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Volumn 8, Issue , 2017, Pages

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

(22)  Seki, Ryohei a,b   Li, Cai c,d,e   Fang, Qi c,d   Hayashi, Shinichi b,f   Egawa, Shiro b   Hu, Jiang c   Xu, Luohao c   Pan, Hailin c,d   Kondo, Mao b   Sato, Tomohiko b   Matsubara, Haruka b   Kamiyama, Namiko b   Kitajima, Keiichi b   Saito, Daisuke b   Liu, Yang c   Gilbert, M Thomas P e,g   Zhou, Qi h   Xu, Xing i   Shiroishi, Toshihiko a   Irie, Naoki j   more..


Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR SOX2; TRANSCRIPTOME; HISTONE; TRANSCRIPTION FACTOR;

EID: 85011884569     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms14229     Document Type: Article
Times cited : (53)

References (75)
  • 1
    • 84863885448 scopus 로고    scopus 로고
    • Comparative studies of gene expression and the evolution of gene regulation
    • Romero, I. G., Ruvinsky, I. & Gilad, Y. Comparative studies of gene expression and the evolution of gene regulation. Nat. Rev. Genet. 13, 505-516 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 505-516
    • Romero, I.G.1    Ruvinsky, I.2    Gilad, Y.3
  • 2
    • 0242354129 scopus 로고    scopus 로고
    • The origin of new genes: Glimpses from the young and old
    • Long, M., Betran, E., Thornton, K. & Wang, W. The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4, 865-875 (2003).
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 865-875
    • Long, M.1    Betran, E.2    Thornton, K.3    Wang, W.4
  • 3
    • 34247100893 scopus 로고    scopus 로고
    • Birds as dinosaurs
    • Sereno, P. Birds as dinosaurs. Acta Zool. Sinica 50, 991-1001 (2004).
    • (2004) Acta Zool. Sinica , vol.50 , pp. 991-1001
    • Sereno, P.1
  • 5
    • 0036737060 scopus 로고    scopus 로고
    • The evolutionary origin and diversification of feathers
    • Prum, R. O. & Brush, A. H. The evolutionary origin and diversification of feathers. Q. Rev. Biol. 77, 261-295 (2002).
    • (2002) Q. Rev. Biol. , vol.77 , pp. 261-295
    • Prum, R.O.1    Brush, A.H.2
  • 6
    • 22444442306 scopus 로고    scopus 로고
    • Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs
    • O'Connor, P. M. & Claessens, L. P. Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs. Nature 436, 253-256 (2005).
    • (2005) Nature , vol.436 , pp. 253-256
    • O'Connor, P.M.1    Claessens, L.P.2
  • 7
    • 84917691034 scopus 로고    scopus 로고
    • An integrative approach to understanding bird origins
    • Xu, X. et al. An integrative approach to understanding bird origins. Science 346, 1253293 (2014).
    • (2014) Science , vol.346 , pp. 1253293
    • Xu, X.1
  • 8
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
    • (2005) Genome Res. , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 9
    • 80054973803 scopus 로고    scopus 로고
    • A high-resolution map of human evolutionary constraint using 29 mammals
    • Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476-482 (2011).
    • (2011) Nature , vol.478 , pp. 476-482
    • Lindblad-Toh, K.1
  • 10
    • 84917678595 scopus 로고    scopus 로고
    • Comparative genomics reveals insights into avian genome evolution and adaptation
    • Zhang, G. et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346, 1311-1320 (2014).
    • (2014) Science , vol.346 , pp. 1311-1320
    • Zhang, G.1
  • 11
    • 84917708482 scopus 로고    scopus 로고
    • Whole-genome analyses resolve early branches in the tree of life of modern birds
    • Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320-1331 (2014).
    • (2014) Science , vol.346 , pp. 1320-1331
    • Jarvis, E.D.1
  • 12
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107-116 (1975).
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 13
    • 10644271562 scopus 로고    scopus 로고
    • A genetic variation map for chicken with 2. 8 million single-nucleotide polymorphisms
    • Wong, G. K. et al. A genetic variation map for chicken with 2. 8 million single-nucleotide polymorphisms. Nature 432, 717-722 (2004).
