메뉴 건너뛰기




Volumn 50, Issue 3, 2018, Pages 424-431

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Author keywords

[No Author keywords available]

Indexed keywords

GAMMA INTERFERON; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; STAT2 PROTEIN; TRANSCRIPTION FACTOR PU 1; PROTEIN BINDING; TRANSCRIPTION FACTOR;

EID: 85041133831     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/s41588-018-0046-7     Document Type: Article
Times cited : (207)

References (75)
  • 1
    • 84976892875 scopus 로고    scopus 로고
    • Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi
    • Li, Y. et al. Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi. Nat. Med. 22, 952-960 (2016).
    • (2016) Nat. Med. , vol.22 , pp. 952-960
    • Li, Y.1
  • 2
    • 84856387609 scopus 로고    scopus 로고
    • Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosisinfection
    • Barreiro, L. B. et al. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosisinfection. Proc. Natl Acad. Sci. USA 109, 1204-1209 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 1204-1209
    • Barreiro, L.B.1
  • 3
    • 84896742056 scopus 로고    scopus 로고
    • Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression
    • Fairfax, B. P. et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343, 1246949 (2014).
    • (2014) Science , vol.343 , pp. 1246949
    • Fairfax, B.P.1
  • 4
    • 84922809120 scopus 로고    scopus 로고
    • Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes
    • Kim, S. et al. Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes. Nat. Commun. 5, 5236 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 5236
    • Kim, S.1
  • 5
    • 84896759364 scopus 로고    scopus 로고
    • Common genetic variants modulate pathogen-sensing responses in human dendritic cells
    • Lee, M. N. et al. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 343, 1246980 (2014).
    • (2014) Science , vol.343 , pp. 1246980
    • Lee, M.N.1
  • 6
    • 84930336482 scopus 로고    scopus 로고
    • Host genetic variation influences gene expression response to rhinovirus infection
    • Çalişkan, M., Baker, S. W., Gilad, Y. &Ober, C. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet. 11, e1005111 (2015).
    • (2015) PLoS Genet. , vol.11 , pp. e1005111
    • Çalişkan, M.1    Baker, S.W.2    Gilad, Y.3    Ober, C.4
  • 7
    • 84992381901 scopus 로고    scopus 로고
    • Genetic ancestry and natural selection drive population differences in immune responses to pathogens
    • Nédélec, Y. et al. Genetic ancestry and natural selection drive population differences in immune responses to pathogens. Cell 167, 657-66.e21 (2016).
    • (2016) Cell , vol.167 , pp. 657-666
    • Nédélec, Y.1
  • 8
    • 85008712412 scopus 로고    scopus 로고
    • Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease
    • de Lange, K. M. et al. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat. Genet. 49, 256-261 (2017).
    • (2017) Nat. Genet. , vol.49 , pp. 256-261
    • De Lange, K.M.1
  • 9
    • 85027524031 scopus 로고    scopus 로고
    • Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations
    • Kim-Hellmuth, S. et al. Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nat. Commun. 8, 266 (2017).
    • (2017) Nat. Commun. , vol.8 , pp. 266
    • Kim-Hellmuth, S.1
  • 10
    • 84857111200 scopus 로고    scopus 로고
    • DNase i sensitivity QTLs are a major determinant of human expression variation
    • Degner, J. F. et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390-394 (2012).
    • (2012) Nature , vol.482 , pp. 390-394
    • Degner, J.F.1
  • 11
    • 79955081425 scopus 로고    scopus 로고
    • PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers
    • Jin, F., Li, Y. &Ren, B. &Natarajan, R. PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proc. Natl. Acad. Sci. USA 108, 5290-5295 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 5290-5295
    • Jin, F.1    Li, Y.2    Ren, B.3    Natarajan, R.4
  • 12
    • 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
  • 13
    • 84888641656 scopus 로고    scopus 로고
    • Effect of natural genetic variation on enhancer selection and function
    • Heinz, S. et al. Effect of natural genetic variation on enhancer selection and function. Nature 503, 487-492 (2013).
