메뉴 건너뛰기




Volumn 18, Issue 1, 2017, Pages

MATCHER: Manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Author keywords

Manifold alignment; Manifold learning; Single cell epigenomics; Single cell RNA seq

Indexed keywords

DNA; RNA; TRANSCRIPTOME; HISTONE;

EID: 85025599203     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-017-1269-0     Document Type: Article
Times cited : (123)

References (56)
  • 1
    • 84894630323 scopus 로고    scopus 로고
    • Entering the era of single-cell transcriptomics in biology and medicine
    • Sandberg R. Entering the era of single-cell transcriptomics in biology and medicine. Nat Methods. 2013;11:22-4.
    • (2013) Nat Methods. , vol.11 , pp. 22-24
    • Sandberg, R.1
  • 2
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro E, Biezuner T, Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet. 2013;14:618-30.
    • (2013) Nat Rev Genet. , vol.14 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 3
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32:381-6.
    • (2014) Nat Biotechnol. , vol.32 , pp. 381-386
    • Trapnell, C.1    Cacchiarelli, D.2    Grimsby, J.3    Pokharel, P.4    Li, S.5    Morse, M.6
  • 4
    • 84941008542 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals a population of dormant neural stem cells that become activated upon brain injury
    • Llorens-Bobadilla E, Zhao S, Baser A, Saiz-Castro G, Zwadlo K, Martin-Villalba A. Single-cell transcriptomics reveals a population of dormant neural stem cells that become activated upon brain injury. Cell Stem Cell. 2015;17:329-40.
    • (2015) Cell Stem Cell. , vol.17 , pp. 329-340
    • Llorens-Bobadilla, E.1    Zhao, S.2    Baser, A.3    Saiz-Castro, G.4    Zwadlo, K.5    Martin-Villalba, A.6
  • 5
    • 84958103478 scopus 로고    scopus 로고
    • Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells
    • Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, Voet T, et al. Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Rep. 2016;14:966-77.
    • (2016) Cell Rep. , vol.14 , pp. 966-977
    • Macaulay, I.C.1    Svensson, V.2    Labalette, C.3    Ferreira, L.4    Hamey, F.5    Voet, T.6
  • 6
    • 84949035291 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis
    • Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, et al. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Science. 2015;350:1251-5.
    • (2015) Science. , vol.350 , pp. 1251-1255
    • Hanchate, N.K.1    Kondoh, K.2    Lu, Z.3    Kuang, D.4    Ye, X.5    Qiu, X.6
  • 7
    • 84900529199 scopus 로고    scopus 로고
    • Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
    • Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature. 2014;509:371-5.
    • (2014) Nature. , vol.509 , pp. 371-375
    • Treutlein, B.1    Brownfield, D.G.2    Wu, A.R.3    Neff, N.F.4    Mantalas, G.L.5    Espinoza, F.H.6
  • 9
    • 84969505817 scopus 로고    scopus 로고
    • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
    • Welch JD, Hartemink AJ, Prins JF. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biol. 2016;17:106.
    • (2016) Genome Biol. , vol.17 , pp. 106
    • Welch, J.D.1    Hartemink, A.J.2    Prins, J.F.3
  • 12
  • 15
    • 84949227165 scopus 로고    scopus 로고
    • Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
    • Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, et al. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature. 2015;528:142-6.
    • (2015) Nature. , vol.528 , pp. 142-146
    • Jin, W.1    Tang, Q.2    Wan, M.3    Cui, K.4    Zhang, Y.5    Ren, G.6
  • 16
    • 85025581111 scopus 로고    scopus 로고
    • Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution
    • Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, et al. Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell. 2017;338:1622-6.
    • (2017) Cell Stem Cell. , vol.338 , pp. 1622-1626
    • Zhu, C.1    Gao, Y.2    Guo, H.3    Xia, B.4    Song, J.5    Wu, X.6
  • 17
    • 84981312051 scopus 로고    scopus 로고
    • Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
    • Mooijman D, Dey SS, Boisset J-C, Crosetto N, van Oudenaarden A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat Biotechnol. 2016;34:852-6.
