메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Expression divergence measured by transcriptome sequencing of four yeast species

Author keywords

Comparative transcriptomics; RNA Seq; S. bayanus; S. cerevisiae; S. mikatae; S. paradoxus

Indexed keywords

ARTICLE; CONTROLLED STUDY; FUNGAL STRAIN; GENE CLUSTER; GENE DOSAGE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC CROSS; GENETIC VARIABILITY; NONHUMAN; PHYLOGENETIC TREE; RNA SEQUENCE; SACCHAROMYCES; SACCHAROMYCES BAYANUS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES MIKATAE; SACCHAROMYCES PARADOXUS; SPECIES COMPARISON; SPECIES DIFFERENCE; SPECIES DISTRIBUTION; SPECIES DIVERSITY; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; CLASSIFICATION; GENETICS; POLYMERASE CHAIN REACTION;

EID: 84855182518     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-635     Document Type: Article
Times cited : (21)

References (40)
  • 1
    • 33747519617 scopus 로고    scopus 로고
    • Evolution of primate gene expression
    • 10.1038/nrg1940, 16921347
    • Khaitovich P, Enard W, Lachmann M, Paabo S. Evolution of primate gene expression. Nat Rev Genet 2006, 7(9):693-702. 10.1038/nrg1940, 16921347.
    • (2006) Nat Rev Genet , vol.7 , Issue.9 , pp. 693-702
    • Khaitovich, P.1    Enard, W.2    Lachmann, M.3    Paabo, S.4
  • 3
    • 77953010033 scopus 로고    scopus 로고
    • Regulatory divergence in Drosophila revealed by mRNA-seq
    • 10.1101/gr.102491.109, 2877578, 20354124
    • McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res 2010, 20(6):816-825. 10.1101/gr.102491.109, 2877578, 20354124.
    • (2010) Genome Res , vol.20 , Issue.6 , pp. 816-825
    • McManus, C.J.1    Coolon, J.D.2    Duff, M.O.3    Eipper-Mains, J.4    Graveley, B.R.5    Wittkopp, P.J.6
  • 4
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • 10.1038/ng1819, 16783381
    • Tirosh I, Weinberger A, Carmi M, Barkai N. A genetic signature of interspecies variations in gene expression. Nat Genet 2006, 38(7):830-834. 10.1038/ng1819, 16783381.
    • (2006) Nat Genet , vol.38 , Issue.7 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2    Carmi, M.3    Barkai, N.4
  • 5
    • 73349095713 scopus 로고    scopus 로고
    • Roles of trans and cis variation in yeast intraspecies evolution of gene expression
    • 10.1093/molbev/msp171, 2767097, 19648464
    • Sung HM, Wang TY, Wang D, Huang YS, Wu JP, Tsai HK, Tzeng J, Huang CJ, Lee YC, Yang P, et al. Roles of trans and cis variation in yeast intraspecies evolution of gene expression. Mol Biol Evol 2009, 26(11):2533-2538. 10.1093/molbev/msp171, 2767097, 19648464.
    • (2009) Mol Biol Evol , vol.26 , Issue.11 , pp. 2533-2538
    • Sung, H.M.1    Wang, T.Y.2    Wang, D.3    Huang, Y.S.4    Wu, J.P.5    Tsai, H.K.6    Tzeng, J.7    Huang, C.J.8    Lee, Y.C.9    Yang, P.10
  • 6
    • 17744376961 scopus 로고    scopus 로고
    • Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
    • 10.1093/molbev/msi122, 15746013
    • Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol 2005, 22(5):1345-1354. 10.1093/molbev/msi122, 15746013.
    • (2005) Mol Biol Evol , vol.22 , Issue.5 , pp. 1345-1354
    • Lemos, B.1    Bettencourt, B.R.2    Meiklejohn, C.D.3    Hartl, D.L.4
  • 7
    • 33646882591 scopus 로고    scopus 로고
    • Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution
    • 10.1093/molbev/msj119, 16520335
    • Liao BY, Zhang J. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 2006, 23(6):1119-1128. 10.1093/molbev/msj119, 16520335.
    • (2006) Mol Biol Evol , vol.23 , Issue.6 , pp. 1119-1128
    • Liao, B.Y.1    Zhang, J.2
  • 8
    • 33244455951 scopus 로고    scopus 로고
    • Evolutionary conservation of expression profiles between human and mouse orthologous genes
    • Liao BY, Zhang J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 2006, 23(3):530-540.