    • (2013) Nature , vol.503 , pp. 487-492
    • Heinz, S.1
  • 14
    • 84926180401 scopus 로고    scopus 로고
    • Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates
    • Wang, A. et al. Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. Cell Stem Cell 16, 386-399 (2015).
    • (2015) Cell Stem Cell , vol.16 , pp. 386-399
    • Wang, A.1
  • 15
    • 84915805486 scopus 로고    scopus 로고
    • Adistal locus element mediates IFN-γ priming of lipopolysaccharide-stimulated TNF gene expression
    • Chow, N. A., Jasenosky, L. D. &Goldfeld, A. E. A distal locus element mediates IFN-γ priming of lipopolysaccharide-stimulated TNF gene expression. Cell Rep. 9, 1718-1728 (2014).
    • (2014) Cell Rep. , vol.9 , pp. 1718-1728
    • Chow, N.A.1    Jasenosky, L.D.2    Goldfeld, A.E.3
  • 16
    • 84976878643 scopus 로고    scopus 로고
    • Hierarchy within the mammary STAT5-driven Wap super-enhancer
    • Shin, H. Y. et al. Hierarchy within the mammary STAT5-driven Wap super-enhancer. Nat. Genet. 48, 904-911 (2016).
    • (2016) Nat. Genet. , vol.48 , pp. 904-911
    • Shin, H.Y.1
  • 17
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
    • (2012) Nature , vol.489 , pp. 75-82
    • Thurman, R.E.1
  • 18
    • 85039994149 scopus 로고    scopus 로고
    • Impact of regulatory variation across human iPSCs and differentiated cells
    • Banovich, N. E. et al. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 28, 122-131 (2017).
    • (2017) Genome Res. , vol.28 , pp. 122-131
    • Banovich, N.E.1
  • 19
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi, R. et al. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21, 447-455 (2011).
    • (2011) Genome Res. , vol.21 , pp. 447-455
    • Pique-Regi, R.1
  • 20
    • 84893863046 scopus 로고    scopus 로고
    • Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
    • Sherwood, R. I. et al. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat. Biotechnol. 32, 171-178 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 171-178
    • Sherwood, R.I.1
  • 21
    • 84938319366 scopus 로고    scopus 로고
    • Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription
    • Alasoo, K. et al. Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription. Sci. Rep. 5, 12524 (2015).
    • (2015) Sci. Rep. , vol.5 , pp. 12524
    • Alasoo, K.1
  • 22
    • 85020793872 scopus 로고    scopus 로고
    • Common genetic variation drives molecular heterogeneity in human iPSCs
    • Kilpinen, H. et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 546, 370-375 (2017).
    • (2017) Nature , vol.546 , pp. 370-375
    • Kilpinen, H.1
  • 23
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. &Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
    • (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
  • 24
    • 70349736116 scopus 로고    scopus 로고
    • Cross-regulation of signaling pathways by interferongamma: Implications for immune responses and autoimmune diseases
    • Hu, X. &Ivashkiv, L. B. Cross-regulation of signaling pathways by interferongamma: implications for immune responses and autoimmune diseases. Immunity 31, 539-550 (2009).
    • (2009) Immunity , vol.31 , pp. 539-550
    • Hu, X.1    Ivashkiv, L.B.2
  • 25
    • 84884355522 scopus 로고    scopus 로고
    • Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling
    • Qiao, Y. et al. Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling. Immunity 39, 454-469 (2013).
    • (2013) Immunity , vol.39 , pp. 454-469
    • Qiao, Y.1
  • 26
    • 84956678036 scopus 로고    scopus 로고
    • Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
    • Kumasaka, N., Knights, A. J. &Gaffney, D. J. Fine-mapping cellular QTLs with RASQUAL and ATAC-seq. Nat. Genet. 48, 206-213 (2016).
    • (2016) Nat. Genet. , vol.48 , pp. 206-213
    • Kumasaka, N.1    Knights, A.J.2    Gaffney, D.J.3
  • 27
    • 84940391986 scopus 로고    scopus 로고
    • Genetic control of chromatin states in humans involves local and distal chromosomal interactions
    • Grubert, F. et al. Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Cell 162, 1051-1065 (2015).
