C. Myc, /. Max, J. A. Bilmes, and E. Birney, Integrative annotation of chromatin elements from ENCODE data, GSE29073.GATA3.mcf7_e2 GSE26831.FOXA1.mcf7_e2 GSE40129.GATA3.mcf7_e2 GSE40129.ESR1.mcf7_e2 GSE25021.ESR1.mcf7_e2 GSE41561.ESR1.mcf7 GSE40129.ESR1.mcf7_gatakd_e2 GSE25021.ESR1.mcf7_untreat GSE41561.ESR1.mcf7_xeno GSE21770.ESR2.u2os_notreated GSE21770.ESR2.u2os_e2 GSE25710.ESR1, pp.827-841, 2013.

N. Negre, C. D. Brown, L. Ma, C. A. Bristow, S. W. Miller et al., A cis-regulatory map of the Drosophila genome, Nature, vol.20, issue.7339, pp.527-531, 2011.
DOI : 10.1038/nature09990

Y. Shen, F. Yue, D. F. Mccleary, Z. Ye, L. Edsall et al., A map of the cis-regulatory sequences in the mouse genome, Nature, vol.6, issue.7409, pp.116-120, 2012.
DOI : 10.1038/nature11243

S. Neph, J. Vierstra, A. B. Stergachis, A. P. Reynolds, E. Haugen et al., An expansive human regulatory lexicon encoded in transcription factor footprints, Nature, vol.3, issue.7414, pp.83-90, 2012.
DOI : 10.1038/nature11212

D. Hnisz, B. J. Abraham, T. I. Lee, A. Lau, V. Saint-andré et al., Super-Enhancers in the Control of Cell Identity and Disease, Cell, vol.155, issue.4, pp.934-947, 2013.
DOI : 10.1016/j.cell.2013.09.053

B. Chapuy, M. R. Mckeown, C. Y. Lin, S. Monti, M. G. Roemer et al., Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma, Cancer Cell, vol.24, issue.6, pp.777-790, 2013.
DOI : 10.1016/j.ccr.2013.11.003

R. Andersson, C. Gebhard, I. Miguel-escalada, I. Hoof, J. Bornholdt et al., An atlas of active enhancers across human cell types and tissues, Nature, vol.45, issue.7493, pp.455-461, 2014.
DOI : 10.1093/bioinformatics/btq033

T. Liu, J. A. Ortiz, L. Taing, C. A. Meyer, B. Lee et al., Cistrome: an integrative platform for transcriptional regulation studies, Genome Biology, vol.12, issue.8, p.83, 2011.
DOI : 10.1101/gr.115519.110
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245621

G. K. Marinov, A. Kundaje, P. J. Park, and B. J. Wold, Large-Scale Quality Analysis of Published ChIP-seq Data, G3 (Bethesda), pp.209-223, 2014.
DOI : 10.1534/g3.113.008680

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381

Y. Zhang, T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson et al., Model-based Analysis of ChIP-Seq (MACS), Genome Biology, vol.9, issue.9, p.137, 2008.
DOI : 10.1186/gb-2008-9-9-r137

M. Salmon-divon, H. Dvinge, K. Tammoja, and P. Bertone, PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci, BMC Bioinformatics, vol.11, issue.1, p.415, 2010.
DOI : 10.1186/1471-2105-11-415

S. G. Landt, G. K. Marinov, A. Kundaje, P. Kheradpour, F. Pauli et al., ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia, Genome Research, vol.22, issue.9, pp.1813-1831, 2012.
DOI : 10.1101/gr.136184.111

P. V. Kharchenko, M. Y. Tolstorukov, and P. J. Park, Design and analysis of ChIP-seq experiments for DNA-binding proteins, Nature Biotechnology, vol.26, issue.12, pp.1351-1359, 2008.
DOI : 10.1016/S0167-9473(99)00100-0

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-842, 2010.
DOI : 10.1093/bioinformatics/btq033

H. Shin, T. Liu, A. K. Manrai, and X. S. Liu, CEAS: cis-regulatory element annotation system, Bioinformatics, vol.25, issue.19, pp.2605-2606, 2009.
DOI : 10.1093/bioinformatics/btp479
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2605

M. Thomas-chollier, C. Herrmann, M. Defrance, O. Sand, D. Thieffry et al., RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets, Nucleic Acids Research, vol.40, issue.4, p.31, 2012.
DOI : 10.1093/nar/gkr1104

J. Wang, J. Zhuang, S. Iyer, X. Lin, M. C. Greven et al., Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium, Nucleic Acids Research, vol.41, issue.D1, pp.171-176, 2013.
DOI : 10.1093/nar/gks1221

A. Mathelier, X. Zhao, A. W. Zhang, F. Parcy, R. Worsley-hunt et al., JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles, Nucleic Acids Research, vol.42, issue.D1, pp.142-147, 2014.
DOI : 10.1093/nar/gkt997
URL : https://hal.archives-ouvertes.fr/hal-00943558

