메뉴 건너뛰기




Volumn 3, Issue October2014, 2014, Pages 1-29

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(22)  Ballester, Benoit a,b   Medina Rivera, Alejandra c   Schmidt, Dominic d,i   Gonzàlez Porta, Mar a   Carlucci, Matthew c   Chen, Xiaoting e   Chessman, Kyle c   Faure, Andre J a   Funnell, Alister P W f   Goncalves, Angela a   Kutter, Claudia d   Lukk, Margus d   Menon, Suraj d   McLaren, William M a   Stefflova, Klara d,j   Watt, Stephen a,d   Weirauch, Matthew T g   Crossley, Merlin f   Marioni, John C a   Odom, Duncan T a,d   more..


Author keywords

[No Author keywords available]

Indexed keywords


EID: 84922313916     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.02626     Document Type: Article
Times cited : (72)

References (92)
  • 11
    • 0025286228 scopus 로고
    • Disruption of a C/EBP binding site in the factor IX promoter is associated with haemophilia B
    • Crossley M, Brownlee GG. 1990. Disruption of a C/EBP binding site in the factor IX promoter is associated with haemophilia B. Nature 345:444-446. doi: 10.1038/345444a0.
    • (1990) Nature , vol.345 , pp. 444-446
    • Crossley, M.1    Brownlee, G.G.2
  • 12
    • 0026767136 scopus 로고
    • Recovery from hemophilia B Leyden: An androgen-responsive element in the factor IX promoter
    • Crossley M, Ludwig M, Stowell KM, De Vos P, Olek K, Brownlee GG. 1992. Recovery from hemophilia B Leyden: an androgen-responsive element in the factor IX promoter. Science 257:377-379. doi: 10.1126/science.1631558.
    • (1992) Science , vol.257 , pp. 377-379
    • Crossley, M.1    Ludwig, M.2    Stowell, K.M.3    De Vos, P.4    Olek, K.5    Brownlee, G.G.6
  • 13
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74. doi: 10.1038/nature11247.
    • (2012) Nature , vol.489 , pp. 57-74
  • 14
    • 84880064679 scopus 로고    scopus 로고
    • Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
    • Ernst J, Kellis M. 2013. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Research 23:1142-1154. doi: 10.1101/gr.144840.112.
    • (2013) Genome Research , vol.23 , pp. 1142-1154
    • Ernst, J.1    Kellis, M.2
  • 19
    • 84869502241 scopus 로고    scopus 로고
    • ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions
    • Furey TS. 2012. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nature Reviews Genetics 13:840-852. doi: 10.1038/nrg3306.
    • (2012) Nature Reviews Genetics , vol.13 , pp. 840-852
    • Furey, T.S.1
  • 23
    • 0025333289 scopus 로고
    • Evolution of the P450 gene superfamily: Animal-plant 'warfare', molecular drive and human genetic differences in drug oxidation
    • Gonzalez FJ, Nebert DW. 1990. Evolution of the P450 gene superfamily: animal-plant 'warfare', molecular drive and human genetic differences in drug oxidation. Trends in Genetics 6:182-186. doi: 10.1016/0168-9525(90)90174-5.
    • (1990) Trends in Genetics , vol.6 , pp. 182-186
    • Gonzalez, F.J.1    Nebert, D.W.2
  • 25
    • 77951266764 scopus 로고    scopus 로고
    • Finding regulatory DNA motifs using alignment-free evolutionary conservation information
    • Gordân R, Narlikar L, Hartemink AJ. 2010. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Research 38:e90. doi: 10.1093/nar/gkp1166.
    • (2010) Nucleic Acids Research , vol.38
    • Gordân, R.1    Narlikar, L.2    Hartemink, A.J.3
  • 26
    • 84866086842 scopus 로고    scopus 로고
    • High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    • Guo Y, Mahony S, Gifford DK. 2012. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLOS Computational Biology 8:e1002638. doi: 10.1371/journal.pcbi.1002638.
    • (2012) PLOS Computational Biology , vol.8
    • Guo, Y.1    Mahony, S.2    Gifford, D.K.3
  • 27
    • 84863890567 scopus 로고    scopus 로고