    • (2015) Cell , vol.162 , pp. 1051-1065
    • Grubert, F.1
  • 28
    • 84940419146 scopus 로고    scopus 로고
    • Population variation and genetic control of modular chromatin architecture in humans
    • Waszak, S. M. et al. Population variation and genetic control of modular chromatin architecture in humans. Cell 162, 1039-1050 (2015).
    • (2015) Cell , vol.162 , pp. 1039-1050
    • Waszak, S.M.1
  • 30
    • 84901631426 scopus 로고    scopus 로고
    • Bayesian test for colocalisation between pairs of genetic association studies using summary statistics
    • Giambartolomei, C. et al. Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet. 10, e1004383 (2014).
    • (2014) PLoS Genet. , vol.10 , pp. e1004383
    • Giambartolomei, C.1
  • 31
    • 84940771118 scopus 로고    scopus 로고
    • Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations
    • Liu, J. Z. et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat. Genet. 47, 979-986 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 979-986
    • Liu, J.Z.1
  • 32
    • 84894288992 scopus 로고    scopus 로고
    • Genetics of rheumatoid arthritis contributes to biology and drug discovery
    • Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376-381 (2014).
    • (2014) Nature , vol.506 , pp. 376-381
    • Okada, Y.1
  • 33
    • 84961927084 scopus 로고    scopus 로고
    • Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
    • Zhu, Z. et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nat. Genet. 48, 481-487 (2016).
    • (2016) Nat. Genet. , vol.48 , pp. 481-487
    • Zhu, Z.1
  • 34
    • 84888317489 scopus 로고    scopus 로고
    • Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease
    • Lambert, J. C. et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat. Genet. 45, 1452-1458 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1452-1458
    • Lambert, J.C.1
  • 35
    • 84868337361 scopus 로고    scopus 로고
    • Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
    • Morris, A. P. et al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat. Genet. 44, 981-990 (2012).
    • (2012) Nat. Genet. , vol.44 , pp. 981-990
    • Morris, A.P.1
  • 36
    • 85018726619 scopus 로고    scopus 로고
    • Conditional eQTL analysis reveals allelic heterogeneity of gene expression
    • Jansen, R. et al. Conditional eQTL analysis reveals allelic heterogeneity of gene expression. Hum. Mol. Genet. 26, 1444-1451 (2017).
    • (2017) Hum. Mol. Genet. , vol.26 , pp. 1444-1451
    • Jansen, R.1
  • 37
    • 84949097483 scopus 로고    scopus 로고
    • Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus
    • Bentham, J. et al. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat. Genet. 47, 1457-1464 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 1457-1464
    • Bentham, J.1
  • 38
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
    • (2012) Science , vol.337 , pp. 1190-1195
    • Maurano, M.T.1
  • 39
    • 84923326765 scopus 로고    scopus 로고
    • Genetic and epigenetic fine mapping of causal autoimmune disease variants
    • Farh, K. K.-H. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337-343 (2015).
    • (2015) Nature , vol.518 , pp. 337-343
    • Farh, K.K.-H.1
  • 40
    • 84930422605 scopus 로고    scopus 로고
    • Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases
    • Guo, H. et al. Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases. Hum. Mol. Genet. 24, 3305-3313 (2015).
    • (2015) Hum. Mol. Genet. , vol.24 , pp. 3305-3313
    • Guo, H.1
  • 41
    • 85013155806 scopus 로고    scopus 로고
    • Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types
    • Chun, S. et al. Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat. Genet. 49, 600-605 (2017).
    • (2017) Nat. Genet. , vol.49 , pp. 600-605
    • Chun, S.1
  • 42
    • 85031313737 scopus 로고    scopus 로고
    • Genetic effects on gene expression across human tissues
    • Battle, A. et al. Genetic effects on gene expression across human tissues. Nature 550, 204-213 (2017).
    • (2017) Nature , vol.550 , pp. 204-213
    • Battle, A.1
  • 43
    • 84995792545 scopus 로고    scopus 로고
    • Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters
    • Javierre, B. M. et al. Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167, 1369-1384. e19 (2016).
