Separating cause from effect: how does insulin/IGF signalling control lifespan in worms, flies and mice?
    • 10.1111/j.1365-2796.2007.01906.x, 18226095
    • Piper MDW, Selman C, McElwee JJ, Partridge L. Separating cause from effect: how does insulin/IGF signalling control lifespan in worms, flies and mice?. J Intern Med 2008, 263:179-191. 10.1111/j.1365-2796.2007.01906.x, 18226095.
    • (2008) J Intern Med , vol.263 , pp. 179-191
    • Piper, M.D.W.1    Selman, C.2    McElwee, J.J.3    Partridge, L.4
  • 5
    • 27744540845 scopus 로고    scopus 로고
    • Annual fishes of the genus Nothobranchius as a model system for aging research
    • 10.1111/j.1474-9726.2005.00165.x, 16164422
    • Genade T, Benedetti M, Terzibasi E, Roncaglia P, Valenzano DR, Cattaneo A, Cellerino A. Annual fishes of the genus Nothobranchius as a model system for aging research. Aging Cell 2005, 4:223-233. 10.1111/j.1474-9726.2005.00165.x, 16164422.
    • (2005) Aging Cell , vol.4 , pp. 223-233
    • Genade, T.1    Benedetti, M.2    Terzibasi, E.3    Roncaglia, P.4    Valenzano, D.R.5    Cattaneo, A.6    Cellerino, A.7
  • 6
    • 0242589902 scopus 로고
    • A new Nothobranchius (Pisces, Cyprinodontidae) from Southeastern Rhodesia
    • Jubb RA. A new Nothobranchius (Pisces, Cyprinodontidae) from Southeastern Rhodesia. J Am Killifish Assoc 1971, 8:314-321.
    • (1971) J Am Killifish Assoc , vol.8 , pp. 314-321
    • Jubb, R.A.1
  • 7
    • 57349135308 scopus 로고    scopus 로고
    • Large Differences in Aging Phenotype between Strains of the Short-Lived Annual Fish Nothobranchius furzeri
    • 10.1371/journal.pone.0003866, 2585814, 19052641
    • Terzibasi E, Valenzano DR, Benedetti M, Roncaglia P, Cattaneo A, Domenici L, Cellerino A. Large Differences in Aging Phenotype between Strains of the Short-Lived Annual Fish Nothobranchius furzeri. PLoS One 2008, 3(12):e3866. 10.1371/journal.pone.0003866, 2585814, 19052641.
    • (2008) PLoS One , vol.3 , Issue.12
    • Terzibasi, E.1    Valenzano, D.R.2    Benedetti, M.3    Roncaglia, P.4    Cattaneo, A.5    Domenici, L.6    Cellerino, A.7
  • 8
    • 0242574697 scopus 로고    scopus 로고
    • Extremely short lifespan in the annual fish Nothobranchius furzeri
    • 1809958, 14667379
    • Valdesalici S, Cellerino A. Extremely short lifespan in the annual fish Nothobranchius furzeri. Proc. Biol. Sci 2003, 270(Suppl 2):S189-S191. 1809958, 14667379.
    • (2003) Proc. Biol. Sci , vol.270 , Issue.SUPPL. 2
    • Valdesalici, S.1    Cellerino, A.2
  • 10
    • 33744454400 scopus 로고    scopus 로고
    • Temperature affects longevity and age-related locomotor and cognitive decay in the short-lived fish Nothobranchius furzeri
    • 10.1111/j.1474-9726.2006.00212.x, 16842500
    • Valenzano DR, Terzibasi E, Cattaneo A, Domenici L, Cellerino A. Temperature affects longevity and age-related locomotor and cognitive decay in the short-lived fish Nothobranchius furzeri. Aging Cell 2006, 5:275-278. 10.1111/j.1474-9726.2006.00212.x, 16842500.