    • (2004) Nature , vol.432 , pp. 717-722
    • Wong, G.K.1
  • 14
    • 1842584883 scopus 로고    scopus 로고
    • RNA regulation: A new genetics
    • Mattick, J. S. RNA regulation: A new geneticsNat. Rev. Genet. 5, 316-323 (2004).
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 316-323
    • Mattick, J.S.1
  • 15
    • 34249876564 scopus 로고    scopus 로고
    • Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells
    • Masui, S. et al. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat. Cell Biol. 9, 625-635 (2007).
    • (2007) Nat. Cell Biol. , vol.9 , pp. 625-635
    • Masui, S.1
  • 16
    • 78650304236 scopus 로고    scopus 로고
    • Charting histone modifications and the functional organization of mammalian genomes
    • Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7-18 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 7-18
    • Zhou, V.W.1    Goren, A.2    Bernstein, B.E.3
  • 17
    • 84879911829 scopus 로고    scopus 로고
    • The evolution of lineage-specific regulatory activities in the human embryonic limb
    • Cotney, J. et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154, 185-196 (2013).
    • (2013) Cell , vol.154 , pp. 185-196
    • Cotney, J.1
  • 18
    • 84924926133 scopus 로고
    • A series of normal stages in the development of the chick embryo
    • Hamburger, V. & Hamilton, H. L. A series of normal stages in the development of the chick embryo. J. Morphol. 88, 49-92 (1951).
    • (1951) J. Morphol , vol.88 , pp. 49-92
    • Hamburger, V.1    Hamilton, H.L.2
  • 19
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst, J. & Kellis, M. ChromHMM: Automating chromatin-state discovery and characterization. Nat. Methods 9, 215-216 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 20
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931-21936 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1
  • 21
    • 33845930303 scopus 로고    scopus 로고
    • Discs-large homolog 1 regulates smooth muscle orientation in the mouse ureter
    • Mahoney, Z. X. et al. Discs-large homolog 1 regulates smooth muscle orientation in the mouse ureter. Proc. Natl Acad. Sci. USA 103, 19872-19877 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 19872-19877
    • Mahoney, Z.X.1
  • 22
    • 84878729685 scopus 로고    scopus 로고
    • The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
    • Wang, Z. et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat. Genet. 45, 701-706 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 701-706
    • Wang, Z.1
  • 23
    • 79953113902 scopus 로고    scopus 로고
    • Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis
    • Irie, N. & Kuratani, S. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat. Commun. 2, 248 (2011).
    • (2011) Nat. Commun. , vol.2 , pp. 248
    • Irie, N.1    Kuratani, S.2
  • 25
    • 84867037816 scopus 로고    scopus 로고
    • Evolutionary and developmental aspects of avian-specific traits in limb skeletal pattern
    • Seki, R. et al. Evolutionary and developmental aspects of avian-specific traits in limb skeletal pattern. Zoolog. Sci. 29, 631-644 (2012).
    • (2012) Zoolog. Sci. , vol.29 , pp. 631-644
    • Seki, R.1
  • 26
    • 79951483773 scopus 로고    scopus 로고
    • Embryological evidence identifies wing digits in birds as digits 1. 2, and 3
    • Tamura, K., Nomura, N., Seki, R., Yonei-Tamura, S. & Yokoyama, H. Embryological evidence identifies wing digits in birds as digits 1, 2, and 3. Science 331, 753-757 (2011).
    • (2011) Science , vol.331 , pp. 753-757
    • Tamura, K.1    Nomura, N.2    Seki, R.3    Yonei-Tamura, S.4    Yokoyama, H.5
  • 29
    • 0032169255 scopus 로고    scopus 로고
    • Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities
    • Peters, H., Neubuser, A., Kratochwil, K. & Balling, R. Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities. Genes Dev. 12, 2735-2747 (1998).
    • (1998) Genes Dev. , vol.12 , pp. 2735-2747
    • Peters, H.1    Neubuser, A.2    Kratochwil, K.3    Balling, R.4
  • 30
    • 34547679699 scopus 로고    scopus 로고
    • Derivation of a mouse model for conditional inactivation of Pax9
    • Kist, R., Greally, E. & Peters, H. Derivation of a mouse model for conditional inactivation of Pax9. Genesis. 45, 460-464 (2007).