    • (2016) Cell , vol.167 , pp. 1369-1384
    • Javierre, B.M.1
  • 44
    • 84887620842 scopus 로고    scopus 로고
    • A high-resolution map of the three-dimensional chromatin interactome in human cells
    • Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-294 (2013).
    • (2013) Nature , vol.503 , pp. 290-294
    • Jin, F.1
  • 45
    • 84905593782 scopus 로고    scopus 로고
    • Enhancer loops appear stable during development and are associated with paused polymerase
    • Ghavi-Helm, Y. et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96-100 (2014).
    • (2014) Nature , vol.512 , pp. 96-100
    • Ghavi-Helm, Y.1
  • 46
    • 84868154284 scopus 로고    scopus 로고
    • The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
    • Pai, A. A. et al. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 8, e1003000 (2012).
    • (2012) PLoS Genet. , vol.8 , pp. e1003000
    • Pai, A.A.1
  • 47
    • 80155137594 scopus 로고    scopus 로고
    • Master transcription factors determine cell-type-specific responses to TGF-β signaling
    • Mullen, A. C. et al. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 147, 565-576 (2011).
    • (2011) Cell , vol.147 , pp. 565-576
    • Mullen, A.C.1
  • 48
    • 80155123782 scopus 로고    scopus 로고
    • Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration
    • Trompouki, E. et al. Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147, 577-589 (2011).
    • (2011) Cell , vol.147 , pp. 577-589
    • Trompouki, E.1
  • 49
    • 84872522528 scopus 로고    scopus 로고
    • Latent enhancers activated by stimulation in differentiated cells
    • Ostuni, R. et al. Latent enhancers activated by stimulation in differentiated cells. Cell 152, 157-171 (2013).
    • (2013) Cell , vol.152 , pp. 157-171
    • Ostuni, R.1
  • 50
    • 80054084614 scopus 로고    scopus 로고
    • Pioneer factors: Directing transcriptional regulators within the chromatin environment
    • Magnani, L., Eeckhoute, J. &Lupien, M. Pioneer factors: directing transcriptional regulators within the chromatin environment. Trends Genet. 27, 465-474 (2011).
    • (2011) Trends Genet. , vol.27 , pp. 465-474
    • Magnani, L.1    Eeckhoute, J.2    Lupien, M.3
  • 51
    • 67649669255 scopus 로고    scopus 로고
    • A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
    • Ramirez-Carrozzi, V. R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114-128 (2009).
    • (2009) Cell , vol.138 , pp. 114-128
    • Ramirez-Carrozzi, V.R.1
  • 52
    • 85019057713 scopus 로고    scopus 로고
    • Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements
    • Bojcsuk, D., Nagy, G. &Balint, B. L. Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements. Nucleic Acids Res. 45, 3693-3706 (2017).
    • (2017) Nucleic Acids Res. , vol.45 , pp. 3693-3706
    • Bojcsuk, D.1    Nagy, G.2    Balint, B.L.3
  • 53
    • 77950343791 scopus 로고    scopus 로고
    • Pattern recognition receptors and inflammation
    • Takeuchi, O. &Akira, S. Pattern recognition receptors and inflammation. Cell 140, 805-820 (2010).
    • (2010) Cell , vol.140 , pp. 805-820
    • Takeuchi, O.1    Akira, S.2
  • 54
    • 0842266786 scopus 로고    scopus 로고
    • Interferon-gamma: An overview of signals, mechanisms and functions
    • Schroder, K., Hertzog, P. J., Ravasi, T. &Hume, D. A. Interferon-gamma: An overview of signals, mechanisms and functions. J. Leukoc. Biol. 75, 163-189 (2004).
    • (2004) J. Leukoc. Biol. , vol.75 , pp. 163-189
    • Schroder, K.1    Hertzog, P.J.2    Ravasi, T.3    Hume, D.A.4
  • 55
    • 84969945169 scopus 로고    scopus 로고
    • Fast and efficient QTL mapper for thousands of molecular phenotypes
    • Ongen, H., Buil, A., Brown, A. A., Dermitzakis, E. T. &Delaneau, O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics 32, 1479-1485 (2016).