    • (2006) Aging Cell , vol.5 , pp. 275-278
    • Valenzano, D.R.1    Terzibasi, E.2    Cattaneo, A.3    Domenici, L.4    Cellerino, A.5
  • 12
    • 0029312158 scopus 로고
    • Toward simplifying and accurately formulating fragment assembly
    • 10.1089/cmb.1995.2.275, 7497129
    • Myers EW. Toward simplifying and accurately formulating fragment assembly. J Comput Biol 1995, 2:275-290. 10.1089/cmb.1995.2.275, 7497129.
    • (1995) J Comput Biol , vol.2 , pp. 275-290
    • Myers, E.W.1
  • 15
    • 70349685077 scopus 로고    scopus 로고
    • PAVE: program for assembling and viewing ESTs
    • 10.1186/1471-2164-10-400, 2748094, 19709403
    • Soderlund C, Johnson E, Bomhoff M, Descour A. PAVE: program for assembling and viewing ESTs. BMC Genomics 2009, 10:400. 10.1186/1471-2164-10-400, 2748094, 19709403.
    • (2009) BMC Genomics , vol.10 , pp. 400
    • Soderlund, C.1    Johnson, E.2    Bomhoff, M.3    Descour, A.4
  • 16
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • 10.1093/bioinformatics/btp324, 2705234, 19451168
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 18
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • 10.1093/nar/gki476, 539979, 15608248
    • Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33:D501-D504. 10.1093/nar/gki476, 539979, 15608248.
    • (2005) Nucleic Acids Res , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 21
    • 3042855210 scopus 로고    scopus 로고
    • UniGene: a unified view of the transcriptome
    • Bethesda (MD): National Center for Biotechnology Information, Available:
    • Pontius J, Wagner L, Schuler G. UniGene: a unified view of the transcriptome. The NCBI Handbook 2003, Bethesda (MD): National Center for Biotechnology Information, Available: http://www.ncbi.nlm.nih.gov/books/NBK21101/.
    • (2003) The NCBI Handbook
    • Pontius, J.1    Wagner, L.2    Schuler, G.3
  • 23
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: Complete, Duplication-Aware Phylogenetic Trees in Vertebrates
    • 2652215, 19029536
    • Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, Duplication-Aware Phylogenetic Trees in Vertebrates. Genome Res 2009, 19:327-335. 2652215, 19029536.
    • (2009) Genome Res , vol.19 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5    Birney, E.6
  • 25
    • 0037351989 scopus 로고    scopus 로고
    • Genome duplication, a trait shared by 22000 species of ray-finned fish
    • 10.1101/gr.640303, 430266, 12618368
    • Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 2003, 13:382-390. 10.1101/gr.640303, 430266, 12618368.
    • (2003) Genome Res , vol.13 , pp. 382-390
    • Taylor, J.S.1    Braasch, I.2    Frickey, T.3    Meyer, A.4    Van de Peer, Y.5
  • 26
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • 10.1186/gb-2010-11-10-r106, 3218662, 20979621
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 27
  • 28
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 29
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Gen 2011, 12:671-682.
    • (2011) Nat Rev Gen , vol.12 , pp. 671-682
    • Martin, J.A.1    Wang, Z.2
  • 30
    • 78549246241 scopus 로고    scopus 로고
    • Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
    • 10.1186/1471-2164-11-663, 3152782, 21106091
    • Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 2010, 11:663. 10.1186/1471-2164-11-663, 3152782, 21106091.
    • (2010) BMC Genomics , vol.11 , pp. 663
    • Martin, J.1    Bruno, V.M.2    Fang, Z.3    Meng, X.4    Blow, M.5    Zhang, T.6    Sherlock, G.7    Snyder, M.8    Wang, Z.9
  • 35
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 3146043, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 3146043, 20436464.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Kwan, G.6    Van Baren, M.J.7    Salzberg, S.L.8    Wold, B.J.9    Pachter, L.10
  • 38
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • 10.1186/1471-2105-12-323, 3163565, 21816040
    • Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011, 12:323. 10.1186/1471-2105-12-323, 3163565, 21816040.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 40
    • 16344391539 scopus 로고    scopus 로고
    • Variation in tissue-specific gene expression among natural populations
    • 10.1186/gb-2005-6-2-r13, 551533, 15693942
    • Whitehead A, Crawford DL. Variation in tissue-specific gene expression among natural populations. Genome Biol 2005, 6:R13. 10.1186/gb-2005-6-2-r13, 551533, 15693942.
