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Volumn 45, Issue 5, 2017, Pages 2354-2367

Models of global gene expression define major domains of cell type and tissue identity

Author keywords

[No Author keywords available]

Indexed keywords

NERVE CELL ADHESION MOLECULE; TRANSCRIPTION FACTOR SOX9; UVOMORULIN; TRANSCRIPTION FACTOR;

EID: 85018239525     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx054     Document Type: Article
Times cited : (43)

References (75)
  • 1
    • 77956476869 scopus 로고    scopus 로고
    • Transitions between epithelial and mesenchymal states and the morphogenesis of the early mouse embryo
    • Ferrer-Vaquer, A., Viotti, M. and Hadjantonakis, A.K. (2010) Transitions between epithelial and mesenchymal states and the morphogenesis of the early mouse embryo. Cell Adhesion Migration, 4, 447-457.
    • (2010) Cell Adhesion Migration , vol.4 , pp. 447-457
    • Ferrer-Vaquer, A.1    Viotti, M.2    Hadjantonakis, A.K.3
  • 2
    • 33745618439 scopus 로고    scopus 로고
    • Building the mouse gastrula: Signals, asymmetry and lineages
    • Tam, P.P., Loebel, D.A. and Tanaka, S.S. (2006) Building the mouse gastrula: Signals, asymmetry and lineages. Curr. Opin. Genet. Dev., 16, 419-425.
    • (2006) Curr. Opin. Genet. Dev. , vol.16 , pp. 419-425
    • Tam, P.P.1    Loebel, D.A.2    Tanaka, S.S.3
  • 3
    • 1642430626 scopus 로고    scopus 로고
    • Origin and evolution of endoderm and mesoderm
    • Technau, U. and Scholz, C.B. (2003) Origin and evolution of endoderm and mesoderm. Int. J. Dev. Biol., 47, 531-539.
    • (2003) Int. J. Dev. Biol. , vol.47 , pp. 531-539
    • Technau, U.1    Scholz, C.B.2
  • 4
    • 84961241937 scopus 로고    scopus 로고
    • Spatial transcriptome for the molecular annotation of lineage fates and cell identity in mid-gastrula mouse embryo
    • Peng, G., Suo, S., Chen, J., Chen, W., Liu, C., Yu, F., Wang, R., Chen, S., Sun, N., Cui, G. et al. (2016) Spatial transcriptome for the molecular annotation of lineage fates and cell identity in mid-gastrula mouse embryo. Dev. Cell, 36, 681-697.
    • (2016) Dev. Cell , vol.36 , pp. 681-697
    • Peng, G.1    Suo, S.2    Chen, J.3    Chen, W.4    Liu, C.5    Yu, F.6    Wang, R.7    Chen, S.8    Sun, N.9    Cui, G.10
  • 6
    • 84925497456 scopus 로고    scopus 로고
    • Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer
    • Hashimshony, T., Feder, M., Levin, M., Hall, B.K. and Yanai, I. (2015) Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature, 519, 219-222.
    • (2015) Nature , vol.519 , pp. 219-222
    • Hashimshony, T.1    Feder, M.2    Levin, M.3    Hall, B.K.4    Yanai, I.5
  • 7
    • 0020858899 scopus 로고
    • The embryonic cell lineage of the nematode Caenorhabditis elegans
    • Sulston, J.E., Schierenberg, E., White, J.G. and Thomson, J.N. (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol., 100, 64-119.
    • (1983) Dev. Biol. , vol.100 , pp. 64-119
    • Sulston, J.E.1    Schierenberg, E.2    White, J.G.3    Thomson, J.N.4
  • 8
    • 69949184406 scopus 로고    scopus 로고
    • Redefining the progression of lineage segregations during mammalian embryogenesis by clonal analysis
    • Tzouanacou, E., Wegener, A., Wymeersch, F.J., Wilson, V. and Nicolas, J.F. (2009) Redefining the progression of lineage segregations during mammalian embryogenesis by clonal analysis. Dev. Cell, 17, 365-376.