    • (2016) Bioinformatics , vol.32 , pp. 1479-1485
    • Ongen, H.1    Buil, A.2    Brown, A.A.3    Dermitzakis, E.T.4    Delaneau, O.5
  • 56
    • 84871809302 scopus 로고    scopus 로고
    • STAR: Ultrafast universal RNA-seq aligner
    • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1
  • 57
    • 84868490540 scopus 로고    scopus 로고
    • Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data
    • Jun, G. et al. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. Am. J. Hum. Genet. 91, 839-848 (2012).
    • (2012) Am. J. Hum. Genet. , vol.91 , pp. 839-848
    • Jun, G.1
  • 58
    • 84897397058 scopus 로고    scopus 로고
    • FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao, Y., Smyth, G. K. &Shi, W. featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 59
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for the ENCODE Project
    • Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1760-1774
    • Harrow, J.1
  • 60
    • 84872033704 scopus 로고    scopus 로고
    • Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
    • Wagner, G. P., Kin, K. &Lynch, V. J. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 131, 281-285 (2012).
    • (2012) Theory Biosci. , vol.131 , pp. 281-285
    • Wagner, G.P.1    Kin, K.2    Lynch, V.J.3
  • 61
    • 84858068675 scopus 로고    scopus 로고
    • Removing technical variability in RNA-seq data using conditional quantile normalization
    • Hansen, K. D., Irizarry, R. A. &Wu, Z. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13, 204-216 (2012).
    • (2012) Biostatistics , vol.13 , pp. 204-216
    • Hansen, K.D.1    Irizarry, R.A.2    Wu, Z.3
  • 62
    • 84861734626 scopus 로고    scopus 로고
    • Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
    • Stegle, O., Parts, L., Piipari, M., Winn, J. &Durbin, R. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc. 7, 500-507 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 500-507
    • Stegle, O.1    Parts, L.2    Piipari, M.3    Winn, J.4    Durbin, R.5
  • 63
    • 84903513963 scopus 로고    scopus 로고
    • Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads
    • Jiang, H., Lei, R., Ding, S.-W. &Zhu, S. Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15, 182 (2014).
    • (2014) BMC Bioinformatics , vol.15 , pp. 182
    • Jiang, H.1    Lei, R.2    Ding, S.-W.3    Zhu, S.4
  • 65
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. &Hall, I. M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 66
    • 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
  • 68
    • 84897373336 scopus 로고    scopus 로고
    • CrossMap: A versatile tool for coordinate conversion between genome assemblies
    • Zhao, H. et al. CrossMap: A versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30, 1006-1007 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1006-1007
    • Zhao, H.1
  • 69
    • 84870820953 scopus 로고    scopus 로고
    • A high-performance computing toolset for relatedness and principal component analysis of SNP data
    • Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326-3328 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 3326-3328
    • Zheng, X.1
  • 70
    • 84954372770 scopus 로고    scopus 로고
    • An efficient multiple-testing adjustment for eqtl studies that accounts for linkage disequilibrium between variants
    • Davis, J. R. et al. An efficient multiple-testing adjustment for eqtl studies that accounts for linkage disequilibrium between variants. Am. J. Hum. Genet. 98, 216-224 (2016).
    • (2016) Am. J. Hum. Genet. , vol.98 , pp. 216-224
    • Davis, J.R.1
  • 72
    • 84970044605 scopus 로고    scopus 로고
    • TFBSTools: An R/bioconductor package for transcription factor binding site analysis
    • Tan, G. &Lenhard, B. TFBSTools: An R/bioconductor package for transcription factor binding site analysis. Bioinformatics 32, 1555-1556 (2016).
    • (2016) Bioinformatics , vol.32 , pp. 1555-1556
    • Tan, G.1    Lenhard, B.2
  • 73
    • 84907413210 scopus 로고    scopus 로고
    • Determination and inference of eukaryotic transcription factor sequence specificity
    • Weirauch, M. T. et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158, 1431-1443 (2014).
    • (2014) Cell , vol.158 , pp. 1431-1443
    • Weirauch, M.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.