메뉴 건너뛰기




Volumn 114, Issue 25, 2017, Pages E4914-E4923

Modeling gene regulation from paired expression and chromatin accessibility data

Author keywords

Chromatin activity; Chromatin regulator; Gene regulation; Regulatory element; Transcription factor

Indexed keywords

TRANSCRIPTION FACTOR; PROTEIN BINDING;

EID: 85021162442     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1704553114     Document Type: Article
Times cited : (142)

References (29)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 2
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren B, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
    • (2000) Science , vol.290 , pp. 2306-2309
    • Ren, B.1
  • 3
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 4
    • 38649099445 scopus 로고    scopus 로고
    • High-resolution mapping and characterization of open chromatin across the genome
    • Boyle AP, et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311-322.
    • (2008) Cell , vol.132 , pp. 311-322
    • Boyle, A.P.1
  • 5
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNAbinding proteins and nucleosome position
    • Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNAbinding proteins and nucleosome position. Nat Methods 10:1213-1218.
    • (2013) Nat Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 6
    • 84947776702 scopus 로고    scopus 로고
    • MsCentipede: Modeling heterogeneity across genomic sites and replicates improves accuracy in the inference of transcription factor binding
    • Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M (2015) msCentipede: Modeling heterogeneity across genomic sites and replicates improves accuracy in the inference of transcription factor binding. PLoS One 10:e0138030.
    • (2015) PLoS One , vol.10 , pp. e0138030
    • Raj, A.1    Shim, H.2    Gilad, Y.3    Pritchard, J.K.4    Stephens, M.5
  • 7
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi R, et al. (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 21:447-455.
    • (2011) Genome Res , vol.21 , pp. 447-455
    • Pique-Regi, R.1
  • 8
    • 84893863046 scopus 로고    scopus 로고
    • Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
    • Sherwood RI, et al. (2014) Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol 32:171-178.
    • (2014) Nat Biotechnol , vol.32 , pp. 171-178
    • Sherwood, R.I.1
  • 9
    • 84930224883 scopus 로고    scopus 로고
    • Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism
    • Blatti C, Kazemian M, Wolfe S, Brodsky M, Sinha S (2015) Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Res 43:3998-4012.
    • (2015) Nucleic Acids Res , vol.43 , pp. 3998-4012
    • Blatti, C.1    Kazemian, M.2    Wolfe, S.3    Brodsky, M.4    Sinha, S.5
  • 10
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28:817-825.
    • (2010) Nat Biotechnol , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 11
    • 85014282428 scopus 로고    scopus 로고
    • Improved regulatory element prediction based on tissue-specific local epigenomic signatures
    • He Y, et al. (2017) Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci USA 114:E1633-E1640.
    • (2017) Proc Natl Acad Sci USA , vol.114 , pp. E1633-E1640
    • He, Y.1
  • 12
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen Y, et al. (2012) A map of the cis-regulatory sequences in the mouse genome. Nature 488:116-120.
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 13
    • 84946716550 scopus 로고    scopus 로고
    • A systematic approach to identify candidate transcription factors that control cell identity
    • D'Alessio AC, et al. (2015) A systematic approach to identify candidate transcription factors that control cell identity. Stem Cell Rep 5:763-775.
    • (2015) Stem Cell Rep , vol.5 , pp. 763-775
    • D'Alessio, A.C.1
  • 14
    • 84878679046 scopus 로고    scopus 로고
    • A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity
    • Zhang B, et al. (2013) A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res 23:917-927.
    • (2013) Genome Res , vol.23 , pp. 917-927
    • Zhang, B.1
  • 15
    • 84872224226 scopus 로고    scopus 로고
    • The potential of HDAC inhibitors as cognitive enhancers
    • Gräff J, Tsai L-H (2013) The potential of HDAC inhibitors as cognitive enhancers. Annu Rev Pharmacol Toxicol 53:311-330.
    • (2013) Annu Rev Pharmacol Toxicol , vol.53 , pp. 311-330
    • Gräff, J.1    Tsai, L.-H.2
  • 16
    • 84904811353 scopus 로고    scopus 로고
    • Bromodomain protein BRD4 is required for estrogen receptordependent enhancer activation and gene transcription
    • Nagarajan S, et al. (2014) Bromodomain protein BRD4 is required for estrogen receptordependent enhancer activation and gene transcription. Cell Reports 8:460-469.