    • (2006) Mol Biol Evol , vol.23 , Issue.3 , pp. 530-540
    • Liao, B.Y.1    Zhang, J.2
  • 9
    • 54749157499 scopus 로고    scopus 로고
    • Single-species microarrays and comparative transcriptomics
    • 10.1371/journal.pone.0003279, 2533705, 18815615
    • Chain FJ, Ilieva D, Evans BJ. Single-species microarrays and comparative transcriptomics. PLoS One 2008, 3(9):e3279. 10.1371/journal.pone.0003279, 2533705, 18815615.
    • (2008) PLoS One , vol.3 , Issue.9
    • Chain, F.J.1    Ilieva, D.2    Evans, B.J.3
  • 10
    • 19844365733 scopus 로고    scopus 로고
    • Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    • 10.1101/gr.3335705, 1088295, 15867429
    • Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 2005, 15(5):674-680. 10.1101/gr.3335705, 1088295, 15867429.
    • (2005) Genome Res , vol.15 , Issue.5 , pp. 674-680
    • Gilad, Y.1    Rifkin, S.A.2    Bertone, P.3    Gerstein, M.4    White, K.P.5
  • 11
    • 79551495627 scopus 로고    scopus 로고
    • A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
    • 3025565, 20864445
    • Liu S, Lin L, Jiang P, Wang D, Xing Y. A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res 2010, 39(2):578-588. 3025565, 20864445.
    • (2010) Nucleic Acids Res , vol.39 , Issue.2 , pp. 578-588
    • Liu, S.1    Lin, L.2    Jiang, P.3    Wang, D.4    Xing, Y.5
  • 12
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • 10.1101/gr.079558.108, 2527709, 18550803
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18(9):1509-1517. 10.1101/gr.079558.108, 2527709, 18550803.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 13
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • 10.1126/science.1158441, 2951732, 18451266
    • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320(5881):1344-1349. 10.1126/science.1158441, 2951732, 18451266.
    • (2008) Science , vol.320 , Issue.5881 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 14
    • 77955504378 scopus 로고    scopus 로고
    • Statistical design and analysis of RNA sequencing data
    • 10.1534/genetics.110.114983, 2881125, 20439781
    • Auer PL, Doerge RW. Statistical design and analysis of RNA sequencing data. Genetics 2010, 185(2):405-416. 10.1534/genetics.110.114983, 2881125, 20439781.
    • (2010) Genetics , vol.185 , Issue.2 , pp. 405-416
    • Auer, P.L.1    Doerge, R.W.2
  • 15
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644, 12748633
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423(6937):241-254. 10.1038/nature01644, 12748633.
    • (2003) Nature , vol.423 , Issue.6937 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 16
    • 0032579440 scopus 로고    scopus 로고
    • Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications
    • 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2, 9483801
    • Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 1998, 14(2):115-132. 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2, 9483801.
    • (1998) Yeast , vol.14 , Issue.2 , pp. 115-132
    • Brachmann, C.B.1    Davies, A.2    Cost, G.J.3    Caputo, E.4    Li, J.5    Hieter, P.6    Boeke, J.D.7
  • 17
    • 69749090013 scopus 로고    scopus 로고
    • Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
    • 10.1101/gr.091868.109, 2752135, 19546169
    • McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009, 19(9):1527-1541. 10.1101/gr.091868.109, 2752135, 19546169.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1527-1541
    • McKernan, K.J.1    Peckham, H.E.2    Costa, G.L.3    McLaughlin, S.F.4    Fu, Y.5    Tsung, E.F.6    Clouser, C.R.7    Duncan, C.8    Ichikawa, J.K.9    Lee, C.C.10
  • 18
    • 25444486426 scopus 로고    scopus 로고
    • Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?
    • 10.1186/1471-2164-6-59, 1142514, 15854232
    • Dallas PB, Gottardo NG, Firth MJ, Beesley AH, Hoffmann K, Terry PA, Freitas JR, Boag JM, Cummings AJ, Kees UR. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?. BMC Genomics 2005, 6(1):59. 10.1186/1471-2164-6-59, 1142514, 15854232.
