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Volumn 19, Issue 4, 2016, Pages 623-633

Integrated genomics and proteomics define huntingtin CAG length-dependent networks in mice

(22)  Langfelder, Peter a   Cantle, Jeffrey P a,b,c   Chatzopoulou, Doxa b   Wang, Nan a,b,c   Gao, Fuying a,b   Al Ramahi, Ismael d,e   Lu, Xiao Hong a,b,c   Ramos, Eliana Marisa a,b   El Zein, Karla d,e   Zhao, Yining b   Deverasetty, Sandeep b   Tebbe, Andreas f   Schaab, Christoph f   Lavery, Daniel J g   Howland, David g   Kwak, Seung g   Botas, Juan d,e   Aaronson, Jeffrey S g   Rosinski, Jim g   Coppola, Giovanni a,b,c   more..


Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP; FIBROBLAST GROWTH FACTOR; GLUCOCORTICOID; GLUTAMATE RECEPTOR; HUNTINGTIN; MESSENGER RNA; PHOSPHOPROTEIN DARPP 32; PROTOCADHERIN; TRANSCRIPTOME; UNCLASSIFIED DRUG; HTT PROTEIN, MOUSE; NERVE PROTEIN; NUCLEAR PROTEIN;

EID: 84959086071     PISSN: 10976256     EISSN: 15461726     Source Type: Journal    
DOI: 10.1038/nn.4256     Document Type: Article
Times cited : (290)

References (75)
  • 1
    • 84898017417 scopus 로고    scopus 로고
    • Huntington disease: Natural history biomarkers and prospects for therapeutics
    • Ross, C.A., et al. Huntington disease: natural history, biomarkers and prospects for therapeutics. Nat. Rev. Neurol. 10, 204-216 (2014
    • (2014) Nat. Rev. Neurol , vol.10 , pp. 204-216
    • Ross, C.A.1
  • 3
    • 0027480960 scopus 로고
    • A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington?s disease chromosomes
    • The Huntington?s Disease Collaborative Research Group
    • The Huntington?s Disease Collaborative Research Group. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington?s disease chromosomes. Cell 72 971-983 (1993
    • (1993) Cell , vol.72 , pp. 971-983
  • 4
    • 34547692622 scopus 로고    scopus 로고
    • Trinucleotide repeat disorders
    • Orr, H.T., & Zoghbi, H.Y. Trinucleotide repeat disorders. Annu. Rev. Neurosci. 30, 575-621 (2007
    • (2007) Annu. Rev. Neurosci , vol.30 , pp. 575-621
    • Orr, H.T.1    Zoghbi, H.Y.2
  • 5
    • 0034329159 scopus 로고    scopus 로고
    • Molecular genetics: Unmasking polyglutamine triggers in neurodegenerative disease
    • Gusella, J.F., & MacDonald, M.E. Molecular genetics: unmasking polyglutamine triggers in neurodegenerative disease. Nat. Rev. Neurosci. 1, 109-115 (2000
    • (2000) Nat. Rev. Neurosci , vol.1 , pp. 109-115
    • Gusella, J.F.1    MacDonald, M.E.2
  • 6
    • 33747768203 scopus 로고    scopus 로고
    • Huntington?s disease: Seeing the pathogenic process through a genetic lens
    • Gusella, J.F., & MacDonald, M.E. Huntington?s disease: seeing the pathogenic process through a genetic lens. Trends Biochem. Sci. 31, 533-540 (2006
    • (2006) Trends Biochem. Sci , vol.31 , pp. 533-540
    • Gusella, J.F.1    MacDonald, M.E.2
  • 7
    • 84906929865 scopus 로고    scopus 로고
    • Regional atrophy associated with cognitive and motor function in prodromal Huntington disease
    • PREDICT-HD Investigators and Coordinators of the Huntington Study Group
    • Aylward E.H., et al. PREDICT-HD Investigators and Coordinators of the Huntington Study Group. Regional atrophy associated with cognitive and motor function in prodromal Huntington disease. J. Huntingtons Dis. 2, 477-489 (2013
    • (2013) J. Huntingtons Dis , vol.2 , pp. 477-489
    • Aylward, E.H.1
  • 8
    • 84930421685 scopus 로고    scopus 로고
    • Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation
    • Biagioli M., et al. Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation. Hum. Mol. Genet. 24, 2442-2457 (2015
    • (2015) Hum. Mol. Genet , vol.24 , pp. 2442-2457
    • Biagioli, M.1
  • 9