    • (2009) Dev. Cell , vol.17 , pp. 365-376
    • Tzouanacou, E.1    Wegener, A.2    Wymeersch, F.J.3    Wilson, V.4    Nicolas, J.F.5
  • 9
    • 84927138368 scopus 로고    scopus 로고
    • SOX17 links gut endoderm morphogenesis and germ layer segregation
    • Viotti, M., Nowotschin, S. and Hadjantonakis, A.K. (2014) SOX17 links gut endoderm morphogenesis and germ layer segregation. Nat. Cell Biol., 16, 1146-1156.
    • (2014) Nat. Cell Biol. , vol.16 , pp. 1146-1156
    • Viotti, M.1    Nowotschin, S.2    Hadjantonakis, A.K.3
  • 10
    • 0033934034 scopus 로고    scopus 로고
    • The neural crest as a fourth germ layer and vertebrates as quadroblastic not triploblastic
    • Hall, B.K. (2000) The neural crest as a fourth germ layer and vertebrates as quadroblastic not triploblastic. Evol. Dev., 2, 3-5.
    • (2000) Evol. Dev. , vol.2 , pp. 3-5
    • Hall, B.K.1
  • 11
    • 84924777822 scopus 로고    scopus 로고
    • Genomic analysis of LPS-stimulated myeloid cells identifies a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses
    • Hutchins, A.P., Takahashi, Y. and Miranda-Saavedra, D. (2015) Genomic analysis of LPS-stimulated myeloid cells identifies a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses. Scientific Rep., 5, 9100.
    • (2015) Scientific Rep. , vol.5 , pp. 9100
    • Hutchins, A.P.1    Takahashi, Y.2    Miranda-Saavedra, D.3
  • 12
    • 84920550975 scopus 로고    scopus 로고
    • A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
    • SEQC/MAQC-III Consortium. (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat. Biotechnol., 32, 903-914.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 903-914
  • 16
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B. and Dewey, C.N. (2011) RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 19
    • 84988231210 scopus 로고    scopus 로고
    • Glbase: A framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data
    • Hutchins, A.P., Jauch, R., Dyla, M. and Miranda-Saavedra, D. (2014) glbase: A framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data. Cell Regener., 3, 1.
    • (2014) Cell Regener. , vol.3 , pp. 1
    • Hutchins, A.P.1    Jauch, R.2    Dyla, M.3    Miranda-Saavedra, D.4
  • 23
    • 84964238187 scopus 로고    scopus 로고
    • Where cell fate conversions meet Chinese philosophy
    • Zheng, H., Hutchins, A.P., Pan, G., Li, Y., Pei, D. and Pei, G. (2014) Where cell fate conversions meet Chinese philosophy. Cell Res., 24, 1162-1163.
    • (2014) Cell Res. , vol.24 , pp. 1162-1163
    • Zheng, H.1    Hutchins, A.P.2    Pan, G.3    Li, Y.4    Pei, D.5    Pei, G.6
  • 26
    • 84945456655 scopus 로고    scopus 로고
    • Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs
    • Hutchins, A.P. and Pei, D. (2015) Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs. Sci. Bull., 60, 1722-1733.
    • (2015) Sci. Bull. , vol.60 , pp. 1722-1733
    • Hutchins, A.P.1    Pei, D.2
  • 27
    • 84920267059 scopus 로고    scopus 로고
    • The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters
    • Bao, X., Wu, H., Zhu, X., Guo, X., Hutchins, A.P., Luo, Z., Song, H., Chen, Y., Lai, K., Yin, M. et al. (2015) The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Res., 25, 80-92.
    • (2015) Cell Res. , vol.25 , pp. 80-92
    • Bao, X.1    Wu, H.2    Zhu, X.3    Guo, X.4    Hutchins, A.P.5    Luo, Z.6    Song, H.7    Chen, Y.8    Lai, K.9    Yin, M.10
  • 29
    • 0344464733 scopus 로고    scopus 로고
    • Gene Expression Dynamics Inspector (GEDI): For integrative analysis of expression profiles
    • Eichler, G.S., Huang, S. and Ingber, D.E. (2003) Gene Expression Dynamics Inspector (GEDI): For integrative analysis of expression profiles. Bioinformatics, 19, 2321-2322.