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 59
    • Dallas, P.B.1    Gottardo, N.G.2    Firth, M.J.3    Beesley, A.H.4    Hoffmann, K.5    Terry, P.A.6    Freitas, J.R.7    Boag, J.M.8    Cummings, A.J.9    Kees, U.R.10
  • 19
    • 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(10):R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
    • (2010) Genome Biol , vol.11 , Issue.10
    • Anders, S.1    Huber, W.2
  • 20
    • 0003775965 scopus 로고    scopus 로고
    • Fundamentals of biostatistics
    • Belmont, CA: Thomson-Brooks/Cole, 6
    • Rosner B. Fundamentals of biostatistics. 2006, Belmont, CA: Thomson-Brooks/Cole, 6.
    • (2006)
    • Rosner, B.1
  • 21
    • 58849139595 scopus 로고    scopus 로고
    • Genetic interactions between transcription factors cause natural variation in yeast
    • 10.1126/science.1166426, 19164747
    • Gerke J, Lorenz K, Cohen B. Genetic interactions between transcription factors cause natural variation in yeast. Science 2009, 323(5913):498-501. 10.1126/science.1166426, 19164747.
    • (2009) Science , vol.323 , Issue.5913 , pp. 498-501
    • Gerke, J.1    Lorenz, K.2    Cohen, B.3
  • 22
    • 58349111875 scopus 로고    scopus 로고
    • AmiGO: online access to ontology and annotation data
    • 10.1093/bioinformatics/btn615, 2639003, 19033274
    • Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics 2009, 25(2):288-289. 10.1093/bioinformatics/btn615, 2639003, 19033274.
    • (2009) Bioinformatics , vol.25 , Issue.2 , pp. 288-289
    • Carbon, S.1    Ireland, A.2    Mungall, C.J.3    Shu, S.4    Marshall, B.5    Lewis, S.6
  • 23
    • 1542328960 scopus 로고    scopus 로고
    • Identification and distinct regulation of yeast TATA box-containing genes
    • 10.1016/S0092-8674(04)00205-3, 15006352
    • Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell 2004, 116(5):699-709. 10.1016/S0092-8674(04)00205-3, 15006352.
    • (2004) Cell , vol.116 , Issue.5 , pp. 699-709
    • Basehoar, A.D.1    Zanton, S.J.2    Pugh, B.F.3
  • 24
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • 10.1186/1471-2105-7-113, 1435934, 16522208
    • MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 2006, 7:113. 10.1186/1471-2105-7-113, 1435934, 16522208.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.D.1    Wang, T.2    Gordon, D.B.3    Gifford, D.K.4    Stormo, G.D.5    Fraenkel, E.6
  • 26
    • 22144440528 scopus 로고    scopus 로고
    • Toward a neutral evolutionary model of gene expression
    • 10.1534/genetics.104.037135, 1450413, 15834146
    • Khaitovich P, Paabo S, Weiss G. Toward a neutral evolutionary model of gene expression. Genetics 2005, 170(2):929-939. 10.1534/genetics.104.037135, 1450413, 15834146.
    • (2005) Genetics , vol.170 , Issue.2 , pp. 929-939
    • Khaitovich, P.1    Paabo, S.2    Weiss, G.3
  • 27
    • 34347330290 scopus 로고    scopus 로고
    • Quantifying variation in gene expression
    • 10.1111/j.1365-294X.2007.03354.x, 17594433
    • Clark TA, Townsend JP. Quantifying variation in gene expression. Mol Ecol 2007, 16(13):2613-2616. 10.1111/j.1365-294X.2007.03354.x, 17594433.
    • (2007) Mol Ecol , vol.16 , Issue.13 , pp. 2613-2616
    • Clark, T.A.1    Townsend, J.P.2
  • 28
    • 43049097860 scopus 로고    scopus 로고
    • Differential gene expression in incipient species of Anopheles gambiae
    • 10.1111/j.1365-294X.2008.03774.x, 18430144
    • Cassone BJ, Mouline K, Hahn MW, White BJ, Pombi M, Simard F, Costantini C, Besansky NJ. Differential gene expression in incipient species of Anopheles gambiae. Mol Ecol 2008, 17(10):2491-2504. 10.1111/j.1365-294X.2008.03774.x, 18430144.