    • Genomic approaches towards finding cis-regulatory modules in animals
    • Hardison RC, Taylor J. 2012. Genomic approaches towards finding cis-regulatory modules in animals. Nature Reviews Genetics 13:469-483. doi: 10.1038/nrg3242.
    • (2012) Nature Reviews Genetics , vol.13 , pp. 469-483
    • Hardison, R.C.1    Taylor, J.2
  • 28
    • 33751381461 scopus 로고    scopus 로고
    • TimeTree: A public knowledge-base of divergence times among organisms
    • Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972. doi: 10.1093/bioinformatics/btl505.
    • (2006) Bioinformatics , vol.22 , pp. 2971-2972
    • Hedges, S.B.1    Dudley, J.2    Kumar, S.3
  • 29
    • 84880968176 scopus 로고    scopus 로고
    • GAT: A simulation framework for testing the association of genomic intervals
    • Heger A, Webber C, Goodson M, Ponting CP, Lunter G. 2013. GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics 29:2046-2048. doi: 10.1093/bioinformatics/btt343.
    • (2013) Bioinformatics , vol.29 , pp. 2046-2048
    • Heger, A.1    Webber, C.2    Goodson, M.3    Ponting, C.P.4    Lunter, G.5
  • 32
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4:44-57. doi: 10.1038/nprot.2008.211.
    • (2009) Nature Protocols , vol.4 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 33
    • 78651250284 scopus 로고    scopus 로고
    • FOXA1 is a key determinant of estrogen receptor function and endocrine response
    • Hurtado A, Holmes KA, Ross-Innes CS, Schmidt D, Carroll JS. 2011. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nature Genetics 43:27-33. doi: 10.1038/ng.730.
    • (2011) Nature Genetics , vol.43 , pp. 27-33
    • Hurtado, A.1    Holmes, K.A.2    Ross-Innes, C.S.3    Schmidt, D.4    Carroll, J.S.5
  • 36
  • 37
    • 80053383499 scopus 로고    scopus 로고
    • Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes
    • Kutter C, Brown GD, Goncalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT. 2011. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nature Genetics 43:948-955. doi: 10.1038/ng.906.
    • (2011) Nature Genetics , vol.43 , pp. 948-955
    • Kutter, C.1    Brown, G.D.2    Goncalves, A.3    Wilson, M.D.4    Watt, S.5    Brazma, A.6    White, R.J.7    Odom, D.T.8
  • 38
    • 33747370376 scopus 로고    scopus 로고
    • Plasticity and expanding complexity of the hepatic transcription factor network during liver development
    • Kyrmizi I, Hatzis P, Katrakili N, Tronche F, Gonzalez FJ, Talianidis I. 2006. Plasticity and expanding complexity of the hepatic transcription factor network during liver development. Genes & Development 20:2293-2305. doi: 10.1101/gad.390906.
    • (2006) Genes & Development , vol.20 , pp. 2293-2305
    • Kyrmizi, I.1    Hatzis, P.2    Katrakili, N.3    Tronche, F.4    Gonzalez, F.J.5    Talianidis, I.6
  • 40
    • 0036677662 scopus 로고    scopus 로고
    • TFBS: Computational framework for transcription factor binding site analysis
    • Lenhard B, Wasserman WW. 2002. TFBS: computational framework for transcription factor binding site analysis. Bioinformatics 18:1135-1136. doi: 10.1093/bioinformatics/18.8.1135.
    • (2002) Bioinformatics , vol.18 , pp. 1135-1136
    • Lenhard, B.1    Wasserman, W.W.2
  • 41
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18:1851-1858. doi: 10.1101/gr.078212.108.
    • (2008) Genome Research , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 44
    • 33645978405 scopus 로고    scopus 로고
    • Design-based stereological estimation of hepatocyte number, by combining the smooth optical fractionator and immunocytochemistry with anti-carcinoembryonic antigen polyclonal antibodies