    • (2007) Genesis. , vol.45 , pp. 460-464
    • Kist, R.1    Greally, E.2    Peters, H.3
  • 31
    • 67449168569 scopus 로고    scopus 로고
    • Sim1 and Sim2 expression during chick and mouse limb development
    • Coumailleau, P. & Duprez, D. Sim1 and Sim2 expression during chick and mouse limb development. Int. J. Dev. Biol. 53, 149-157 (2009).
    • (2009) Int. J. Dev. Biol. , vol.53 , pp. 149-157
    • Coumailleau, P.1    Duprez, D.2
  • 32
    • 0028888334 scopus 로고
    • Involvement of the Sonic hedgehog gene in chick feather formation
    • Nohno, T. et al. Involvement of the Sonic hedgehog gene in chick feather formation. Biochem. Biophys. Res. Commun. 206, 33-39 (1995).
    • (1995) Biochem. Biophys. Res. Commun. , vol.206 , pp. 33-39
    • Nohno, T.1
  • 33
    • 0032780157 scopus 로고    scopus 로고
    • The role of long range, local and direct signalling molecules during chick feather bud development involving the BMPs, follistatin and the Eph receptor tyrosine kinase Eph-A4
    • Patel, K., Makarenkova, H. & Jung, H. S. The role of long range, local and direct signalling molecules during chick feather bud development involving the BMPs, follistatin and the Eph receptor tyrosine kinase Eph-A4. Mech. Dev. 86, 51-62 (1999).
    • (1999) Mech. Dev. , vol.86 , pp. 51-62
    • Patel, K.1    Makarenkova, H.2    Jung, H.S.3
  • 34
    • 84962211170 scopus 로고    scopus 로고
    • Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species
    • Domyan, E. T. et al. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. Elife 5, e12115 (2016).
    • (2016) Elife , vol.5 , pp. e12115
    • Domyan, E.T.1
  • 35
    • 84966054025 scopus 로고
    • W. H. Freeman and Company
    • Gill, F. Ornithology (W. H. Freeman and Company, 1995).
    • (1995) Ornithology
    • Gill, F.1
  • 36
    • 0000446890 scopus 로고    scopus 로고
    • Two feathered dinosaur from China
    • Ji, Q., Currie, P. J., Norell, M. A. & Ji, S.-A. Two feathered dinosaur from China. Nature 393, 753-761 (1998).
    • (1998) Nature , vol.393 , pp. 753-761
    • Ji, Q.1    Currie, P.J.2    Norell, M.A.3    Ji, S.-A.4
  • 37
    • 0000335360 scopus 로고    scopus 로고
    • Important features of Caudipteryx-evidence from two nearly complete new specimens
    • Zhou, Z.-H., Wang, X.-L., Zhang, F.-C. & Xu, X. Important features of Caudipteryx-evidence from two nearly complete new specimens. Vertebrat. PalAsiatic. 38, 241-254 (2000).
    • (2000) Vertebrat. PalAsiatic. , vol.38 , pp. 241-254
    • Zhou, Z.-H.1    Wang, X.-L.2    Zhang, F.-C.3    Xu, X.4
  • 38
    • 0037461733 scopus 로고    scopus 로고
    • Four-winged dinosaurs from China
    • Xu, X. et al. Four-winged dinosaurs from China. Nature 421, 335-340 2003
    • (2003) Nature , vol.421 , pp. 335-340
    • Xu, X.1
  • 39
    • 70349667478 scopus 로고    scopus 로고
    • A pre-Archaeopteryx troodontid from China with long feathers on the metatarsus
    • Hu, D. Y., Hou, L.-H., Zhang, L. J. & Xu, X. A pre-Archaeopteryx troodontid from China with long feathers on the metatarsus. Nature 461, 640-643 (2009).
