메뉴 건너뛰기




Volumn 31, Issue 1, 2015, Pages 17-24

SignalSpider: Probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

EID: 84922385856     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu604     Document Type: Article
Times cited : (24)

References (44)
  • 1
    • 84901838628 scopus 로고    scopus 로고
    • Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
    • Ay,F. et al. (2014) Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res., 24, 999-1011.
    • (2014) Genome Res. , vol.24 , pp. 999-1011
    • Ay, F.1
  • 2
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger,M.F. et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1429-1435
    • Berger, M.F.1
  • 3
    • 84874947727 scopus 로고    scopus 로고
    • The BioGRID interaction database: 2013 update
    • Chatr-Aryamontri,A. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D816-D823
    • Chatr-Aryamontri, A.1
  • 4
    • 79351469446 scopus 로고    scopus 로고
    • MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-ChIP or ChIP-seq data
    • Chen,Y. et al. (2011) MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-ChIP or ChIP-seq data. Genome Biol, 12, R11.
    • (2011) Genome Biol. , vol.12 , pp. R11
    • Chen, Y.1
  • 5
    • 84865712383 scopus 로고    scopus 로고
    • Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    • Cheng,C. et al. (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res., 22, 1658-1667.
    • (2012) Genome Res. , vol.22 , pp. 1658-1667
    • Cheng, C.1
  • 6
    • 80053908619 scopus 로고    scopus 로고
    • Resveratrol, through NF-Y/p53/Sin3/HDAC1 complex phosphorylation, inhibits estrogen receptor alpha gene expression via p38MAPK/CK2 signaling in human breast cancer cells
    • De Amicis,F. et al. (2011) Resveratrol, through NF-Y/p53/Sin3/HDAC1 complex phosphorylation, inhibits estrogen receptor alpha gene expression via p38MAPK/CK2 signaling in human breast cancer cells. FASEB J., 25, 3695-3707.
    • (2011) FASEB J. , vol.25 , pp. 3695-3707
    • De Amicis, F.1
  • 7
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Encode
    • ENCODE. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
    • (2012) Nature. , vol.489 , pp. 57-74
  • 8
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst,J. and Kellis,M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
    • (2012) Nat. Methods. , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 9
    • 77956654773 scopus 로고    scopus 로고
    • De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
    • Fordyce,P.M. et al. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol., 28, 970-975.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 970-975
    • Fordyce, P.M.1
  • 10
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • Gerstein,M.B. et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.
    • (2012) Nature. , vol.489 , pp. 91-100
    • Gerstein, M.B.1
  • 11
    • 84881171276 scopus 로고    scopus 로고
    • Inferring chromatin-bound protein complexes from genome-wide binding assays
    • Giannopoulou,E.G. and Elemento,O. (2013) Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res., 23, 1295-1306.
    • (2013) Genome Res. , vol.23 , pp. 1295-1306
    • Giannopoulou, E.G.1    Elemento, O.2
  • 12
    • 84866086842 scopus 로고    scopus 로고
    • High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    • Guo,Y. et al. (2012) High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput. Biol., 8, e1002638.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002638
    • Guo, Y.1
  • 13
    • 0035676057 scopus 로고    scopus 로고
    • On clustering validation techniques
    • Halkidi,M. et al. (2001) On clustering validation techniques. J. Intell. Inf. Syst., 17, 107-145.
    • (2001) J. Intell. Inf. Syst. , vol.17 , pp. 107-145
    • Halkidi, M.1
  • 14
    • 0033553541 scopus 로고    scopus 로고
    • Ras regulates the association of serum response factor and CCAAT/enhancer-binding protein beta
    • Hanlon,M. and Sealy,L. (1999) Ras regulates the association of serum response factor and CCAAT/enhancer-binding protein beta. J. Biol. Chem., 274, 14224-14228.
    • (1999) J. Biol. Chem. , vol.274 , pp. 14224-14228
    • Hanlon, M.1    Sealy, L.2
  • 15
    • 12344252237 scopus 로고    scopus 로고
    • AP-1 subunits: Quarrel and harmony among siblings
    • Hess,J. et al. (2004) AP-1 subunits: quarrel and harmony among siblings. J. Cell. Sci., 117 (Pt 25), 5965-5973.
