Anders, S. and W. Huber (2010): “Differential expression analysis for sequence count data,” Genome Biol., 11, R106.CrossrefGoogle Scholar

Carroll, J. S., C. A. Meyer, J. Song, W. Li, T. R. Geistlinger, J. Eeckhoute, A. S. Brodsky, E. K. K. Keeton, K. C. Fertuck, G. F. Hall, Q. Wang, S. Bekiranov, V. Sementchenko, E. A. Fox, P. A. Silver, T. R. Gingeras, X. S. Liu and M. Brown (2006): “Genome-wide analysis of estrogen receptor binding sites,” Nat. Genet., 38, 1289–1297.Google Scholar

de Wit, E. and W. de Laat (2012): “A decade of 3c technologies: insights into nuclear organization,” Genes Develop., 26, 11–24.Google Scholar

Dekker, J., K. Rippe, M. Dekker and N. Kleckner (2002): “Capturing chromosome conformation,” Science, 295, 1306–1311.Google Scholar

Dostie, J., T. Richmond, R. Arnaout, R. Selzer, W. Lee, T. Honan, E. Rubio, A. Krumm, J. Lamb, C. Nusbaum, R. Green and J. Dekker (2006): “Chromosome conformation capture carbon copy (5c): A massively parallel solution for mapping interactions between genomic elements,” Genome Res., 16, 1299–1309.CrossrefGoogle Scholar

Fullwood, M. J., M. H. Liu, Y. F. Pan, J. Liu, H. Xu, Y. B. Mohamed, Y. L. Orlov, S. Velkov, A. Ho, P. H. Mei, E. G. Chew, P. Y. Huang, W. J. Welboren, Y. Han, H. S. Ooi, P. N. Ariyaratne, V. B. Vega, Y. Luo, P. Y. Tan, P. Y. Choy, K. D. Wansa, B. Zhao, K. S. Lim, S. C. Leow, J. S. Yow, R. Joseph, H. Li, K. V. Desai, J. S. Thomsen, Y. K. Lee, R. K. Karuturi, T. Herve, G. Bourque, H. G. Stunnenberg, X. Ruan, V. Cacheux-Rataboul, W. K. Sung, E. T. Liu, C. L. Wei, E. Cheung and Y. Ruan (2009): “An oestrogen-receptor-alpha-bound human chromatin interactome,” Nature, 462, 58–64.Web of SciencePubMedCrossrefGoogle Scholar

Gelman, A. and D. B. Rubin (1992): “Inference from iterative simulation using multiple sequences,” Stat. Sci., 7, 457–472.Google Scholar

Horike, S.-i., S. Cai, M. Miyano, J.-F. F. Cheng and T. Kohwi-Shigematsu (2005): “Loss of silent-chromatin looping and impaired imprinting of dlx5 in rett syndrome,” Nat. Genet., 37, 31–40.Google Scholar

Jia, L., B. P. Berman, U. Jariwala, X. Yan, J. P. Cogan, A. Walters, T. Chen, G. Buchanan, B. Frenkel and G. A. Coetzee (2008): “Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity,” PLoS One, 3, e3645.Google Scholar

Jiang, H. and W. H. Wong (2009): “Statistical inferences for isoform expression in rna-seq,” Bioinformatics, 25, 1026–1032.Web of ScienceCrossrefPubMedGoogle Scholar

Karolchik, D., G. P. Barber, J. Casper, H. Clawson, M. S. Cline, M. Diekhans, T. R. Dreszer, P. A. Fujita, L. Guruvadoo, M. Haeussler, R. A. Harte, S. Heitner, A. S. Hinrichs, K. Learned, B. T. Lee, C. H. Li, B. J. Raney, B. Rhead, K. R. Rosenbloom, C. A. Sloan, M. L. Speir, A. S. Zweig, D. Haussler, R. M. Kuhn and W. J. Kent. (2014): “The ucsc genome browser database: 2014 update,” Nucleic Acids Res., 42, D764–D770.CrossrefGoogle Scholar

Labhart, P., S. Karmakar, E. M. Salicru, B. S. Egan, V. Alexiadis, B. W. O’Malley and C. L. Smith (2005): “Identification of target genes in breast cancer cells directly regulated by the src-3/aib1 coactivator,” Proc. Natl. Acad. Sci. USA, 102, 1339–1344.CrossrefGoogle Scholar

Li, G., M. J. Fullwood, H. Xu, F. H. H. Mulawadi, S. Velkov, V. Vega, P. N. N. Ariyaratne, Y. B. B. Mohamed, H.-S. S. Ooi, C. Tennakoon, C.-L. L. Wei, Y. Ruan and W.-K. K. Sung (2010): “Chia-pet tool for comprehensive chromatin interaction analysis with paired-end tag sequencing,” Genome Biol., 11, R22+.CrossrefWeb of ScienceGoogle Scholar

Lieberman-Aiden, E., N. L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B. R. Lajoie, P. J. Sabo, M. O. Dorschner, R. Sandstrom, B. Bernstein, M. A. Bender, M. Groudine, A. Gnirke, J. Stamatoyannopoulos, L. A. Mirny, E. S. Lander and J. Dekker (2009): “Comprehensive mapping of long-range interactions reveals folding principles of the human genome,” Science, 326, 289–293.CrossrefWeb of ScienceGoogle Scholar

Marioni, J. C., C. E. Mason, S. M. Mane, M. Stephens and Y. Gilad (2008): “Rnaseq: an assessment of technical reproducibility and comparison with gene expression arrays,” Genome Res., 18, 1509–1517.CrossrefWeb of SciencePubMedGoogle Scholar