    • (2008) Mol Ecol , vol.17 , Issue.10 , pp. 2491-2504
    • Cassone, B.J.1    Mouline, K.2    Hahn, M.W.3    White, B.J.4    Pombi, M.5    Simard, F.6    Costantini, C.7    Besansky, N.J.8
  • 29
    • 14144255920 scopus 로고    scopus 로고
    • Rapid evolution of expression and regulatory divergences after yeast gene duplication
    • 10.1073/pnas.0409186102, 545572, 15647348
    • Gu X, Zhang Z, Huang W. Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci USA 2005, 102(3):707-712. 10.1073/pnas.0409186102, 545572, 15647348.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.3 , pp. 707-712
    • Gu, X.1    Zhang, Z.2    Huang, W.3
  • 30
    • 34548527460 scopus 로고    scopus 로고
    • Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
    • 10.1186/gb-2007-8-4-r50, 1895995, 17411427
    • Tirosh I, Barkai N. Comparative analysis indicates regulatory neofunctionalization of yeast duplicates. Genome Biol 2007, 8(4):R50. 10.1186/gb-2007-8-4-r50, 1895995, 17411427.
    • (2007) Genome Biol , vol.8 , Issue.4
    • Tirosh, I.1    Barkai, N.2
  • 31
    • 77950388941 scopus 로고    scopus 로고
    • Polygenic and directional regulatory evolution across pathways in Saccharomyces
    • 10.1073/pnas.0912959107, 2841874, 20194736
    • Bullard JH, Mostovoy Y, Dudoit S, Brem RB. Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci USA 2010, 107(11):5058-5063. 10.1073/pnas.0912959107, 2841874, 20194736.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.11 , pp. 5058-5063
    • Bullard, J.H.1    Mostovoy, Y.2    Dudoit, S.3    Brem, R.B.4
  • 32
    • 65549086559 scopus 로고    scopus 로고
    • A yeast hybrid provides insight into the evolution of gene expression regulation
    • 10.1126/science.1169766, 19407207
    • Tirosh I, Reikhav S, Levy AA, Barkai N. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 2009, 324(5927):659-662. 10.1126/science.1169766, 19407207.
    • (2009) Science , vol.324 , Issue.5927 , pp. 659-662
    • Tirosh, I.1    Reikhav, S.2    Levy, A.A.3    Barkai, N.4
  • 33
    • 79958151996 scopus 로고    scopus 로고
    • BamTools: a C++ API and toolkit for analyzing and managing BAM files
    • 10.1093/bioinformatics/btr174, 21493652
    • Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 2011, 27(12):1691-1692. 10.1093/bioinformatics/btr174, 21493652.
    • (2011) Bioinformatics , vol.27 , Issue.12 , pp. 1691-1692
    • Barnett, D.W.1    Garrison, E.K.2    Quinlan, A.R.3    Stromberg, M.P.4    Marth, G.T.5
  • 34
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • 10.1038/nmeth.1226, 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
    • (2008) Nat Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 35
    • 0001454867 scopus 로고
    • On the criterion that a given system of deviations from the probable in the case of a correlated system of variables is such that it can be reasonably supposed to have arisen from random sampling
    • Pearson K. On the criterion that a given system of deviations from the probable in the case of a correlated system of variables is such that it can be reasonably supposed to have arisen from random sampling. London 1900,
    • (1900) London
    • Pearson, K.1
  • 36
    • 0003570262 scopus 로고    scopus 로고
    • Statistical methods for psychology
    • Belmont, CA: Duxbury Press, 4
    • Howell DC. Statistical methods for psychology. 1997, Belmont, CA: Duxbury Press, 4.
    • (1997)
    • Howell, D.C.1
  • 37
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • 10.1186/gb-2010-11-3-r25, 2864565, 20196867
    • Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 2010, 11(3):R25. 10.1186/gb-2010-11-3-r25, 2864565, 20196867.
    • (2010) Genome Biol , vol.11 , Issue.3
    • Robinson, M.D.1    Oshlack, A.2
  • 38
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 11(10):R106.
    • Genome Biol , vol.11 , Issue.10
    • Anders, S.1    Huber, W.2
  • 39
    • 0003478714 scopus 로고
    • Data reduction and error analysis for the physical sciences
    • New York: McGraw-Hill
    • Bevington PR. Data reduction and error analysis for the physical sciences. 1969, New York: McGraw-Hill.
    • (1969)
    • Bevington, P.R.1
  • 40
    • 0003493777 scopus 로고
    • Statistical methods for research workers
    • Edinburgh [etc.]: Oliver and Boyd, 4
    • Fisher RA. Statistical methods for research workers. 1932, Edinburgh [etc.]: Oliver and Boyd, 4.
    • (1932)
    • Fisher, R.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.