    • (2004) J. Cell. Sci. , vol.117 , pp. 5965-5973
    • Hess, J.1
  • 16
    • 33745614618 scopus 로고    scopus 로고
    • Linking DNA-binding proteins to their recognition sequences by using protein microarrays
    • Ho,S.W. et al. (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc. Natl Acad. Sci. USA, 103, 9940-9945.
    • (2006) Proc. Natl Acad. Sci. USA. , vol.103 , pp. 9940-9945
    • Ho, S.W.1
  • 17
    • 84862785201 scopus 로고    scopus 로고
    • Unsupervised pattern discovery in human chromatin structure through genomic segmentation
    • Hoffman,M.M. et al. (2012) Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods, 9, 473-476.
    • (2012) Nat. Methods. , vol.9 , pp. 473-476
    • Hoffman, M.M.1
  • 18
    • 84875448918 scopus 로고    scopus 로고
    • Integrative annotation of chromatin elements from ENCODE data
    • Hoffman,M.M. et al. (2013) Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res., 41, 827-841.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 827-841
    • Hoffman, M.M.1
  • 19
    • 70350340058 scopus 로고    scopus 로고
    • Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling
    • Hu,S. et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell, 139, 610-622.
    • (2009) Cell. , vol.139 , pp. 610-622
    • Hu, S.1
  • 20
    • 36048976921 scopus 로고    scopus 로고
    • USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier
    • Huang,S. et al. (2007) USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Mol. Cell. Biol., 27, 7991-8002.
    • (2007) Mol. Cell. Biol. , vol.27 , pp. 7991-8002
    • Huang, S.1
  • 21
    • 84876855559 scopus 로고    scopus 로고
    • Differential principal component analysis of ChIP-seq
    • Ji,H. et al. (2013) Differential principal component analysis of ChIP-seq. Proc. Natl Acad. Sci. USA, 110, 6789-6794.
    • (2013) Proc. Natl Acad. Sci. USA. , vol.110 , pp. 6789-6794
    • Ji, H.1
  • 22
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson,D.S. et al. (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
  • 23
    • 74549114755 scopus 로고    scopus 로고
    • A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
    • Laajala,T.D. et al. (2009) A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics, 10, 618.
    • (2009) BMC Genomics. , vol.10 , pp. 618
    • Laajala, T.D.1
  • 24
    • 84859582058 scopus 로고    scopus 로고
    • Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
    • Lickwar,C.R. et al. (2012) Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature, 484, 251-255.
    • (2012) Nature. , vol.484 , pp. 251-255
    • Lickwar, C.R.1
  • 25
    • 39149109887 scopus 로고    scopus 로고
    • The structural basis of protein acetylation by the p300/CBP transcriptional coactivator
    • Liu,X. et al. (2008) The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. Nature, 451, 846-850.
    • (2008) Nature. , vol.451 , pp. 846-850
    • Liu, X.1
  • 26
    • 84897436870 scopus 로고    scopus 로고
    • An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding
    • Mahony,S. et al. (2014) An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding. PLoS Comput. Biol., 10, e1003501.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003501
    • Mahony, S.1
  • 27
    • 0037370029 scopus 로고    scopus 로고
    • Cascade of distinct histone modifications during collagenase gene activation
    • Martens,J.H. et al. (2003) Cascade of distinct histone modifications during collagenase gene activation. Mol. Cell. Biol., 23, 1808-1816.
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 1808-1816
    • Martens, J.H.1
  • 28
    • 84884516365 scopus 로고    scopus 로고
    • Architecture of an RNA polymerase II transcription preinitiation complex
    • Murakami,K. et al. (2013) Architecture of an RNA polymerase II transcription preinitiation complex. Science, 342, 1238724.
    • (2013) Science. , vol.342 , pp. 1238724
    • Murakami, K.1
  • 29
    • 0033201447 scopus 로고    scopus 로고
    • Bcl3, an IkappaB protein, stimulates activating protein-1 transactivation and cellular proliferation
    • Na,S.Y. et al. (1999) Bcl3, an IkappaB protein, stimulates activating protein-1 transactivation and cellular proliferation. J. Biol. Chem., 274, 28491-28496.
    • (1999) J. Biol. Chem. , vol.274 , pp. 28491-28496
    • Na, S.Y.1
  • 30
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • Palla,G. et al. (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature, 435, 814-818.