    • 26444441008 scopus 로고    scopus 로고
    • HD CAG repeat implicates a dominant property of huntingtin in mitochondrial energy metabolism
    • Seong I.S., et al. HD CAG repeat implicates a dominant property of huntingtin in mitochondrial energy metabolism. Hum. Mol. Genet. 14, 2871-2880 (2005
    • (2005) Hum. Mol. Genet , vol.14 , pp. 2871-2880
    • Seong, I.S.1
  • 10
    • 84902996303 scopus 로고    scopus 로고
    • Neuronal targets for reducing mutant huntingtin expression to ameliorate disease in a mouse model of Huntington?s disease
    • Wang N., et al. Neuronal targets for reducing mutant huntingtin expression to ameliorate disease in a mouse model of Huntington?s disease. Nat. Med. 20, 536-541 (2014
    • (2014) Nat. Med , vol.20 , pp. 536-541
    • Wang, N.1
  • 11
    • 84884537922 scopus 로고    scopus 로고
    • Choosing an animal model for the study of Huntington?s disease
    • Pouladi, M.A., Morton, A.J., & Hayden, M.R. Choosing an animal model for the study of Huntington?s disease. Nat. Rev. Neurosci. 14, 708-721 (2013
    • (2013) Nat. Rev. Neurosci , vol.14 , pp. 708-721
    • Pouladi, M.A.1    Morton, A.J.2    Hayden, M.R.3
  • 12
    • 84871422859 scopus 로고    scopus 로고
    • Comprehensive behavioral and molecular characterization of a new knock-in mouse model of Huntington?s disease: ZQ175
    • Menalled L.B., et al. Comprehensive behavioral and molecular characterization of a new knock-in mouse model of Huntington?s disease: zQ175. PLoS One 7, e49838 (2012
    • (2012) PLoS One , vol.7 , pp. e49838
    • Menalled, L.B.1
  • 13
    • 0037107191 scopus 로고    scopus 로고
    • Early motor dysfunction and striosomal distribution of huntingtin microaggregates in Huntington?s disease knock-in mice
    • Menalled L.B., et al. Early motor dysfunction and striosomal distribution of huntingtin microaggregates in Huntington?s disease knock-in mice. J. Neurosci. 22, 8266-8276 (2002
    • (2002) J. Neurosci , vol.22 , pp. 8266-8276
    • Menalled, L.B.1
  • 14
    • 84905667224 scopus 로고    scopus 로고
    • Progressive axonal transport and synaptic protein changes correlate with behavioral and neuropathological abnormalities in the heterozygous Q175 KI mouse model of Huntington?s disease
    • Smith G.A., et al. Progressive axonal transport and synaptic protein changes correlate with behavioral and neuropathological abnormalities in the heterozygous Q175 KI mouse model of Huntington?s disease. Hum. Mol. Genet. 23, 4510-4527 (2014
    • (2014) Hum. Mol. Genet , vol.23 , pp. 4510-4527
    • Smith, G.A.1
  • 15
    • 34248531227 scopus 로고    scopus 로고
    • Testicular degeneration in Huntington disease
    • Van Raamsdonk J.M., et al. Testicular degeneration in Huntington disease. Neurobiol. Dis. 26, 512-520 (2007
    • (2007) Neurobiol. Dis , vol.26 , pp. 512-520
    • Van Raamsdonk, J.M.1
  • 16
    • 84944718721 scopus 로고    scopus 로고
    • Dysfunction of the CNS-heart axis in mouse models of Huntington?s disease
    • Mielcarek M., et al. Dysfunction of the CNS-heart axis in mouse models of Huntington?s disease. PLoS Genet. 10, e1004550 (2014
    • (2014) PLoS Genet , vol.10 , pp. e1004550
    • Mielcarek, M.1
  • 17
    • 41449085571 scopus 로고    scopus 로고
    • Eigengene networks for studying the relationships between co-expression modules
    • Langfelder, P., & Horvath, S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst. Biol. 1, 54 (2007
    • (2007) BMC Syst. Biol , vol.1 , pp. 54
    • Langfelder, P.1    Horvath, S.2
  • 18
    • 50949084896 scopus 로고    scopus 로고
    • Geometric interpretation of gene coexpression network analysis
    • Horvath, S., & Dong, J. Geometric interpretation of gene coexpression network analysis. PLOS Comput. Biol. 4, e1000117 (2008