    • (2009) Nature , vol.461 , pp. 640-643
    • Hu, D.Y.1    Hou, L.-H.2    Zhang, L.J.3    Xu, X.4
  • 40
    • 77949412176 scopus 로고    scopus 로고
    • The origin and early evolution of feathers: Insights from recent paleontological and neontological data
    • Xu, X. & Guo, Y. The origin and early evolution of feathers: insights from recent paleontological and neontological data. Vertebrat. PalAsiatic. 47, 311-329 (2009).
    • (2009) Vertebrat. PalAsiatic. , vol.47 , pp. 311-329
    • Xu, X.1    Guo, Y.2
  • 41
    • 77951873991 scopus 로고    scopus 로고
    • Exceptional dinosaur fossils show ontogenetic development of early feathers
    • Xu, X., Zheng, X. T. & You, H. L. Exceptional dinosaur fossils show ontogenetic development of early feathers. Nature 464, 1338-1341 (2010).
    • (2010) Nature , vol.464 , pp. 1338-1341
    • Xu, X.1    Zheng, X.T.2    You, H.L.3
  • 42
    • 84903714669 scopus 로고    scopus 로고
    • New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers
    • Foth, C., Tischlinger, H. & Rauhut, O. W. M. New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers. Nature 511, 79-82 (2014).
    • (2014) Nature , vol.511 , pp. 79-82
    • Foth, C.1    Tischlinger, H.2    Rauhut, O.W.M.3
  • 43
    • 84922566884 scopus 로고    scopus 로고
    • Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight
    • Feo, T. J., Field, D. J. & Prum, R. O. Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight. Proc. Biol. Sci. 282, 20142864 (2015).
    • (2015) Proc. Biol. Sci. , vol.282 , pp. 20142864
    • Feo, T.J.1    Field, D.J.2    Prum, R.O.3
  • 44
    • 0037500141 scopus 로고    scopus 로고
    • Evolution by gene duplication: An update
    • Zhang, J. Evolution by gene duplication: An update. Trends Ecol. Evol. 18, 292-298 (2003).
    • (2003) Trends Ecol. Evol. , vol.18 , pp. 292-298
    • Zhang, J.1
  • 46
    • 78649231644 scopus 로고    scopus 로고
    • Origins, evolution, and phenotypic impact of new genes
    • Kaessmann, H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 20, 1313-1326 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1313-1326
    • Kaessmann, H.1
  • 47
    • 77952381192 scopus 로고    scopus 로고
    • Narrow primary feather rachises in Confuciusornis and Archaeopteryx suggest poor flight ability
    • Nudds, R. L. & Dyke, G. J. Narrow primary feather rachises in Confuciusornis and Archaeopteryx suggest poor flight ability. Science 328, 887-889 (2010).
    • (2010) Science , vol.328 , pp. 887-889
    • Nudds, R.L.1    Dyke, G.J.2
  • 48
    • 78651320424 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: Update 2011
    • Fujita, P. A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876-D882 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D876-D882
    • Fujita, P.A.1
  • 49
    • 33644876458 scopus 로고    scopus 로고
    • TreeFam: A curated database of phylogenetic trees of animal gene families
    • Li, H. et al. TreeFam: A curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. D572-D580
    • Li, H.1
  • 51
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W. & Haussler, D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA 100, 11484-11489 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5
  • 52
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004).
    • (2004) Genome Res. , vol.14 , pp. 708-715
    • Blanchette, M.1
  • 53
    • 79551634894 scopus 로고    scopus 로고
    • PHAST and RPHAST: Phylogenetic analysis with space/time models
    • Hubisz, M. J., Pollard, K. S. & Siepel, A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinform. 12, 41-51 (2011).
    • (2011) Brief. Bioinform. , vol.12 , pp. 41-51
    • Hubisz, M.J.1    Pollard, K.S.2    Siepel, A.3
  • 54
    • 75549083247 scopus 로고    scopus 로고
    • JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
    • Portales-Casamar, E. et al. JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105-D110 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. D105-D110
    • Portales-Casamar, E.1
  • 55
    • 57549089243 scopus 로고    scopus 로고
    • Using TESS to predict transcription factor binding sites in DNA sequence
    • Schug, J. Using TESS to predict transcription factor binding sites in DNA sequence. Curr. Protoc. Bioinformatics 2, 15 (2008).