    • (2005) Nature. , vol.435 , pp. 814-818
    • Palla, G.1
  • 31
    • 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
  • 32
    • 0028971290 scopus 로고
    • Human TAFII250 interacts with RAP74: Implications for RNA polymerase II initiation
    • Ruppert,S. and Tjian,R. (1995) Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation. Genes Dev., 9, 2747-2755.
    • (1995) Genes Dev. , vol.9 , pp. 2747-2755
    • Ruppert, S.1    Tjian, R.2
  • 33
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel,A. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
    • (2005) Genome Res. , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 34
    • 34250376736 scopus 로고    scopus 로고
    • Synergistic activation of the tumor suppressor, HLJ1, by the transcription factors YY1 and activator protein 1
    • Wang,C.C. et al. (2007) Synergistic activation of the tumor suppressor, HLJ1, by the transcription factors YY1 and activator protein 1 Cancer Res., 67, 4816-4826.
    • (2007) Cancer Res. , vol.67 , pp. 4816-4826
    • Wang, C.C.1
  • 36
    • 84870063111 scopus 로고    scopus 로고
    • Iaseq: Integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets
    • Wei,Y. et al. (2012) iaseq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets. BMC Genomics, 13, 681.
    • (2012) BMC Genomics. , vol.13 , pp. 681
    • Wei, Y.1
  • 37
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in ChIP-seq peak detection
    • Wilbanks,E.G. and Facciotti,M.T. (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One, 5, e11471.
    • (2010) PLoS One. , vol.5 , pp. e11471
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 38
    • 84887011782 scopus 로고    scopus 로고
    • DNA motif elucidation using belief propagation
    • Wong,K.C. et al. (2013) DNA Motif Elucidation using Belief Propagation. Nucleic Acids Research, 41, e153.
    • (2013) Nucleic Acids Research. , vol.41 , pp. e153
    • Wong, K.C.1
  • 39
    • 84886780296 scopus 로고    scopus 로고
    • Dynamic trans-acting factor colocalization in human cells
    • Xie,D. et al. (2013) Dynamic trans-acting factor colocalization in human cells. Cell, 155, 713-724.
    • (2013) Cell. , vol.155 , pp. 713-724
    • Xie, D.1
  • 40
    • 34447527890 scopus 로고    scopus 로고
    • Extracellular matrix-regulated gene expression requires cooperation of SWI/SNF and transcription factors
    • Xu,R. et al. (2007) Extracellular matrix-regulated gene expression requires cooperation of SWI/SNF and transcription factors. J. Biol. Chem., 282, 14992-14999.
    • (2007) J. Biol. Chem. , vol.282 , pp. 14992-14999
    • Xu, R.1
  • 41
    • 33846214719 scopus 로고    scopus 로고
    • Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
    • Yang,C. et al. (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene, 389, 52-65.
    • (2007) Gene. , vol.389 , pp. 52-65
    • Yang, C.1
  • 42
    • 84879357102 scopus 로고    scopus 로고
    • JMOSAiCS: Joint analysis of multiple ChIP-seq datasets
    • Zeng,X. et al. (2013) jMOSAiCS: joint analysis of multiple ChIP-seq datasets. Genome Biol., 14, R38.
    • (2013) Genome Biol. , vol.14 , pp. R38
    • Zeng, X.1
  • 43
    • 34548504321 scopus 로고    scopus 로고
    • A novel role of Brg1 in the regulation of SRF/MRTFAdependent smooth muscle-specific gene expression
    • Zhang,M. et al. (2007) A novel role of Brg1 in the regulation of SRF/MRTFAdependent smooth muscle-specific gene expression. J. Biol. Chem., 282, 25708-25716.
    • (2007) J. Biol. Chem. , vol.282 , pp. 25708-25716
    • Zhang, M.1
  • 44
    • 0037869164 scopus 로고    scopus 로고
    • Criterion functions for document clustering: Experiments and analysis
    • In: Technical report. University of Minnesota
    • Zhao,Y. and Karypis,G. (2002) Criterion functions for document clustering: experiments and analysis. In: Technical report. Department of Computer Science, University of Minnesota.
    • (2002) Department of Computer Science.
    • Zhao, Y.1    Karypis, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.