Murrell, A., S. Heeson and W. Reik (2004): “Interaction between differentially methylated regions partitions the imprinted genes igf2 and h19 into parent-specific chromatin loops,” Nat. Genet., 36, 889–893.Google Scholar

Parisi, F., B. Sonderegger, P. Wirapati, M. Delorenzi and F. Naef (2009): “Relationship between estrogen receptor α location and gene induction reveals the importance of downstream sites and cofactors,” BMC Genom., 10, 381.CrossrefGoogle Scholar

Pruitt, K. D., G. R. Brown, S. M. Hiatt, F. Thibaud-Nissen, A. Astashyn, O. Ermolaeva, C. M. Farrell, J. Hart, M. J. Landrum, K. M. McGarvey, M. R. Murphy, N. A. O’Leary, S. Pujar, B. Rajput, S. H. Rangwala, L. D. Riddick, A. Shkeda, H. Sun, P. Tamez, R. E. Tully, C. Wallin, D. Webb, J. Weber, W. Wu, M. DiCuccio, P. Kitts, D. R. Maglott, T. D. Murphy and J. M. Ostell (2014): “Refseq: an update on mammalian reference sequences,” Nucleic Acids Res., 42, D756–D763.Web of ScienceCrossrefGoogle Scholar

Raftery, A. E. and S. M. Lewis (1995): The number of iterations, convergence diagnostics and generic metropolis algorithms. In: Gilks, W. R., Spiegelhalter, D. J. and Richardson S. (Eds.), Practical Markov Chain Monte Carlo, Chapman and Hall, pp. 115–130.Google Scholar

Robinson, M. D., D. J. McCarthy and G. K. Smyth (2010): “Edger: a bioconductor package for differential expression analysis of digital gene expression data,” Bioinformatics, 26, 139–140.CrossrefPubMedGoogle Scholar

Rousseau, M., J. Fraser, M. Ferraiuolo, J. Dostie and M. Blanchette (2011): “Three-dimensional modeling of chromatin structure from interaction frequency data using markov chain monte carlo sampling,” BMC Bioinform., 12, 414.CrossrefGoogle Scholar

Simonis, M., P. Klous, E. Splinter, Y. Moshkin, R. Willemsen, E. de Wit, B. van Steensel and W. de Laat (2006): “Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4c),” Nat. Genet., 38, 1348–1354.Google Scholar

Spilianakis, C. G. and R. A. Flavell (2004): “Long-range intrachromosomal interactions in the t helper type 2 cytokine locus,” Nat. Immunol., 5, 1017–1027.Google Scholar

Srivastava, S. and L. Chen (2010): “A two-parameter generalized poisson model to improve the analysis of rna-seq data,” Nucleic Acids Res., 38, e170–e170.Web of ScienceCrossrefGoogle Scholar

Tolhuis, B., R.-J. Palstra, E. Splinter, F. Grosveld and W. de Laat (2002): “Looping and interaction between hypersensitive sites in the active β-globin locus,” Mol. Cell., 10, 1453–1465.Google Scholar

Vernimmen, D., M. De Gobbi, J. A. Sloane-Stanley, W. G. Wood and D. R. Higgs (2007): “Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression,” The EMBO J., 26, 2041–2051.CrossrefGoogle Scholar

Wang, Q., W. Li, Y. Zhang, X. Yuan, K. Xu, J. Yu, Z. Chen, R. Beroukhim, H. Wang, M. Lupien, T. Wu, M. M. Regan, C. A. Meyer, J. S. Carroll, A. K. K. Manrai, O. A. Jänne, S. P. Balk, R. Mehra, B. Han, A. M. Chinnaiyan, M. A. Rubin, L. True, M. Fiorentino, C. Fiore, M. Loda, P. W. Kantoff, X. S. Liu and M. Brown (2009): “Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer,” Cell, 138, 245–256.Google Scholar

Wright, P. K., F. E. May, S. Darby, R. Saif, T. W. Lennard and B. R. Westley (2009): “Estrogen regulates vesicle trafficking gene expression in eff-3, efm-19 and mcf-7 breast cancer cells,” Int. J. Clin. Exp. Pathol., 2, 463.Google Scholar

Yang, J.-H., J.-H. Li, S. Jiang, H. Zhou and L.-H. Qu (2013): “Chipbase: a database for decoding the transcriptional regulation of long non-coding rna and microrna genes from chip-seq data,” Nucleic Acids Res., 41, D177–D187.CrossrefGoogle Scholar

Yu, J., J. Yu, R.-S. Mani, Q. Cao, C. J. Brenner, X. Cao, X. Wang, L. Wu, J. Li, M. Hu, Y. Gong, H. Cheng, B. Laxman, A. Vellaichamy, S. Shankar, Y. Li, S. M. Dhanasekaran, R. Morey, T. Barrette, R. J. Lonigro, S. A. Tomlins, S. Varambally, Z. S. Qin and A. M. Chinnaiyan (2010): “An integrated network of androgen receptor, polycomb, and tmprss2-erg gene fusions in prostate cancer progression,” Cancer Cell., 17, 443–454.Web of ScienceGoogle Scholar

Zhao, Z., G. Tavoosidana, M. Sjölinder, A. Göndör, P. Mariano, S. Wang, C. Kanduri, M. Lezcano, K. S. S. Sandhu, U. Singh, V. Pant, V. Tiwari, S. Kurukuti and R. Ohlsson (2006): “Circular chromosome conformation capture (4c) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions,” Nat. Genet., 38, 1341–1347.Google Scholar

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