    • (2014) Cell Reports , vol.8 , pp. 460-469
    • Nagarajan, S.1
  • 17
    • 84922363112 scopus 로고    scopus 로고
    • Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression
    • Kasper LH, Qu C, Obenauer JC, McGoldrick DJ, Brindle PK (2014) Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression. Nucleic Acids Res 42:11363-11382.
    • (2014) Nucleic Acids Res , vol.42 , pp. 11363-11382
    • Kasper, L.H.1    Qu, C.2    Obenauer, J.C.3    McGoldrick, D.J.4    Brindle, P.K.5
  • 18
    • 58049189381 scopus 로고    scopus 로고
    • Liver X receptors (LXRalpha and LXRbeta) are potent regulators for hepatic Dec1 expression
    • Noshiro M, et al. (2009) Liver X receptors (LXRalpha and LXRbeta) are potent regulators for hepatic Dec1 expression. Genes Cells 14:29-40.
    • (2009) Genes Cells , vol.14 , pp. 29-40
    • Noshiro, M.1
  • 19
    • 84943257078 scopus 로고    scopus 로고
    • Reg Network: Anintegrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
    • Liu Z-P, Wu C, Miao H, Wu H (2015) Reg Network: Anintegrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database 2015:bav095.
    • (2015) Database , vol.2015 , pp. bav095
    • Liu, Z.-P.1    Wu, C.2    Miao, H.3    Wu, H.4
  • 20
    • 84951765264 scopus 로고    scopus 로고
    • 3CPET: Finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
    • Djekidel MN, et al. (2015) 3CPET: Finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biol 16:288.
    • (2015) Genome Biol , vol.16 , pp. 288
    • Djekidel, M.N.1
  • 21
    • 84977126727 scopus 로고    scopus 로고
    • Knockdown of EWSR1/FLI1 expression alters the transcriptome of Ewing sarcoma cells in vitro
    • Wang J, et al. (2016) Knockdown of EWSR1/FLI1 expression alters the transcriptome of Ewing sarcoma cells in vitro. J Bone Oncol 5:153-158.
    • (2016) J Bone Oncol , vol.5 , pp. 153-158
    • Wang, J.1
  • 22
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073-1081.
    • (2009) Nat Protoc , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 23
    • 11844267259 scopus 로고    scopus 로고
    • Genetic determinants influencing the response to injury, inflammation, and sepsis
    • De Maio A, Torres MB, Reeves RH (2005) Genetic determinants influencing the response to injury, inflammation, and sepsis. Shock 23:11-17.
    • (2005) Shock , vol.23 , pp. 11-17
    • De Maio, A.1    Torres, M.B.2    Reeves, R.H.3
  • 24
    • 0033738311 scopus 로고    scopus 로고
    • Quantitative trait loci modulate neutrophil infiltration in the liver during LPS-induced inflammation
    • Matesic LE, Niemitz EL, De Maio A, Reeves RH (2000) Quantitative trait loci modulate neutrophil infiltration in the liver during LPS-induced inflammation. FASEB J 14:2247-2254.
    • (2000) FASEB J , vol.14 , pp. 2247-2254
    • Matesic, L.E.1    Niemitz, E.L.2    De Maio, A.3    Reeves, R.H.4
  • 25
    • 84895545435 scopus 로고    scopus 로고
    • Neuronal nicotinic acetylcholine receptors are important targets for alcohol reward and dependence
    • Wu J, Gao M, Taylor DH (2014) Neuronal nicotinic acetylcholine receptors are important targets for alcohol reward and dependence. Acta Pharmacol Sin 35:311-315.
    • (2014) Acta Pharmacol Sin , vol.35 , pp. 311-315
    • Wu, J.1    Gao, M.2    Taylor, D.H.3
  • 26
    • 33845188832 scopus 로고    scopus 로고
    • Buprenorphine reduces alcohol drinking through activation of the nociceptin/orphanin FQ-NOP receptor system
    • Ciccocioppo R, et al. (2007) Buprenorphine reduces alcohol drinking through activation of the nociceptin/orphanin FQ-NOP receptor system. Biol Psychiatry 61:4-12.
    • (2007) Biol Psychiatry , vol.61 , pp. 4-12
    • Ciccocioppo, R.1
  • 27
    • 84890432056 scopus 로고    scopus 로고
    • Chromatin connectivity maps reveal dynamic promoterenhancer long-range associations
    • Zhang Y, et al. (2013) Chromatin connectivity maps reveal dynamic promoterenhancer long-range associations. Nature 504:306-310.
    • (2013) Nature , vol.504 , pp. 306-310
    • Zhang, Y.1
  • 28
    • 0004112391 scopus 로고
    • The data model concept in statistical mapping
    • Jenks GF (1967) The data model concept in statistical mapping. Int Yearb Cartog 7:186-190.
    • (1967) Int Yearb Cartog , vol.7 , pp. 186-190
    • Jenks, G.F.1
  • 29
    • 80055101776 scopus 로고    scopus 로고
    • In vitro differentiation of mouse embryonic stem (mES) cells using the hanging drop method
    • Wang X, Yang P (2008) In vitro differentiation of mouse embryonic stem (mES) cells using the hanging drop method. J Vis Exp 17:e825.
    • (2008) J Vis Exp , vol.17 , pp. e825
    • Wang, X.1    Yang, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.