P. Flicek, B. L. Aken, B. Ballester, K. Beal, E. Bragin et al., Ensembl's 10th year, Nucleic Acids Research, vol.38, issue.Database, pp.557-562, 2010.
DOI : 10.1093/nar/gkp972
URL : http://doi.org/10.1093/nar/gkp972

G. M. Cooper, E. A. Stone, G. Asimenos, E. D. Green, S. Batzoglou et al., Distribution and intensity of constraint in mammalian genomic sequence, Genome Research, vol.15, issue.7, pp.901-913, 2005.
DOI : 10.1101/gr.3577405

M. D. Chikina and O. G. Troyanskaya, An effective statistical evaluation of ChIPseq dataset similarity, Bioinformatics, vol.28, issue.5, pp.607-613, 2012.
DOI : 10.1093/bioinformatics/bts009

M. Bastian, S. Heymann, and M. Jacomy, Gephi: an open source software for exploring and manipulating networks, Intl. AAAI Conf. Weblogs Social Media, 2009.

V. D. Blondel, J. Guillaume, R. Lambiotte, and E. Lefebvre, Fast unfolding of communities in large networks, Journal of Statistical Mechanics: Theory and Experiment, vol.2008, issue.10, p.10008, 2008.
DOI : 10.1088/1742-5468/2008/10/P10008
URL : https://hal.archives-ouvertes.fr/hal-01146070

B. Akhtar-zaidi, R. Cowper-sal-lari, O. Corradin, A. Saiakhova, C. F. Bartels et al., Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer, Science, vol.336, issue.6082, pp.736-739, 2012.
DOI : 10.1126/science.1217277

M. K. Choe, C. Hong, J. Park, S. H. Seo, and T. Roh, Functional elements demarcated by histone modifications in breast cancer cells, Biochemical and Biophysical Research Communications, vol.418, issue.3, pp.475-482, 2012.
DOI : 10.1016/j.bbrc.2012.01.042

T. Barrett, D. B. Troup, S. E. Wilhite, P. Ledoux, D. Rudnev et al., NCBI GEO: mining tens of millions of expression profiles--database and tools update, Nucleic Acids Research, vol.35, issue.Database, pp.760-765, 2007.
DOI : 10.1093/nar/gkl887

H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson et al., ArrayExpress--a public database of microarray experiments and gene expression profiles, Nucleic Acids Research, vol.35, issue.Database, pp.747-750, 2007.
DOI : 10.1093/nar/gkl995

S. Cuddapah, R. Jothi, D. E. Schones, T. Roh, K. Cui et al., Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains, Genome Research, vol.19, issue.1, pp.24-32, 2009.
DOI : 10.1101/gr.082800.108

N. D. Heintzman, G. C. Hon, R. D. Hawkins, P. Kheradpour, A. Stark et al., Histone modifications at human enhancers reflect global cell-type-specific gene expression, Nature, vol.17, issue.7243, pp.108-112, 2009.
DOI : 10.1038/nature07829
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910248

C. Moorman, L. V. Sun, J. Wang, E. De-wit, W. Talhout et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster, Proceedings of the National Academy of Sciences, vol.103, issue.32, pp.12027-12032, 2006.
DOI : 10.1073/pnas.0605003103

J. W. Foley and A. Sidow, Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines, BMC Genomics, vol.14, issue.1, p.720, 2013.
DOI : 10.1093/bioinformatics/14.1.48

B. Lee, A. A. Bhinge, A. Battenhouse, Z. Liu, R. M. Mcdaniell et al., Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells, Genome Research, vol.22, issue.1, pp.9-24, 2011.
DOI : 10.1101/gr.127597.111

D. Xie, A. P. Boyle, L. Wu, J. Zhai, T. Kawli et al., Dynamic trans-Acting Factor Colocalization in Human Cells, Cell, vol.155, issue.3, pp.713-724, 2013.
DOI : 10.1016/j.cell.2013.09.043

D. Vlieghe, A. Sandelin, P. J. Bleser, K. Vleminckx, W. W. Wasserman et al., A new generation of JASPAR, the open-access repository for transcription factor binding site profiles, Nucleic Acids Research, vol.34, issue.90001, pp.95-97, 2006.
DOI : 10.1093/nar/gkj115

D. Schmidt, M. D. Wilson, B. Ballester, P. C. Schwalie, G. D. Brown et al., Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding, Science, vol.328, issue.5981, pp.1036-1040, 2010.
DOI : 10.1126/science.1186176

E. P. Consortium, A user's guide to the encyclopedia of DNA elements (ENCODE), PLoS Biol, vol.9, p.1001046, 2011.

M. Kazemian, H. Pham, S. A. Wolfe, M. H. Brodsky, and S. Sinha, Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development, Nucleic Acids Research, vol.41, issue.17, pp.8237-8252, 2013.
DOI : 10.1093/nar/gkt598

Q. Cheng, M. Kazemian, H. Pham, C. Blatti, S. E. Celniker et al., Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy, PLoS Genetics, vol.456, issue.8, p.1003571, 2013.
DOI : 10.1371/journal.pgen.1003571.s031

M. B. Gerstein, A. Kundaje, M. Hariharan, S. G. Landt, K. Yan et al., Architecture of the human regulatory network derived from ENCODE data, Nature, vol.107, issue.7414, pp.91-100, 2012.
DOI : 10.1038/nature11245