    • (2003) Bioinformatics , vol.19 , pp. 2321-2322
    • Eichler, G.S.1    Huang, S.2    Ingber, D.E.3
  • 30
    • 79960662814 scopus 로고    scopus 로고
    • Expression cartography of human tissues using self organizing maps
    • Wirth, H., Loffler, M., von Bergen, M. and Binder, H. (2011) Expression cartography of human tissues using self organizing maps. BMC Bioinformatics, 12, 306.
    • (2011) BMC Bioinformatics , vol.12 , pp. 306
    • Wirth, H.1    Loffler, M.2    Von Bergen, M.3    Binder, H.4
  • 31
    • 84930195552 scopus 로고    scopus 로고
    • An alternative pluripotent state confers interspecies chimaeric competency
    • Wu, J., Okamura, D., Li, M., Suzuki, K., Luo, C., Ma, L., He, Y., Li, Z., Benner, C., Tamura, I. et al. (2015) An alternative pluripotent state confers interspecies chimaeric competency. Nature, 521, 316-321.
    • (2015) Nature , vol.521 , pp. 316-321
    • Wu, J.1    Okamura, D.2    Li, M.3    Suzuki, K.4    Luo, C.5    Ma, L.6    He, Y.7    Li, Z.8    Benner, C.9    Tamura, I.10
  • 32
    • 84920749813 scopus 로고    scopus 로고
    • Waddington's valleys and Captain Cook's islands
    • Sieweke, M.H. (2015) Waddington's valleys and Captain Cook's islands. Cell Stem Cell, 16, 7-8.
    • (2015) Cell Stem Cell , vol.16 , pp. 7-8
    • Sieweke, M.H.1
  • 34
    • 78149487692 scopus 로고    scopus 로고
    • Pluripotency and cellular reprogramming: Facts, hypotheses, unresolved issues
    • Hanna, J.H., Saha, K. and Jaenisch, R. (2010) Pluripotency and cellular reprogramming: Facts, hypotheses, unresolved issues. Cell, 143, 508-525.
    • (2010) Cell , vol.143 , pp. 508-525
    • Hanna, J.H.1    Saha, K.2    Jaenisch, R.3
  • 35
    • 84975736328 scopus 로고    scopus 로고
    • Plasticity in the adult: How should the waddington diagram be applied to regenerating tissues?
    • Rajagopal, J. and Stanger, B.Z. (2016) Plasticity in the adult: How should the waddington diagram be applied to regenerating tissues? Dev. Cell, 36, 133-137.
    • (2016) Dev. Cell , vol.36 , pp. 133-137
    • Rajagopal, J.1    Stanger, B.Z.2
  • 36
    • 23844528776 scopus 로고    scopus 로고
    • The Snail genes as inducers of cell movement and survival: Implications in development and cancer
    • Barrallo-Gimeno, A. and Nieto, M.A. (2005) The Snail genes as inducers of cell movement and survival: Implications in development and cancer. Development, 132, 3151-3161.
    • (2005) Development , vol.132 , pp. 3151-3161
    • Barrallo-Gimeno, A.1    Nieto, M.A.2
  • 37
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • Ramskold, D., Wang, E.T., Burge, C.B. and Sandberg, R. (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol., 5, e1000598.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000598
    • Ramskold, D.1    Wang, E.T.2    Burge, C.B.3    Sandberg, R.4
  • 39
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V.B., Wong, E., Orlov, Y.L., Zhang, W., Jiang, J. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117.
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1    Xu, H.2    Yuan, P.3    Fang, F.4    Huss, M.5    Vega, V.B.6    Wong, E.7    Orlov, Y.L.8    Zhang, W.9    Jiang, J.10
  • 40
    • 84874292408 scopus 로고    scopus 로고
    • Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells
    • Hutchins, A.P., Choo, S.H., Mistri, T.K., Rahmani, M., Woon, C.T., Ng, C.K., Jauch, R. and Robson, P. (2013) Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells. Stem Cells, 31, 269-281.