    • Marcos R, Monteiro RA, Rocha E. 2006. Design-based stereological estimation of hepatocyte number, by combining the smooth optical fractionator and immunocytochemistry with anti-carcinoembryonic antigen polyclonal antibodies. Liver International 26:116-124. doi: 10.1111/j.1478-3231.2005.01201.x.
    • (2006) Liver International , vol.26 , pp. 116-124
    • Marcos, R.1    Monteiro, R.A.2    Rocha, E.3
  • 45
    • 84894573097 scopus 로고    scopus 로고
    • Large-scale quality analysis of published ChIP-seq data
    • Marinov GK, Kundaje A, Park PJ, Wold BJ. 2014. Large-scale quality analysis of published ChIP-seq data. G3 4:209-223. doi: 10.1534/g3.113.008680.
    • (2014) G3 , vol.4 , pp. 209-223
    • Marinov, G.K.1    Kundaje, A.2    Park, P.J.3    Wold, B.J.4
  • 51
  • 55
    • 58149200952 scopus 로고    scopus 로고
    • UniPROBE: An online database of protein binding microarray data on protein-DNA interactions
    • Newburger DE, Bulyk ML. 2009. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Research 37:D77-D82. doi: 10.1093/nar/gkn660.
    • (2009) Nucleic Acids Research , vol.37 , pp. D77-D82
    • Newburger, D.E.1    Bulyk, M.L.2
  • 58
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. 2008. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research 18:1814-1828. doi: 10.1101/gr.076554.108.
    • (2008) Genome Research , vol.18 , pp. 1814-1828
    • Paten, B.1    Herrero, J.2    Beal, K.3    Fitzgerald, S.4    Birney, E.5
  • 60
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. 2011. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research 21:447-455. doi: 10.1101/gr.112623.110.
    • (2011) Genome Research , vol.21 , pp. 447-455
    • Pique-Regi, R.1    Degner, J.F.2    Pai, A.A.3    Gaffney, D.J.4    Gilad, Y.5    Pritchard, J.K.6
  • 63
    • 54949127160 scopus 로고    scopus 로고
    • iRefIndex: A consolidated protein interaction database with provenance
    • Razick S, Magklaras G, Donaldson IM. 2008. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 9:405. doi: 10.1186/1471-2105-9-405.
    • (2008) BMC Bioinformatics , vol.9 , pp. 405
    • Razick, S.1    Magklaras, G.2    Donaldson, I.M.3
  • 65
    • 0027159448 scopus 로고
    • Hemophilia B Leyden: Substitution of thymine for guanine at position-21 results in a disruption of a hepatocyte nuclear factor 4 binding site in the factor IX promoter
    • Reijnen MJ, Peerlinck K, Maasdam D, Bertina RM, Reitsma PH. 1993. Hemophilia B Leyden: substitution of thymine for guanine at position-21 results in a disruption of a hepatocyte nuclear factor 4 binding site in the factor IX promoter. Blood 82:151-158.
    • (1993) Blood , vol.82 , pp. 151-158
    • Reijnen, M.J.1    Peerlinck, K.2    Maasdam, D.3    Bertina, R.M.4    Reitsma, P.H.5
  • 66
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    • Rhee HS, Pugh BF. 2011. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147:1408-1419. doi: 10.1016/j.cell.2011.11.013.
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 69
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. 2004. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research 32:D91-D94. doi: 10.1093/nar/gkh012.
    • (2004) Nucleic Acids Research , vol.32 , pp. D91-D94
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 70
    • 84865777825 scopus 로고    scopus 로고
    • Linking disease associations with regulatory information in the human genome
    • Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. 2012. Linking disease associations with regulatory information in the human genome. Genome Research 22:1748-1759. doi: 10.1101/gr.136127.111.
    • (2012) Genome Research , vol.22 , pp. 1748-1759
    • Schaub, M.A.1    Boyle, A.P.2    Kundaje, A.3    Batzoglou, S.4    Snyder, M.5
  • 72
    • 67649834440 scopus 로고    scopus 로고
    • ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions
    • Schmidt D, Wilson M, Spyrou C, Brown G, Hadfield J, Odom D. 2009. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48:240-248. doi: 10.1016/j.ymeth.2009.03.001.
    • (2009) Methods , vol.48 , pp. 240-248
    • Schmidt, D.1    Wilson, M.2    Spyrou, C.3    Brown, G.4    Hadfield, J.5    Odom, D.6
  • 75
    • 84903169287 scopus 로고    scopus 로고
    • DiffBind: Differential binding analysis of ChIP-Seq peak data
    • Stark R, Brown GD. 2011. DiffBind: differential binding analysis of ChIP-Seq peak data. In R package version 100.
    • (2011) In R package version , pp. 100
    • Stark, R.1    Brown, G.D.2
  • 77
    • 84868343901 scopus 로고    scopus 로고
    • The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution
    • Chapter 1: Unit1 13
    • Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, Cooper DN. 2012. The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Current Protocols in Bioinformatics Chapter 1: Unit1 13. doi: 10.1002/0471250953.bi0113s39.
    • (2012) Current Protocols in Bioinformatics
    • Stenson, P.D.1    Ball, E.V.2    Mort, M.3    Phillips, A.D.4    Shaw, K.5    Cooper, D.N.6
  • 78
    • 35448967958 scopus 로고    scopus 로고
    • Regulation of human protein Z gene expression by liver-enriched transcription factor HNF-4alpha and ubiquitous factor Sp1
    • Sugawara H, Iwata H, Souri M, Ichinose A. 2007. Regulation of human protein Z gene expression by liver-enriched transcription factor HNF-4alpha and ubiquitous factor Sp1. Journal of Thrombosis and Haemostasis 5:2250-2258. doi: 10.1111/j.1538-7836.2007.02738.x.
    • (2007) Journal of Thrombosis and Haemostasis , vol.5 , pp. 2250-2258
    • Sugawara, H.1    Iwata, H.2    Souri, M.3    Ichinose, A.4
  • 79
    • 0023821768 scopus 로고
    • Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints
    • Tagle DA, Koop BF, Goodman M, Slightom JL, Hess DL, Jones RT. 1988. Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. Journal of Molecular Biology 203:439-455. doi: 10.1016/0022-2836(88)90011-3.
    • (1988) Journal of Molecular Biology , vol.203 , pp. 439-455
    • Tagle, D.A.1    Koop, B.F.2    Goodman, M.3    Slightom, J.L.4    Hess, D.L.5    Jones, R.T.6
  • 83
    • 84858779229 scopus 로고    scopus 로고
    • HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    • Ward LD, Kellis M. 2012a. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Research 40:D930-D934. doi: 10.1093/nar/gkr917.
    • (2012) Nucleic Acids Research , vol.40 , pp. D930-D934
    • Ward, L.D.1    Kellis, M.2
  • 84
    • 84869436774 scopus 로고    scopus 로고
    • Interpreting noncoding genetic variation in complex traits and human disease
    • Ward LD, Kellis M. 2012b. Interpreting noncoding genetic variation in complex traits and human disease. Nature Biotechnology 30:1095-1106. doi: 10.1038/nbt.2422.
    • (2012) Nature Biotechnology , vol.30 , pp. 1095-1106
    • Ward, L.D.1    Kellis, M.2
  • 88
    • 77952310528 scopus 로고    scopus 로고
    • A human functional protein interaction network and its application to cancer data analysis
    • Wu G, Feng X, Stein L. 2010. A human functional protein interaction network and its application to cancer data analysis. Genome Biology 11:R53. doi: 10.1186/gb-2010-11-5-r53.
    • (2010) Genome Biology , vol.11
    • Wu, G.1    Feng, X.2    Stein, L.3
  • 92
    • 70449132583 scopus 로고    scopus 로고
    • Combinatorial binding predicts spatio-temporal cis-regulatory activity
    • Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE. 2009. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462:65-70. doi: 10.1038/nature08531.
    • (2009) Nature , vol.462 , pp. 65-70
    • Zinzen, R.P.1    Girardot, C.2    Gagneur, J.3    Braun, M.4    Furlong, E.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.