J. Wang, J. Zhuang, S. Iyer, X. Lin, T. W. Whitfield et al., Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors, Genome Research, vol.22, issue.9, pp.1798-1812, 2012.
DOI : 10.1101/gr.139105.112

J. M. Vaquerizas, S. K. Kummerfeld, S. A. Teichmann, and N. M. Luscombe, A census of human transcription factors: function, expression and evolution, Nature Reviews Genetics, vol.455, issue.4, pp.252-263, 2009.
DOI : 10.1038/nrg2538

S. M. Hawkins, H. A. Loomans, Y. Wan, T. Ghosh-choudhury, D. Coffey et al., Expression and Functional Pathway Analysis of Nuclear Receptor NR2F2 in Ovarian Cancer, The Journal of Clinical Endocrinology & Metabolism, vol.98, issue.7, pp.1152-1162, 2013.
DOI : 10.1210/jc.2013-1081

X. Su, D. Chakravarti, M. S. Cho, L. Liu, Y. J. Gi et al., TAp63 suppresses metastasis through coordinate regulation of Dicer and miRNAs, Nature, vol.5, issue.7318, pp.986-990, 2010.
DOI : 10.1038/nature09459

C. Schaab, T. Geiger, G. Stoehr, J. Cox, and M. Mann, Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database, Molecular & Cellular Proteomics, vol.11, issue.3, pp.111-014068, 2012.
DOI : 10.1074/mcp.M111.014068

W. Tang, M. Dodge, D. Gundapaneni, C. Michnoff, M. Roth et al., A genome-wide RNAi screen for Wnt/??-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer, Proceedings of the National Academy of Sciences, vol.105, issue.28, pp.9697-9702, 2008.
DOI : 10.1073/pnas.0804709105

M. L. Slattery, A. R. Folsom, R. Wolff, J. Herrick, B. J. Caan et al., Transcription Factor 7-like 2 Polymorphism and Colon Cancer, Cancer Epidemiology Biomarkers & Prevention, vol.17, issue.4, pp.978-982, 2008.
DOI : 10.1158/1055-9965.EPI-07-2687
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587179

E. Shaulian and M. Karin, AP-1 as a regulator of cell life and death, Nature Cell Biology, vol.4, issue.5, pp.131-136, 2002.
DOI : 10.1038/ncb0502-e131

L. Teng, B. He, P. Gao, L. Gao, and K. Tan, Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets, Nucleic Acids Research, vol.42, issue.4, pp.1105-1129, 2013.
DOI : 10.1093/nar/gkt1105

J. Ernst and M. Kellis, Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types, Genome Research, vol.23, issue.7, 2013.
DOI : 10.1101/gr.144840.112

M. Mendoza-parra, W. Van-gool, M. Saleem, M. A. Ceschin, D. G. Gronemeyer et al., A quality control system for profiles obtained by ChIP sequencing, Nucleic Acids Research, vol.41, issue.21, p.196, 2013.
DOI : 10.1093/nar/gkt829

E. Khurana, Y. Fu, V. Colonna, X. J. Mu, H. M. Kang et al., Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics, Science, vol.342, issue.6154, pp.342-1235587, 2013.
DOI : 10.1126/science.1235587

G. R. Ritchie, I. Dunham, E. Zeggini, and P. Flicek, Functional annotation of noncoding sequence variants, Nature Methods, vol.12, issue.3, pp.294-296, 2014.
DOI : 10.1093/bioinformatics/btq330

W. A. Whyte, D. A. Orlando, D. Hnisz, B. J. Abraham, C. Y. Lin et al., Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes, Cell, vol.153, issue.2, pp.307-319, 2013.
DOI : 10.1016/j.cell.2013.03.035

J. Lovén, H. A. Hoke, C. Y. Lin, A. Lau, D. A. Orlando et al., Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers, Cell, vol.153, issue.2, pp.320-334, 2013.
DOI : 10.1016/j.cell.2013.03.036

Z. Zhao, G. Tavoosidana, M. Sjölindersj¨sjölinder, A. Ondörond¨ondör, P. Mariano et al., Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions, Nature Genetics, vol.8, issue.11, pp.1341-1347, 2006.
DOI : 10.1038/ng1891

F. Jin, Y. Li, J. R. Dixon, S. Selvaraj, Z. Ye et al., A high-resolution map of the three-dimensional chromatin interactome in human cells, Nature, vol.2, pp.290-294, 2013.
DOI : 10.1038/nature12644

G. Li, X. Ruan, R. K. Auerbach, K. S. Sandhu, M. Zheng et al., Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation, Cell, vol.148, issue.1-2, pp.84-98, 2012.
DOI : 10.1016/j.cell.2011.12.014

Y. Zhang, C. Wong, R. Y. Birnbaum, G. Li, R. Favaro et al., Chromatin connectivity maps reveal dynamic promoter???enhancer long-range associations, Nature, vol.15, issue.7479, pp.306-310, 2013.
DOI : 10.1038/nature12716
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954713