    • (2008) PLOS Comput. Biol , vol.4 , pp. e1000117
    • Horvath, S.1    Dong, J.2
  • 19
    • 84876217807 scopus 로고    scopus 로고
    • When is hub gene selection better than standard meta-Analysis
    • Langfelder, P., Mischel, P.S., & Horvath, S. When is hub gene selection better than standard meta-Analysis?. PLoS One 8, e61505 (2013
    • (2013) PLoS One , vol.8 , pp. e61505
    • Langfelder, P.1    Mischel, P.S.2    Horvath, S.3
  • 20
    • 84919756166 scopus 로고    scopus 로고
    • Targeting ATM ameliorates mutant Huntingtin toxicity in cell and animal models of Huntington?s disease
    • 268ra178
    • Lu X.H., et al. Targeting ATM ameliorates mutant Huntingtin toxicity in cell and animal models of Huntington?s disease. Sci. Transl. Med. 6, 268ra178 (2014
    • (2014) Sci. Transl. Med , vol.6
    • Lu, X.H.1
  • 21
    • 84938389137 scopus 로고    scopus 로고
    • Identification of genetic factors that modify clinical onset of Huntington?s disease
    • Genetic Modifiers of Huntington?s Disease (GeM-HD) Consortium
    • Genetic Modifiers of Huntington?s Disease (GeM-HD) Consortium. Identification of genetic factors that modify clinical onset of Huntington?s disease. Cell 162 516-526 (2015
    • (2015) Cell , vol.162 , pp. 516-526
  • 22
    • 84880730823 scopus 로고    scopus 로고
    • Huntington?s disease: Underlying molecular mechanisms and emerging concepts
    • Labbadia, J., & Morimoto, R.I. Huntington?s disease: underlying molecular mechanisms and emerging concepts. Trends Biochem. Sci. 38, 378-385 (2013
    • (2013) Trends Biochem. Sci , vol.38 , pp. 378-385
    • Labbadia, J.1    Morimoto, R.I.2
  • 23
    • 33750347347 scopus 로고    scopus 로고
    • Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases
    • Lin, M.T., & Beal, M.F. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. Nature 443, 787-795 (2006
    • (2006) Nature , vol.443 , pp. 787-795
    • Lin, M.T.1    Beal, M.F.2
  • 24
    • 33644783812 scopus 로고    scopus 로고
    • Regional and cellular gene expression changes in human Huntington?s disease brain
    • Hodges A., et al. Regional and cellular gene expression changes in human Huntington?s disease brain. Hum. Mol. Genet. 15, 965-977 (2006
    • (2006) Hum. Mol. Genet , vol.15 , pp. 965-977
    • Hodges, A.1
  • 25
    • 84937518757 scopus 로고    scopus 로고
    • Common mechanisms in neurodegeneration and neuroinflammation: A BrainNet Europe gene expression microarray study
    • Durrenberger P.F., et al. Common mechanisms in neurodegeneration and neuroinflammation: a BrainNet Europe gene expression microarray study. J. Neural Transm. (Vienna) 122, 1055-1068 (2015
    • (2015) J. Neural Transm. (Vienna , vol.122 , pp. 1055-1068
    • Durrenberger, P.F.1
  • 26
    • 84876907931 scopus 로고    scopus 로고
    • Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer?s disease
    • Zhang B., et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer?s disease. Cell 153, 707-720 (2013
    • (2013) Cell , vol.153 , pp. 707-720
    • Zhang, B.1
  • 27
    • 34547839797 scopus 로고    scopus 로고
    • Mutant huntingtin?s effects on striatal gene expression in mice recapitulate changes observed in human Huntington?s disease brain and do not differ with mutant huntingtin length or wild-Type huntingtin dosage
    • Kuhn A., et al. Mutant huntingtin?s effects on striatal gene expression in mice recapitulate changes observed in human Huntington?s disease brain and do not differ with mutant huntingtin length or wild-Type huntingtin dosage. Hum. Mol. Genet. 16, 1845-1861 (2007
    • (2007) Hum. Mol. Genet , vol.16 , pp. 1845-1861
    • Kuhn, A.1
  • 28
    • 33846252240 scopus 로고    scopus 로고