    • (2013) Stem Cells , vol.31 , pp. 269-281
    • Hutchins, A.P.1    Choo, S.H.2    Mistri, T.K.3    Rahmani, M.4    Woon, C.T.5    Ng, C.K.6    Jauch, R.7    Robson, P.8
  • 44
    • 84899634426 scopus 로고    scopus 로고
    • Formation of proximal and anterior limb skeleton requires early function of Irx3 and Irx5 and is negatively regulated by Shh signaling
    • Li, D., Sakuma, R., Vakili, N.A., Mo, R., Puviindran, V., Deimling, S., Zhang, X., Hopyan, S. and Hui, C.C. (2014) Formation of proximal and anterior limb skeleton requires early function of Irx3 and Irx5 and is negatively regulated by Shh signaling. Dev. Cell, 29, 233-240.
    • (2014) Dev. Cell , vol.29 , pp. 233-240
    • Li, D.1    Sakuma, R.2    Vakili, N.A.3    Mo, R.4    Puviindran, V.5    Deimling, S.6    Zhang, X.7    Hopyan, S.8    Hui, C.C.9
  • 45
    • 84860838205 scopus 로고    scopus 로고
    • Development and evolution of the neural crest: An overview
    • Bronner, M.E. and LeDouarin, N.M. (2012) Development and evolution of the neural crest: An overview. Dev. Biol., 366, 2-9.
    • (2012) Dev. Biol. , vol.366 , pp. 2-9
    • Bronner, M.E.1    LeDouarin, N.M.2
  • 46
    • 84868484735 scopus 로고    scopus 로고
    • Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
    • Rada-Iglesias, A., Bajpai, R., Prescott, S., Brugmann, S.A., Swigut, T. and Wysocka, J. (2012) Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell, 11, 633-648.
    • (2012) Cell Stem Cell , vol.11 , pp. 633-648
    • Rada-Iglesias, A.1    Bajpai, R.2    Prescott, S.3    Brugmann, S.A.4    Swigut, T.5    Wysocka, J.6
  • 50
    • 84883236090 scopus 로고    scopus 로고
    • Notch signaling represses p63 expression in the developing surface ectoderm
    • Tadeu, A.M. and Horsley, V. (2013) Notch signaling represses p63 expression in the developing surface ectoderm. Development, 140, 3777-3786.
    • (2013) Development , vol.140 , pp. 3777-3786
    • Tadeu, A.M.1    Horsley, V.2
  • 52
    • 0346121540 scopus 로고    scopus 로고
    • Neural crest development is regulated by the transcription factor Sox9
    • Cheung, M. and Briscoe, J. (2003) Neural crest development is regulated by the transcription factor Sox9. Development, 130, 5681-5693.
    • (2003) Development , vol.130 , pp. 5681-5693
    • Cheung, M.1    Briscoe, J.2
  • 53
    • 0037663384 scopus 로고    scopus 로고
    • The Sox9 transcription factor determines glial fate choice in the developing spinal cord
    • Stolt, C.C., Lommes, P., Sock, E., Chaboissier, M.C., Schedl, A. and Wegner, M. (2003) The Sox9 transcription factor determines glial fate choice in the developing spinal cord. Genes Dev., 17, 1677-1689.
    • (2003) Genes Dev. , vol.17 , pp. 1677-1689
    • Stolt, C.C.1    Lommes, P.2    Sock, E.3    Chaboissier, M.C.4    Schedl, A.5    Wegner, M.6
  • 54
    • 0036830491 scopus 로고    scopus 로고
    • The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6
    • Akiyama, H., Chaboissier, M.C., Martin, J.F., Schedl, A. and de Crombrugghe, B. (2002) The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6. Genes Dev., 16, 2813-2828.