    • (2016) Nat Biotechnol. , vol.34 , pp. 852-856
    • Mooijman, D.1    Dey, S.S.2    Boisset, J.-C.3    Crosetto, N.4    Oudenaarden, A.5
  • 18
    • 84924601067 scopus 로고    scopus 로고
    • Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
    • Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, et al. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 2015;10:1386-97.
    • (2015) Cell Rep. , vol.10 , pp. 1386-1397
    • Farlik, M.1    Sheffield, N.C.2    Nuzzo, A.3    Datlinger, P.4    Schönegger, A.5    Klughammer, J.6
  • 19
    • 84982146199 scopus 로고    scopus 로고
    • Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
    • Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-203.
    • (2016) Nat Genet. , vol.48 , pp. 1193-1203
    • Corces, M.R.1    Buenrostro, J.D.2    Wu, B.3    Greenside, P.G.4    Chan, S.M.5    Koenig, J.L.6
  • 20
    • 84969504939 scopus 로고    scopus 로고
    • Multi-omics of single cells: strategies and applications
    • Bock C, Farlik M, Sheffield NC. Multi-omics of single cells: strategies and applications. Trends Biotechnol. 2016;34:605-8.
    • (2016) Trends Biotechnol. , vol.34 , pp. 605-608
    • Bock, C.1    Farlik, M.2    Sheffield, N.C.3
  • 21
    • 85009781625 scopus 로고    scopus 로고
    • Single-cell multiomics: multiple measurements from single cells
    • Macaulay IC, Ponting CP, Voet T. Single-cell multiomics: multiple measurements from single cells. Trends Genet. 2017;33:155-68.
    • (2017) Trends Genet. , vol.33 , pp. 155-168
    • Macaulay, I.C.1    Ponting, C.P.2    Voet, T.3
  • 23
  • 24
    • 84960091878 scopus 로고    scopus 로고
    • Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas
    • Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, et al. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 2016;26:304-19.
    • (2016) Cell Res. , vol.26 , pp. 304-319
    • Hou, Y.1    Guo, H.2    Cao, C.3    Li, X.4    Hu, B.5    Zhu, P.6
  • 27
    • 84862595041 scopus 로고    scopus 로고
    • Semisupervised alignment of manifolds
    • Proc 10th Intnl Conf on Artificial Intelligence and Statistics. SAIS. 2005;120-27
    • Ham J, Lee DD, Saul LK. Semisupervised alignment of manifolds. Proc 10th Intnl Conf on Artificial Intelligence and Statistics. SAIS. 2005;120-27.
    • Ham, J.1    Lee, D.D.2    Saul, L.K.3
  • 28
    • 84887488078 scopus 로고    scopus 로고
    • A general framework for manifold alignment
    • Palo Alto, CA: AAAI
    • Wang C, Mahadevan S. A general framework for manifold alignment. Palo Alto, CA: AAAI; 2009.
    • (2009)
    • Wang, C.1    Mahadevan, S.2
  • 32
    • 84919898241 scopus 로고    scopus 로고
    • Discriminative shared gaussian processes for multiview and view-invariant facial expression recognition
    • Eleftheriadis S, Rudovic O, Pantic M. Discriminative shared gaussian processes for multiview and view-invariant facial expression recognition. IEEE Trans Image Process. 2015;24:189-204.
    • (2015) IEEE Trans Image Process. , vol.24 , pp. 189-204
    • Eleftheriadis, S.1    Rudovic, O.2    Pantic, M.3
  • 33
    • 84898980901 scopus 로고    scopus 로고
    • Gaussian process latent variable models for visualisation of high dimensional data
    • Lawrence ND. Gaussian process latent variable models for visualisation of high dimensional data. Adv Neural Inf Process Syst. 2004;16:329-36.
    • (2004) Adv Neural Inf Process Syst. , vol.16 , pp. 329-336
    • Lawrence, N.D.1
  • 35
    • 84979912168 scopus 로고    scopus 로고
    • Variational inference for latent variables and uncertain inputs in Gaussian processes
    • Damianou AC, Titsias MK, Lawrence ND. Variational inference for latent variables and uncertain inputs in Gaussian processes. J Mach Learn Res. 2016;17:1-62.
    • (2016) J Mach Learn Res. , vol.17 , pp. 1-62
    • Damianou, A.C.1    Titsias, M.K.2    Lawrence, N.D.3
  • 36
    • 84923292191 scopus 로고    scopus 로고
    • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
    • Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol. 2015;33:155-60.
    • (2015) Nat Biotechnol. , vol.33 , pp. 155-160
    • Buettner, F.1    Natarajan, K.N.2    Casale, F.P.3    Proserpio, V.4    Scialdone, A.5    Theis, F.J.6
