메뉴 건너뛰기




Volumn 6, Issue 7, 2010, Pages 37-

Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN; MAMMALS; TRANSCRIPTION;

EID: 77957929225     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000843     Document Type: Article
Times cited : (50)

References (39)
  • 1
    • 70449723389 scopus 로고    scopus 로고
    • Establishing legitimacy and function in the new transcriptome
    • van Bakel H, Hughes TR (2009) Establishing legitimacy and function in the new transcriptome. Brief Funct Genomic Proteomic 8: 424-436.
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 424-436
    • van Bakel, H.1    Hughes, T.R.2
  • 2
    • 60349120914 scopus 로고    scopus 로고
    • Long non-coding RNAs: Insights into functions
    • Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10: 155-159.
    • (2009) Nat Rev Genet , vol.10 , pp. 155-159
    • Mercer, T.R.1    Dinger, M.E.2    Mattick, J.S.3
  • 3
    • 10944229314 scopus 로고    scopus 로고
    • Variation in alternative splicing across human tissues
    • Yeo G, Holste D, Kreiman G, Burge CB (2004) Variation in alternative splicing across human tissues. Genome Biol 5: R74.
    • (2004) Genome Biol , vol.5
    • Yeo, G.1    Holste, D.2    Kreiman, G.3    Burge, C.B.4
  • 4
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 5
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 6
    • 0037066542 scopus 로고    scopus 로고
    • Intra- and interspecific variation in primate gene expression patterns
    • Enard W, Khaitovich P, Klose J, Zöllner S, Heissig F, et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
    • (2002) Science , vol.296 , pp. 340-343
    • Enard, W.1    Khaitovich, P.2    Klose, J.3    Zöllner, S.4    Heissig, F.5
  • 7
    • 0242268390 scopus 로고    scopus 로고
    • Elevated gene expression levels distinguish human from non-human primate brains
    • Cáceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, et al. (2003) Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci USA 100: 13030-13035.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13030-13035
    • Cáceres, M.1    Lachuer, J.2    Zapala, M.A.3    Redmond, J.C.4    Kudo, L.5
  • 8
    • 0037303824 scopus 로고    scopus 로고
    • Induced gene expression in human brain after the split from chimpanzee
    • Gu J, Gu X (2003) Induced gene expression in human brain after the split from chimpanzee. Trends Genet 19: 63-65.
    • (2003) Trends Genet , vol.19 , pp. 63-65
    • Gu, J.1    Gu, X.2
  • 9
    • 33750482555 scopus 로고    scopus 로고
    • Functionality of intergenic transcription: An evolutionary comparison
    • Khaitovich P, Kelso J, Franz H, Visagie J, Giger T, et al. (2006) Functionality of intergenic transcription: an evolutionary comparison. PLoS Genet 2: e171.
    • (2006) PLoS Genet , vol.2
    • Khaitovich, P.1    Kelso, J.2    Franz, H.3    Visagie, J.4    Giger, T.5
  • 11
    • 47949084846 scopus 로고    scopus 로고
    • Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
    • Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, et al. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45: 81-94.
    • (2008) Biotechniques , vol.45 , pp. 81-94
    • Morin, R.1    Bainbridge, M.2    Fejes, A.3    Hirst, M.4    Krzywinski, M.5
  • 12
    • 50949090496 scopus 로고    scopus 로고
    • Poly A- transcripts expressed in HeLa cells
    • Wu Q, Kim YC, Lu J, Xuan Z, Chen J, et al. (2008) Poly A- transcripts expressed in HeLa cells. PLoS One 3: e2803.
    • (2008) PLoS One , vol.3
    • Wu, Q.1    Kim, Y.C.2    Lu, J.3    Xuan, Z.4    Chen, J.5
  • 13
    • 67349173665 scopus 로고    scopus 로고
    • The regulated retrotransposon transcriptome of mammalian cells
    • Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41: 563-571.
    • (2009) Nat Genet , vol.41 , pp. 563-571
    • Faulkner, G.J.1    Kimura, Y.2    Daub, C.O.3    Wani, S.4    Plessy, C.5
  • 14
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel A, Bejerano G, Pedersen J, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research 15: 1034-1050.
    • (2005) Genome Research , vol.15 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.3    Hinrichs, A.S.4    Hou, M.5
  • 15
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 16
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 17
    • 38849101777 scopus 로고    scopus 로고
    • Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
    • Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, et al. (2007) Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Research 17: 1823-1836.
    • (2007) Genome Research , vol.17 , pp. 1823-1836
    • Lin, M.F.1    Carlson, J.W.2    Crosby, M.A.3    Matthews, B.B.4    Yu, C.5
  • 18
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3    French, C.4    Lin, M.F.5
  • 19
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil AM, Guttman M, Huarte M, Garber M, Raj A, et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 11667-11672