    • Genome-wide atlas of gene expression in the adult mouse brain
    • Lein E.S., et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168-176 (2007
    • (2007) Nature , vol.445 , pp. 168-176
    • Lein, E.S.1
  • 29
    • 84898050413 scopus 로고    scopus 로고
    • Cell-Type-based model explaining coexpression patterns of genes in the brain
    • Grange P., et al. Cell-Type-based model explaining coexpression patterns of genes in the brain. Proc. Natl. Acad. Sci. USA 111, 5397-5402 (2014
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 5397-5402
    • Grange, P.1
  • 30
    • 0001589776 scopus 로고
    • Differential loss of striatal projection neurons in Huntington disease
    • Reiner A., et al. Differential loss of striatal projection neurons in Huntington disease. Proc. Natl. Acad. Sci. USA 85, 5733-5737 (1988
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 5733-5737
    • Reiner, A.1
  • 31
    • 55449107738 scopus 로고    scopus 로고
    • A translational profiling approach for the molecular characterization of CNS cell types
    • Heiman M., et al. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738-748 (2008
    • (2008) Cell , vol.135 , pp. 738-748
    • Heiman, M.1
  • 32
    • 33344470365 scopus 로고    scopus 로고
    • FACS-Array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains
    • Lobo, M.K., Karsten, S.L., Gray, M., Geschwind, D.H., & Yang, X.W. FACS-Array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains. Nat. Neurosci. 9, 443-452 (2006
    • (2006) Nat. Neurosci , vol.9 , pp. 443-452
    • Lobo, M.K.1    Karsten, S.L.2    Gray, M.3    Geschwind, D.H.4    Yang, X.W.5
  • 33
    • 84886996159 scopus 로고    scopus 로고
    • The neuron identity problem: Form meets function
    • Fishell, G., & Heintz, N. The neuron identity problem: form meets function. Neuron 80, 602-612 (2013
    • (2013) Neuron , vol.80 , pp. 602-612
    • Fishell, G.1    Heintz, N.2
  • 34
    • 84903382312 scopus 로고    scopus 로고
    • Maintenance of postmitotic neuronal cell identity
    • Deneris, E.S., & Hobert, O. Maintenance of postmitotic neuronal cell identity. Nat. Neurosci. 17, 899-907 (2014
    • (2014) Nat. Neurosci , vol.17 , pp. 899-907
    • Deneris, E.S.1    Hobert, O.2
  • 35
    • 84880953033 scopus 로고    scopus 로고
    • Clustered protocadherins
    • Chen, W.V., & Maniatis, T. Clustered protocadherins. Development 140, 3297-3302 (2013
    • (2013) Development , vol.140 , pp. 3297-3302
    • Chen, W.V.1    Maniatis, T.2
  • 36
    • 84897413565 scopus 로고    scopus 로고
    • Developmental epigenetic modification regulates stochastic expression of clustered protocadherin genes generating single neuron diversity
    • Toyoda, S., et al. Developmental epigenetic modification regulates stochastic expression of clustered protocadherin genes, generating single neuron diversity. Neuron 82, 94-108 (2014
    • (2014) Neuron , vol.82 , pp. 94-108
    • Toyoda, S.1
  • 37
    • 84871398317 scopus 로고    scopus 로고
    • CTCF/cohesin-mediated DNA looping is required for protocadherin a promoter choice
    • Guo Y., et al. CTCF/cohesin-mediated DNA looping is required for protocadherin a promoter choice. Proc. Natl. Acad. Sci. USA 109, 21081-21086 (2012
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 21081-21086
    • Guo, Y.1
  • 38
    • 84861917541 scopus 로고    scopus 로고
    • Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-A gene expression
    • Monahan K., et al. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-A gene expression. Proc. Natl. Acad. Sci. USA 109, 9125-9130 (2012
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 9125-9130
    • Monahan, K.1
  • 39
    • 0041353535 scopus 로고    scopus 로고
    • Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes
    • Zuccato C., et al. Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes. Nat. Genet. 35, 76-83 (2003
    • (2003) Nat. Genet , vol.35 , pp. 76-83
    • Zuccato, C.1
  • 40
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann, M., Kulak, N.A., Nagaraj, N., & Cox, J. The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49, 583-590 (2013
    • (2013) Mol. Cell , vol.49 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3    Cox, J.4
  • 41
    • 84857938446 scopus 로고    scopus 로고
    • Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    • M111 014050
    • Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Molecular & cellular proteomics: MCP 11, M111 014050 (2012
    • (2012) Molecular & Cellular Proteomics: MCP , vol.11
    • Geiger, T.1    Wehner, A.2    Schaab, C.3    Cox, J.4    Mann, M.5
  • 42
    • 84863833900 scopus 로고    scopus 로고
    • Network organization of the huntingtin proteomic interactome in mammalian brain
    • Shirasaki D.I., et al. Network organization of the huntingtin proteomic interactome in mammalian brain. Neuron 75, 41-57 (2012
    • (2012) Neuron , vol.75 , pp. 41-57
    • Shirasaki, D.I.1
  • 43
    • 84907197082 scopus 로고    scopus 로고
    • Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction termed MaxLFQ
    • Cox, J., et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513-2526 (2014
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 2513-2526
    • Cox, J.1
  • 44
    • 84949104386 scopus 로고    scopus 로고
    • Cell type-And brain region-resolved mouse brain proteome
    • Sharma K., et al. Cell type-And brain region-resolved mouse brain proteome. Nat. Neurosci. 18, 1819-1831 (2015
    • (2015) Nat. Neurosci , vol.18 , pp. 1819-1831
    • Sharma, K.1
  • 45
    • 32644434386 scopus 로고    scopus 로고
    • Huntingtin-HAP40 complex is a novel Rab5 effector that regulates early endosome motility and is up-regulated in Huntington?s disease
    • Pal, A., Severin, F., Lommer, B., Shevchenko, A., & Zerial, M. Huntingtin-HAP40 complex is a novel Rab5 effector that regulates early endosome motility and is up-regulated in Huntington?s disease. J. Cell Biol. 172, 605-618 (2006
    • (2006) J. Cell Biol , vol.172 , pp. 605-618
    • Pal, A.1    Severin, F.2    Lommer, B.3    Shevchenko, A.4    Zerial, M.5
  • 46
    • 84906929787 scopus 로고    scopus 로고
    • Striatal synaptosomes from Hdh140Q/140Q knock-in mice have altered protein levels novel sites of methionine oxidation, and excess glutamate release after stimulation
    • Valencia, A., et al. Striatal synaptosomes from Hdh140Q/140Q knock-in mice have altered protein levels, novel sites of methionine oxidation, and excess glutamate release after stimulation. J. Huntingtons Dis. 2, 459-475 (2013
    • (2013) J. Huntingtons Dis , vol.2 , pp. 459-475
    • Valencia, A.1
  • 47
    • 34249715853 scopus 로고    scopus 로고
    • Huntingtin interacting proteins are genetic modifiers of neurodegeneration
    • Kaltenbach L.S., et al. Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet. 3, e82 (2007
    • (2007) PLoS Genet , vol.3 , pp. e82
    • Kaltenbach, L.S.1
  • 48
    • 84897386660 scopus 로고    scopus 로고
    • REST and stress resistance in ageing and Alzheimer?s disease
    • Lu T., et al. REST and stress resistance in ageing and Alzheimer?s disease. Nature 507, 448-454 (2014
    • (2014) Nature , vol.507 , pp. 448-454
    • Lu, T.1
  • 49
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • Phillips, J.E., & Corces, V.G. CTCF: master weaver of the genome. Cell 137, 1194-1211 (2009
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 50