  • 37
    • 84983497196 scopus 로고    scopus 로고
    • Pseudotime estimation: deconfounding single cell time series
    • Reid JE, Wernisch L. Pseudotime estimation: deconfounding single cell time series. Bioinformatics. 2016;32(19):2973-80.
    • (2016) Bioinformatics. , vol.32 , Issue.19 , pp. 2973-2980
    • Reid, J.E.1    Wernisch, L.2
  • 38
    • 84999791835 scopus 로고    scopus 로고
    • Order under uncertainty: robust differential expression analysis using probabilistic models for pseudotime inference
    • Campbell KR, Yau C. Order under uncertainty: robust differential expression analysis using probabilistic models for pseudotime inference. PLOS Comput Biol. 2016;12:e1005212.
    • (2016) PLOS Comput. Biol. , vol.12
    • Campbell, K.R.1    Yau, C.2
  • 40
    • 79851480767 scopus 로고    scopus 로고
    • Shared Gaussian process latent variables models
    • Oxford: Oxford Brookes University
    • Ek CH. Shared Gaussian process latent variables models. Oxford: Oxford Brookes University; 2009.
    • (2009)
    • Ek, C.H.1
  • 43
    • 65549095495 scopus 로고    scopus 로고
    • REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells
    • Jørgensen HF, Terry A, Beretta C, Pereira CF, Leleu M, Chen Z-F, et al. REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells. Development. 2009;136:715-21.
    • (2009) Development. , vol.136 , pp. 715-721
    • Jørgensen, H.F.1    Terry, A.2    Beretta, C.3    Pereira, C.F.4    Leleu, M.5    Chen, Z.-F.6
  • 45
    • 78751662908 scopus 로고    scopus 로고
    • The Polycomb complex PRC2 and its mark in life
    • Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature. 2011;469:343-9.
    • (2011) Nature. , vol.469 , pp. 343-349
    • Margueron, R.1    Reinberg, D.2
  • 47
    • 77956202054 scopus 로고    scopus 로고
    • Polycomb group proteins set the stage for early lineage commitment
    • Surface LE, Thornton SR, Boyer LA. Polycomb group proteins set the stage for early lineage commitment. Cell Stem Cell. 2010;7:288-98.
    • (2010) Cell Stem Cell. , vol.7 , pp. 288-298
    • Surface, L.E.1    Thornton, S.R.2    Boyer, L.A.3
  • 48
    • 84879613132 scopus 로고    scopus 로고
    • USF1 and hSET1A mediated epigenetic modifications regulate lineage differentiation and HoxB4 transcription
    • Deng C, Li Y, Liang S, Cui K, Salz T, Yang H, et al. USF1 and hSET1A mediated epigenetic modifications regulate lineage differentiation and HoxB4 transcription. PLoS Genet. 2013;9:e1003524.
    • (2013) PLoS Genet. , vol.9
    • Deng, C.1    Li, Y.2    Liang, S.3    Cui, K.4    Salz, T.5    Yang, H.6
  • 49
    • 33646070846 scopus 로고    scopus 로고
    • A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    • Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125:315-26.
    • (2006) Cell. , vol.125 , pp. 315-326
    • Bernstein, B.E.1    Mikkelsen, T.S.2    Xie, X.3    Kamal, M.4    Huebert, D.J.5    Cuff, J.6
  • 51
    • 80053063127 scopus 로고    scopus 로고
    • Maintaining embryonic stem cell pluripotency with Wnt signaling
    • Sokol SY. Maintaining embryonic stem cell pluripotency with Wnt signaling. Development. 2011;138:4341-50.
    • (2011) Development. , vol.138 , pp. 4341-4350
    • Sokol, S.Y.1
  • 53
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: scanning for occurrences of a given motif
    • Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27:1017-8.
    • (2011) Bioinformatics. , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 54
    • 84891808382 scopus 로고    scopus 로고
    • JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
    • Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42:D142-7.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D142-D147
    • Mathelier, A.1    Zhao, X.2    Zhang, A.W.3    Parcy, F.4    Worsley-Hunt, R.5    Arenillas, D.J.6
  • 55
    • 84355163093 scopus 로고    scopus 로고
    • DNA-binding factors shape the mouse methylome at distal regulatory regions
    • Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011;480:490-5.
    • (2011) Nature. , vol.480 , pp. 490-495
    • Stadler, M.B.1    Murr, R.2    Burger, L.3    Ivanek, R.4    Lienert, F.5    Schöler, A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.