    • (2008) Curr. Protoc. Bioinformatics , vol.2 , pp. 15
    • Schug, J.1
  • 56
    • 80054976678 scopus 로고    scopus 로고
    • The evolution of gene expression levels in mammalian organs
    • Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343-348 (2011).
    • (2011) Nature , vol.478 , pp. 343-348
    • Brawand, D.1
  • 57
    • 33646272409 scopus 로고    scopus 로고
    • Identification and classification of conserved RNA secondary structures in the human genome
    • Pedersen, J. S. et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2, e33 (2006).
    • (2006) PLoS Comput. Biol. , vol.2 , pp. e33
    • Pedersen, J.S.1
  • 58
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 59
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and samtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 60
    • 84865777819 scopus 로고    scopus 로고
    • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1813-1831
    • Landt, S.G.1
  • 61
    • 84888264156 scopus 로고    scopus 로고
    • Practical guidelines for the comprehensive analysis of ChIP-seq data
    • Bailey, T. et al. Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput. Biol. 9, e1003326 (2013).
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003326
    • Bailey, T.1
  • 62
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 63
    • 84880968176 scopus 로고    scopus 로고
    • GAT: A simulation framework for testing the association of genomic intervals
    • Heger, A., Webber, C., Goodson, M., Ponting, C. P. & Lunter, G. GAT: A simulation framework for testing the association of genomic intervals. Bioinformatics 29, 2046-2048 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2046-2048
    • Heger, A.1    Webber, C.2    Goodson, M.3    Ponting, C.P.4    Lunter, G.5
  • 64
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1
  • 65
    • 84878834064 scopus 로고    scopus 로고
    • DiffReps: Detecting differential chromatin modification sites from ChIP-seq data with biological replicates
    • Shen, L. et al. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS ONE 8, e65598 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e65598
    • Shen, L.1
  • 66
    • 84875391572 scopus 로고    scopus 로고
    • Ensembl 2013
    • Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48-D55 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D48-D55
    • Flicek, P.1
  • 67
    • 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, R106 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 68
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 69
    • 77955298482 scopus 로고    scopus 로고
    • BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle, T. J. & Kelly, K. A. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11, 422 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 70
    • 20144376345 scopus 로고    scopus 로고
    • Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
    • Yanai, I. et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650-659 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 650-659
    • Yanai, I.1
  • 71
    • 77951682635 scopus 로고    scopus 로고
    • KaKs-Calculator 2. 0: A toolkit incorporating gamma-series methods and sliding window strategies
    • Wang, D., Zhang, Y., Zhang, Z., Zhu, J. & Yu, J. KaKs-Calculator 2. 0: A toolkit incorporating gamma-series methods and sliding window strategies. Genom. Proteom. Bioinformatics 8, 77-80 (2010).
    • (2010) Genom. Proteom. Bioinformatics , vol.8 , pp. 77-80
    • Wang, D.1    Zhang, Y.2    Zhang, Z.3    Zhu, J.4    Yu, J.5
  • 72
    • 58149231027 scopus 로고    scopus 로고
    • Normal developmental stages of the Madagascar ground gecko Paroedura pictus with special reference to limb morphogenesis
    • Noro, M., Uejima, A., Abe, G., Manabe, M. & Tamura, K. Normal developmental stages of the Madagascar ground gecko Paroedura pictus with special reference to limb morphogenesis. Dev. Dyn. 238, 100-109 (2009).
    • (2009) Dev. Dyn. , vol.238 , pp. 100-109
    • Noro, M.1    Uejima, A.2    Abe, G.3    Manabe, M.4    Tamura, K.5
  • 73
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    • Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640-6645 (2000).
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 74
    • 84892367532 scopus 로고    scopus 로고
    • A novel regulatory element for Shh expression in the lung and gut of mouse embryos
    • Tsukiji, N., Amano, T. & Shiroishi, T. A novel regulatory element for Shh expression in the lung and gut of mouse embryos. Mech. Dev. 131, 127-136 (2014).
    • (2014) Mech. Dev. , vol.131 , pp. 127-136
    • Tsukiji, N.1    Amano, T.2    Shiroishi, T.3
  • 75
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1


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