    • 84916880365 scopus 로고    scopus 로고
    • Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
    • Dowen J.M., et al. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159, 374-387 (2014
    • (2014) Cell , vol.159 , pp. 374-387
    • Dowen, J.M.1
  • 51
    • 79959796625 scopus 로고    scopus 로고
    • HD CAG-correlated gene expression changes support a simple dominant gain of function
    • Jacobsen J.C., et al. HD CAG-correlated gene expression changes support a simple dominant gain of function. Hum. Mol. Genet. 20, 2846-2860 (2011
    • (2011) Hum. Mol. Genet , vol.20 , pp. 2846-2860
    • Jacobsen, J.C.1
  • 52
    • 0041691176 scopus 로고    scopus 로고
    • Time course of early motor and neuropathological anomalies in a knock-in mouse model of Huntington?s disease with 140 CAG repeats
    • Menalled, L.B., Sison, J.D., Dragatsis, I., Zeitlin, S., & Chesselet, M.F. Time course of early motor and neuropathological anomalies in a knock-in mouse model of Huntington?s disease with 140 CAG repeats. J. Comp. Neurol. 465, 11-26 (2003
    • (2003) J. Comp. Neurol , vol.465 , pp. 11-26
    • Menalled, L.B.1    Sison, J.D.2    Dragatsis, I.3    Zeitlin, S.4    Chesselet, M.F.5
  • 53
    • 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
  • 54
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-A Python framework to work with high-Throughput sequencing data
    • Anders, S., Pyl, P.T., & Huber, W. HTSeq-A Python framework to work with high-Throughput sequencing data. Bioinformatics 31, 166-169 (2015
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 55
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M.I., Huber, W., & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 56
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson, W.E., Li, C., & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127 (2007
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 57
    • 84861970118 scopus 로고    scopus 로고
    • Network methods for describing sample relationships in genomic datasets: Application to Huntington?s disease
    • Oldham, M.C., Langfelder, P., & Horvath, S. Network methods for describing sample relationships in genomic datasets: application to Huntington?s disease. BMC Syst. Biol. 6, 63 (2012
    • (2012) BMC Syst. Biol , vol.6 , pp. 63
    • Oldham, M.C.1    Langfelder, P.2    Horvath, S.3
  • 58
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • Zhang, B., & Horvath, S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4, e17 (2005
    • (2005) Stat. Appl. Genet. Mol. Biol , vol.4 , pp. e17
    • Zhang, B.1    Horvath, S.2
  • 59
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • Langfelder, P., & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 60
    • 84859326067 scopus 로고    scopus 로고
    • Fast R functions for robust correlations and hierarchical clustering
    • Langfelder, P., & Horvath, S. Fast R functions for robust correlations and hierarchical clustering. J. Stat. Softw. 46 (11), 1-17 (2012
    • (2012) J. Stat. Softw , vol.46 , Issue.11 , pp. 1-17
    • Langfelder, P.1    Horvath, S.2
  • 61
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad, B.M., Irizarry, R.A., Astrand, M., & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 62
    • 40049099114 scopus 로고    scopus 로고
    • Defining clusters from a hierarchical cluster tree: The dynamic tree cut package for r
    • Langfelder, P., Zhang, B., & Horvath, S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24, 719-720 (2007
    • (2007) Bioinformatics , vol.24 , pp. 719-720
    • Langfelder, P.1    Zhang, B.2    Horvath, S.3
  • 64
    • 79960277368 scopus 로고    scopus 로고
    • Optimally weighted Z-Test is a powerful method for combining probabilities in meta-Analysis
