SEARCH

SEARCH BY CITATION

References

  • Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T et al (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol 30: 224226
  • Bockamp EO, Fordham JL, Gottgens B, Murrell AM, Sanchez MJ, Green AR (1998) Transcriptional regulation of the stem cell leukemia gene by PU.1 and Elf-1. J Biol Chem 273: 2903229042
  • Bot I, Guo J, Van Eck M, Van Santbrink PJ, Groot PH, Hildebrand RB, Seppen J, Van Berkel TJ, Biessen EA (2005) Lentiviral shRNA silencing of murine bone marrow cell CCR2 leads to persistent knockdown of CCR2 function in vivo. Blood 106: 11471153
  • Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew J-L, Ruan Y, Wei C-L, Ng HH, Liu ET (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18: 17521762
  • Bresnick EH, Katsumura KR, Lee HY, Johnson KD, Perkins AS (2012) Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies. Nucleic Acids Res 40: 58195831
  • Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36: D102D106
  • Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigo R, Birney E, Weng Z, Snyder M, Gerstein M (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res 22: 16581667
  • Cheng C, Gerstein M (2012) Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 40: 553568
  • Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107: 2193121936
  • Du P, Kibbe WA, Lin SM (2008) Lumi: a pipeline for processing Illumina microarray. Bioinformatics 24: 15471548
  • Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 5774
  • Elefanty AG, Cory S (1992) bcr-abl-Induced cell lines can switch from mast cell to erythroid or myeloid differentiation in vitro. Blood 79: 12711281
  • Forsberg EC, Downs KM, Bresnick EH (2000) Direct interaction of NF-E2 with hypersensitive site 2 of the beta-globin locus control region in living cells. Blood 96: 334339
  • Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S et al (2012) A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 47: 810822
  • Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy–analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307315
  • Gottgens B, McLaughlin F, Bockamp EO, Fordham JL, Begley CG, Kosmopoulos K, Elefanty AG, Green AR (1997) Transcription of the SCL gene in erythroid and CD34 positive primitive myeloid cells is controlled by a complex network of lineage-restricted chromatin-dependent and chromatin-independent regulatory elements. Oncogene 15: 24192428
  • Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007) Quantifying similarity between motifs. Genome Biol 8: R24
  • Handstad T, Rye M, Mocnik R, Drablos F, Saetrom P (2012) Cell-type specificity of ChIP-predicted transcription factor binding sites. BMC Genomics 13: 372
  • Hannah R, Joshi A, Wilson NK, Kinston S, Gottgens B (2011) A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms. Exp Hematol 39: 531541
  • Hastie T, Tibshirani R (1986) Generalized additive models. Stat Sci 1: 297310
  • Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576589
  • Huang Z, Dore LC, Li Z, Orkin SH, Feng G, Lin S, Crispino JD (2009) GATA-2 reinforces megakaryocyte development in the absence of GATA-1. Mol Cell Biol 29: 51685180
  • Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318356
  • John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA (2011) Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43: 264268
  • Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 14971502
  • Karlic R, Chung HR, Lasserre J, Vlahovicek K, Vingron M (2010) Histone modification levels are predictive for gene expression. Proc Natl Acad Sci USA 107: 29262931
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860921
  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
  • Lichtinger M, Ingram R, Hannah R, Muller D, Clarke D, Assi SA, Lie ALM, Noailles L, Vijayabaskar MS, Wu M, Tenen DG, Westhead DR, Kouskoff V, Lacaud G, Gottgens B, Bonifer C (2012) RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis. EMBO J 31: 43184333
  • Lodato MA, Ng CW, Wamstad JA, Cheng AW, Thai KK, Fraenkel E, Jaenisch R, Boyer LA (2013) SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state. PLoS Genet 9: e1003288
  • Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M (2012) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Res 22: 13341349