    • (2005) Genome Biol , vol.6
    • Whitehead, A.1    Crawford, D.L.2
  • 42
    • 63549135460 scopus 로고    scopus 로고
    • Meta-analysis of age-related gene expression profiles identifies common signatures of aging
    • 10.1093/bioinformatics/btp073, 2732303, 19189975
    • De Magalhães JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 2009, 25:875-881. 10.1093/bioinformatics/btp073, 2732303, 19189975.
    • (2009) Bioinformatics , vol.25 , pp. 875-881
    • De Magalhães, J.P.1    Curado, J.2    Church, G.M.3
  • 44
    • 67651183792 scopus 로고    scopus 로고
    • Gene expression profiling of aging in multiple mouse strains: identification of aging biomarkers and impact of dietary antioxidants
    • 10.1111/j.1474-9726.2009.00496.x, 2733852, 19555370
    • Park S-K, Kim K, Page GP, Allison DB, Weindruch R, Prolla TA. Gene expression profiling of aging in multiple mouse strains: identification of aging biomarkers and impact of dietary antioxidants. Aging Cell 2009, 8:484-495. 10.1111/j.1474-9726.2009.00496.x, 2733852, 19555370.
    • (2009) Aging Cell , vol.8 , pp. 484-495
    • Park, S.-K.1    Kim, K.2    Page, G.P.3    Allison, D.B.4    Weindruch, R.5    Prolla, T.A.6
  • 45
    • 79952706223 scopus 로고    scopus 로고
    • The short-lived annual fish Nothobranchius furzeri shows a typical teleost aging process reinforced by high incidence of age-dependent neoplasias
    • 10.1016/j.exger.2010.10.011, 21056099
    • Di Cicco E, Tozzini ET, Rossi G, Cellerino A. The short-lived annual fish Nothobranchius furzeri shows a typical teleost aging process reinforced by high incidence of age-dependent neoplasias. Exp Gerontol 2011, 46:249-256. 10.1016/j.exger.2010.10.011, 21056099.
    • (2011) Exp Gerontol , vol.46 , pp. 249-256
    • Di Cicco, E.1    Tozzini, E.T.2    Rossi, G.3    Cellerino, A.4
  • 48
    • 77954238055 scopus 로고    scopus 로고
    • Efficient construction of an assembly string graph using the FM-index
    • 10.1093/bioinformatics/btq217, 2881401, 20529929
    • Simpson JT, Durbin R. Efficient construction of an assembly string graph using the FM-index. Bioinformatics 2010, 26:i367-i373. 10.1093/bioinformatics/btq217, 2881401, 20529929.
    • (2010) Bioinformatics , vol.26
    • Simpson, J.T.1    Durbin, R.2
  • 49
    • 84875364697 scopus 로고    scopus 로고
    • CLC bio http://www.clcbio.com/.
    • CLC bio
  • 50
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • 10.1093/bioinformatics/btl158, 16731699
    • Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 52
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 54
    • 0036581160 scopus 로고    scopus 로고
    • Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR
    • 10.1093/nar/30.9.e36, 113859, 11972351
    • Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 2002, 30:e36. 10.1093/nar/30.9.e36, 113859, 11972351.
    • (2002) Nucleic Acids Res , vol.30
    • Pfaffl, M.W.1    Horgan, G.W.2    Dempfle, L.3
  • 55
    • 10044259013 scopus 로고    scopus 로고
    • Sebastopol, CA, USA: O'Reilly & Associates, Inc
    • Korf I, Yandell M, Bedell J. BLAST Sebastopol, CA, USA: O'Reilly & Associates, Inc.
    • BLAST
    • Korf, I.1    Yandell, M.2    Bedell, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.