    • Khalil, A.M.1    Guttman, M.2    Huarte, M.3    Garber, M.4    Raj, A.5
  • 21
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
    • Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 22
    • 4444287699 scopus 로고    scopus 로고
    • Regional patterns of gene expression in human and chimpanzee brains
    • Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, et al. (2004) Regional patterns of gene expression in human and chimpanzee brains. Genome Research 14: 1462-1473.
    • (2004) Genome Research , vol.14 , pp. 1462-1473
    • Khaitovich, P.1    Muetzel, B.2    She, X.3    Lachmann, M.4    Hellmann, I.5
  • 23
    • 76049088399 scopus 로고    scopus 로고
    • Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain
    • Nowick K, Gernat T, Almaas E, Stubbs L (2009) Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A 106: 22358-22363.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 22358-22363
    • Nowick, K.1    Gernat, T.2    Almaas, E.3    Stubbs, L.4
  • 24
    • 34548346860 scopus 로고    scopus 로고
    • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
    • Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA (2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet 39: 1140-1144.
    • (2007) Nat Genet , vol.39 , pp. 1140-1144
    • Haygood, R.1    Fedrigo, O.2    Hanson, B.3    Yokoyama, K.D.4    Wray, G.A.5
  • 25
    • 33644855479 scopus 로고    scopus 로고
    • Expression profiling in primates reveals a rapid evolution of human transcription factors
    • Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
    • (2006) Nature , vol.440 , pp. 242-245
    • Gilad, Y.1    Oshlack, A.2    Smyth, G.K.3    Speed, T.P.4    White, K.P.5
  • 26
    • 56649102089 scopus 로고    scopus 로고
    • Genomic convergence analysis of schizophrenia: MRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum
    • Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, et al. (2008) Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One 3: e3625.
    • (2008) PLoS One , vol.3
    • Mudge, J.1    Miller, N.A.2    Khrebtukova, I.3    Lindquist, I.E.4    May, G.D.5
  • 27
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 28
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 39 untranslated regions and fewer microRNA target sites
    • Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB (2008) Proliferating cells express mRNAs with shortened 39 untranslated regions and fewer microRNA target sites. Science 320: 1643-1647.
    • (2008) Science , vol.320 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3    Sharp, P.A.4    Burge, C.B.5
  • 29
    • 66049104920 scopus 로고    scopus 로고
    • Progressive lengthening of 39 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
    • Ji Z, Lee JY, Pan Z, Jiang B, Tian B (2009) Progressive lengthening of 39 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci USA 106: 7028-7033.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 7028-7033
    • Ji, Z.1    Lee, J.Y.2    Pan, Z.3    Jiang, B.4    Tian, B.5
  • 30
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: Short oligonucleotide alignment program
    • Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
    • (2008) Bioinformatics , vol.24 , pp. 713-714
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 33
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
    • (2004) Genome Res , vol.14 , pp. 708-715
    • Blanchette, M.1    Kent, W.J.2    Riemer, C.3    Elnitski, L.4    Smit, A.F.5
  • 35
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 36
    • 33847173733 scopus 로고    scopus 로고
    • FUNC: A package for detecting significant associations between gene sets and ontological annotations
    • Prufer K, Muetzel B, Do HH, Weiss G, Khaitovich P, et al. (2007) FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: 41.
    • (2007) BMC Bioinformatics , vol.8 , pp. 41
    • Prufer, K.1    Muetzel, B.2    Do, H.H.3    Weiss, G.4    Khaitovich, P.5
  • 37
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
    • (2005) Nature , vol.437 , pp. 69-87
  • 38
    • 22144447840 scopus 로고    scopus 로고
    • Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
    • Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850-1854.
    • (2005) Science , vol.309 , pp. 1850-1854
    • Khaitovich, P.1    Hellmann, I.2    Enard, W.3    Nowick, K.4    Leinweber, M.5
  • 39
    • 34547609849 scopus 로고    scopus 로고
    • Evolutionary history of mammalian transposons determined by genome-wide defragmentation
    • Giordano J, Ge Y, Gelfand Y, Abrusán G, Benson G, et al. (2007) Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol 3: e137.
    • (2007) PLoS Comput Biol , vol.3
    • Giordano, J.1    Ge, Y.2    Gelfand, Y.3    Abrusán, G.4    Benson, G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.