  • Masuda A, Hashimoto K, Yokoi T, Doi T, Kodama T, Kume H, Ohno K, Matsuguchi T (2007) Essential role of GATA transcriptional factors in the activation of mast cells. J Immunol 178: 360368
  • McKinlay LH, Tymms MJ, Thomas RS, Seth A, Hasthorpe S, Hertzog PJ, Kola I (1998) The role of Ets-1 in mast cell granulocyte-macrophage colony-stimulating factor expression and activation. J Immunol 161: 40984105
  • Moignard V, Macaulay IC, Swiers G, Buettner F, Schutte J, Calero-Nieto FJ, Kinston S, Joshi A, Hannah R, Theis FJ, Jacobsen SE, de Bruijn MF, Gottgens B (2013) Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat Cell Biol 15: 363372
  • Mullen AC, Orlando DA, Newman JJ, Loven J, Kumar RM, Bilodeau S, Reddy J, Guenther MG, DeKoter RP, Young RA (2011) Master transcription factors determine cell type-specific responses to TGF-beta signaling. Cell 147: 565576
  • Ouyang Z, Zhou Q, Wong WH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci 106: 2152121526
  • Pinto do OP, Wandzioch E, Kolterud A, Carlsson L (2001) Multipotent hematopoietic progenitor cells immortalized by Lhx2 self-renew by a cell nonautonomous mechanism. Exp Hematol 29: 10191028
  • Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841842
  • Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA (2010) c-Myc regulates transcriptional pause release. Cell 141: 432445
  • Robasky K, Bulyk ML (2011) UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res 39: D124D128
  • Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651657
  • Salmon JM, Slater NJ, Hall MA, McCormack MP, Nutt SL, Jane SM, Curtis DJ (2007) Aberrant mast-cell differentiation in mice lacking the stem-cell leukemia gene. Blood 110: 35733581
  • Schmidt D, Schwalie PC, Wilson MD, Ballester B, Goncalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT (2012) Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148: 335348
  • Smyth G (2005) Limma: Linear Models for Microarray Data. New York: Springer, pp 397420
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 1554515550
  • Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663676
  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 11051111
  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511515
  • Trompouki E, Bowman TV, Lawton LN, Fan ZP, Wu DC, DiBiase A, Martin CS, Cech JN, Sessa AK, Leblanc JL, Li P, Durand EM, Mosimann C, Heffner GC, Daley GQ, Paulson RF, Young RA, Zon LI (2011) Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147: 577589
  • Tsai FY, Orkin SH (1997) Transcription factor GATA-2 is required for proliferation/survival of early hematopoietic cells and mast cell formation, but not for erythroid and myeloid terminal differentiation. Blood 89: 36363643
  • Walsh JC, DeKoter RP, Lee HJ, Smith ED, Lancki DW, Gurish MF, Friend DS, Stevens RL, Anastasi J, Singh H (2002) Cooperative and antagonistic interplay between PU.1 and GATA-2 in the specification of myeloid cell fates. Immunity 17: 665676
  • Warnes GR, Ben B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B. (2012) gplots: Various R programming tools for plotting data.
  • Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K (2011) Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 35: 299311
  • Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis. New York: Springer.
  • Wilkinson L. (2011) Venneuler: Venn and Euler Diagrams.
  • Wilson NK, Foster SD, Wang X, Knezevic K, Schutte J, Kaimakis P, Chilarska PM, Kinston S, Ouwehand WH, Dzierzak E, Pimanda JE, de Bruijn MF, Gottgens B (2010) Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 7: 532544
  • Wilson NK, Miranda-Saavedra D, Kinston S, Bonadies N, Foster SD, Calero-Nieto F, Dawson MA, Donaldson IJ, Dumon S, Frampton J, Janky R, Sun XH, Teichmann SA, Bannister AJ, Gottgens B (2009) The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood 113: 54565465
  • Wood SN (2011) Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J R Stat Soc B 73: 336
  • Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10: R130
  • Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ (2013) Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites. Skelet Muscle 3: 8
  • Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137
  • Zhu BM, Kang K, Yu JH, Chen W, Smith HE, Lee D, Sun HW, Wei L, Hennighausen L (2012) Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes. Nucleic Acids Res 40: 44614472