    • (2002) Genes Dev. , vol.16 , pp. 2813-2828
    • Akiyama, H.1    Chaboissier, M.C.2    Martin, J.F.3    Schedl, A.4    De Crombrugghe, B.5
  • 56
    • 84924264526 scopus 로고    scopus 로고
    • Direct lineage reprogramming: Strategies, mechanisms, and applications
    • Xu, J., Du, Y. and Deng, H. (2015) Direct lineage reprogramming: Strategies, mechanisms, and applications. Cell Stem Cell, 16, 119-134.
    • (2015) Cell Stem Cell , vol.16 , pp. 119-134
    • Xu, J.1    Du, Y.2    Deng, H.3
  • 58
    • 2542455620 scopus 로고    scopus 로고
    • Stepwise reprogramming of B cells into macrophages
    • Xie, H., Ye, M., Feng, R. and Graf, T. (2004) Stepwise reprogramming of B cells into macrophages. Cell, 117, 663-676.
    • (2004) Cell , vol.117 , pp. 663-676
    • Xie, H.1    Ye, M.2    Feng, R.3    Graf, T.4
  • 59
    • 84941000940 scopus 로고    scopus 로고
    • Polycomb regulates mesoderm cell fate-specification in embryonic stem cells through activation and repression mechanisms
    • Morey, L., Santanach, A., Blanco, E., Aloia, L., Nora, E.P., Bruneau, B.G. and Di Croce, L. (2015) Polycomb regulates mesoderm cell fate-specification in embryonic stem cells through activation and repression mechanisms. Cell Stem Cell, 17, 300-315.
    • (2015) Cell Stem Cell , vol.17 , pp. 300-315
    • Morey, L.1    Santanach, A.2    Blanco, E.3    Aloia, L.4    Nora, E.P.5    Bruneau, B.G.6    Di Croce, L.7
  • 60
    • 84923771297 scopus 로고    scopus 로고
    • CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation
    • Narendra, V., Rocha, P.P., An, D., Raviram, R., Skok, J.A., Mazzoni, E.O. and Reinberg, D. (2015) CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science, 347, 1017-1021.
    • (2015) Science , vol.347 , pp. 1017-1021
    • Narendra, V.1    Rocha, P.P.2    An, D.3    Raviram, R.4    Skok, J.A.5    Mazzoni, E.O.6    Reinberg, D.7
  • 63
    • 28344436489 scopus 로고    scopus 로고
    • Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation
    • Niwa, H., Toyooka, Y., Shimosato, D., Strumpf, D., Takahashi, K., Yagi, R. and Rossant, J. (2005) Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell, 123, 917-929.
    • (2005) Cell , vol.123 , pp. 917-929
    • Niwa, H.1    Toyooka, Y.2    Shimosato, D.3    Strumpf, D.4    Takahashi, K.5    Yagi, R.6    Rossant, J.7
  • 64
    • 76149087152 scopus 로고    scopus 로고
    • Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal
    • Niakan, K.K., Ji, H., Maehr, R., Vokes, S.A., Rodolfa, K.T., Sherwood, R.I., Yamaki, M., Dimos, J.T., Chen, A.E., Melton, D.A. et al. (2010) Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. Genes Dev., 24, 312-326.
    • (2010) Genes Dev. , vol.24 , pp. 312-326
    • Niakan, K.K.1    Ji, H.2    Maehr, R.3    Vokes, S.A.4    Rodolfa, K.T.5    Sherwood, R.I.6    Yamaki, M.7    Dimos, J.T.8    Chen, A.E.9    Melton, D.A.10
  • 72
    • 79954452308 scopus 로고    scopus 로고
    • Mapping gene expression in two Xenopus species: Evolutionary constraints and developmental flexibility
    • Yanai, I., Peshkin, L., Jorgensen, P. and Kirschner, M.W. (2011) Mapping gene expression in two Xenopus species: Evolutionary constraints and developmental flexibility. Dev. Cell, 20, 483-496.
    • (2011) Dev. Cell , vol.20 , pp. 483-496
    • Yanai, I.1    Peshkin, L.2    Jorgensen, P.3    Kirschner, M.W.4
  • 74
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro, E., Biezuner, T. and Linnarsson, S. (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet., 14, 618-630.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.