    • Zaykin, D.V. Optimally weighted Z-Test is a powerful method for combining probabilities in meta-Analysis. J. Evol. Biol. 24, 1836-1841 (2011
    • (2011) J. Evol. Biol , vol.24 , pp. 1836-1841
    • Zaykin, D.V.1
  • 65
    • 79961116748 scopus 로고    scopus 로고
    • Strategies for aggregating gene expression data: The collapseRows R function
    • Miller J.A., et al. Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics 12, 322 (2011
    • (2011) BMC Bioinformatics , vol.12 , pp. 322
    • Miller, J.A.1
  • 66
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen Y., et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 67
    • 84925657284 scopus 로고    scopus 로고
    • N17 Modifies mutant Huntingtin nuclear pathogenesis and severity of disease in HD BAC transgenic mice
    • Gu X., et al. N17 Modifies mutant Huntingtin nuclear pathogenesis and severity of disease in HD BAC transgenic mice. Neuron 85, 726-741 (2015
    • (2015) Neuron , vol.85 , pp. 726-741
    • Gu, X.1
  • 68
    • 84860842187 scopus 로고    scopus 로고
    • Longitudinal analysis of gene expression and behaviour in the HdhQ150 mouse model of Huntington?s disease
    • Giles P., et al. Longitudinal analysis of gene expression and behaviour in the HdhQ150 mouse model of Huntington?s disease. Brain Res. Bull. 88, 199-209 (2012
    • (2012) Brain Res. Bull , vol.88 , pp. 199-209
    • Giles, P.1
  • 69
    • 77952316271 scopus 로고    scopus 로고
    • Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis
    • Becanovic K., et al. Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis. Hum. Mol. Genet. 19, 1438-1452 (2010
    • (2010) Hum. Mol. Genet , vol.19 , pp. 1438-1452
    • Becanovic, K.1
  • 70
    • 79955752894 scopus 로고    scopus 로고
    • Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
    • Wang Y., et al. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 11, 2019-2026 (2011
    • (2011) Proteomics , vol.11 , pp. 2019-2026
    • Wang, Y.1
  • 71
    • 67649400942 scopus 로고    scopus 로고
    • A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    • Cox J., et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protoc. 4, 698-705 (2009
    • (2009) Nat. Protoc , vol.4 , pp. 698-705
    • Cox, J.1
  • 72
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman R.C., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004
    • (2004) Genome Biol , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 73
    • 84962236382 scopus 로고
    • Controlling the false discovery rate-A practical and powerful approach to multiple testing
    • Benjamini, Y., & Hochberg, Y. Controlling the false discovery rate-A practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289-300 (1995
    • (1995) J. R. Stat. Soc. Series B Stat. Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 74
    • 84925657284 scopus 로고    scopus 로고
    • N17 modifies mutant huntingtin nuclear pathogenesis and severity of disease in HD BAC transgenic mice
    • Gu X., et al. N17 modifies mutant huntingtin nuclear pathogenesis and severity of disease in HD BAC transgenic mice. Neuron 85, 726-741 (2015
    • (2015) Neuron , vol.85 , pp. 726-741
    • Gu, X.1
  • 75
    • 33748741301 scopus 로고    scopus 로고
    • CHIP protects from the neurotoxicity of expanded and wild-Type ataxin-1 and promotes their ubiquitination and degradation
    • Al-Ramahi I., et al. CHIP protects from the neurotoxicity of expanded and wild-Type ataxin-1 and promotes their ubiquitination and degradation. J. Biol. Chem. 281, 26714-26724 (2006
    • (2006) J. Biol. Chem , vol.281 , pp. 26714-26724
    • Al-Ramahi, I.1


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