H. Zhang, H. Chen, W. Liu, H. Liu, J. Gong et al., AnimalTFDB: a comprehensive animal transcription factor database, Nucleic Acids Res, vol.40, pp.144-153, 2012.
DOI : 10.1093/nar/gkr965
URL : https://academic.oup.com/nar/article-pdf/40/D1/D144/9483221/gkr965.pdf

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.489, pp.91-100, 2012.

D. Santiago-algarra, L. Dao, L. Pradel, A. España, and S. Spicuglia, Recent advances in high-throughput approaches to dissect enhancer function, F1000Research, vol.6, p.939, 2017.
DOI : 10.12688/f1000research.11581.1
URL : https://hal.archives-ouvertes.fr/hal-01612096

S. R. Grossman, X. Zhang, L. Wang, J. Engreitz, A. Melnikov et al., Systematic dissection of genomic features determining transcription factor binding and enhancer function, Proc Natl Acad Sci U S A, vol.114, pp.1291-300, 2017.
DOI : 10.1073/pnas.1621150114
URL : https://www.pnas.org/content/pnas/114/7/E1291.full.pdf

S. Weingarten-gabbay and E. Segal, The grammar of transcriptional regulation, Hum Genet, vol.133, pp.701-712, 2014.

E. R. Weikum, M. T. Knuesel, E. A. Ortlund, and K. R. Yamamoto, Glucocorticoid receptor control of transcription: precision and plasticity via allostery, Nat Rev Mol Cell Biol, vol.18, pp.159-74, 2017.
DOI : 10.1038/nrm.2016.152
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6257982

M. Boergesen, T. Å. Pedersen, B. Gross, S. J. Van-heeringen, D. Hagenbeek et al., Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor ? in mouse liver reveals extensive sharing of binding sites, Mol Cell Biol, vol.32, pp.852-67, 2012.

S. Heinz, C. E. Romanoski, C. Benner, K. A. Allison, M. U. Kaikkonen et al., Effect of natural genetic variation on enhancer selection and function, Nature, vol.503, pp.487-92, 2013.

T. Pham, J. Minderjahn, C. Schmidl, H. Hoffmeister, S. Schmidhofer et al., Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1, Nucleic Acids Res, vol.41, pp.6391-402, 2013.

L. Magnani, J. Eeckhoute, and M. Lupien, Pioneer factors: directing transcriptional regulators within the chromatin environment, Trends Genet, vol.27, pp.465-74, 2011.
DOI : 10.1016/j.tig.2011.07.002

K. S. Zaret and J. S. Carroll, Pioneer transcription factors: establishing competence for gene expression, Genes Dev, vol.25, pp.2227-2268, 2011.
DOI : 10.1101/gad.176826.111
URL : http://genesdev.cshlp.org/content/25/21/2227.full.pdf

T. E. Reddy, J. Gertz, F. Pauli, K. S. Kucera, K. E. Varley et al., Effects of sequence variation on differential allelic transcription factor occupancy and gene expression, Genome Res, vol.22, pp.860-869, 2012.

K. Stefflova, D. Thybert, M. D. Wilson, I. Streeter, J. Aleksic et al., Cooperativity and rapid evolution of cobound transcription factors in closely related mammals, Cell, vol.154, pp.530-570, 2013.
DOI : 10.1016/j.cell.2013.07.007
URL : https://doi.org/10.1016/j.cell.2013.07.007

J. Roe, C. Hwang, T. Somerville, J. P. Milazzo, E. J. Lee et al., Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis, Cell, vol.170, pp.875-888, 2017.
DOI : 10.1016/j.cell.2017.07.007
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726277

L. A. Barrera, A. Vedenko, J. V. Kurland, J. M. Rogers, S. S. Gisselbrecht et al., Survey of variation in human transcription factors reveals prevalent DNA binding changes, Science, vol.351, pp.1450-1454, 2016.

M. T. Maurano, E. Haugen, R. Sandstrom, J. Vierstra, A. Shafer et al., Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo, Nat Genet, vol.47, pp.1393-401, 2015.

S. Zhou, A. E. Treloar, and M. Lupien, Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations, Cancer Discov, vol.6, pp.1215-1244, 2016.

J. Dubois-chevalier, V. Dubois, H. Dehondt, P. Mazrooei, C. Mazuy et al., The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions

, Genome Res, vol.27, pp.985-96, 2017.

Y. Guo and D. K. Gifford, Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding, BMC Genomics, vol.18, p.45, 2017.
DOI : 10.1101/027953
URL : https://www.biorxiv.org/content/biorxiv/early/2015/09/30/027953.full.pdf

R. Cowper-sal-lari, X. Zhang, J. B. Wright, S. D. Bailey, M. D. Cole et al., Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression, Nat Genet, vol.44, pp.1191-1199, 2012.

S. D. Bailey, K. Desai, K. J. Kron, P. Mazrooei, N. A. Sinnott-armstrong et al., Noncoding somatic and inherited singlenucleotide variants converge to promote ESR1 expression in breast cancer, Nat Genet, vol.48, pp.1260-1266, 2016.
DOI : 10.1038/ng.3650
URL : http://europepmc.org/articles/pmc5042848?pdf=render

I. E. Vorontsov, I. V. Kulakovskiy, G. Khimulya, D. D. Nikolaeva, and V. J. Makeev, PERFECTOS-APE -Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation, pp.102-110, 2017.

A. Soufi, G. Donahue, and K. S. Zaret, Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome, Cell, vol.151, pp.994-1004, 2012.

E. E. Swinstead, T. B. Miranda, V. Paakinaho, S. Baek, I. Goldstein et al., Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions, Cell, vol.165, pp.593-605, 2016.
DOI : 10.1016/j.cell.2016.02.067
URL : https://doi.org/10.1016/j.cell.2016.02.067

A. Isakova, R. Groux, M. Imbeault, P. Rainer, D. Alpern et al., SMiLE-seq identifies binding motifs of single and dimeric transcription factors, Nat Methods, vol.14, pp.316-338, 2017.
DOI : 10.1038/nmeth.4143

A. Jolma, Y. Yin, K. Nitta, D. K. Popov, A. Taipale et al., DNA-dependent formation of transcription factor pairs alters their binding specificity, Nature, vol.527, pp.384-392, 2015.
DOI : 10.1038/nature15518

S. Neph, J. Vierstra, A. Stergachis, A. Reynolds, E. Haugen et al., An expansive human regulatory lexicon encoded in transcription factor footprints, Nature, vol.489, pp.83-90, 2012.
DOI : 10.1038/nature11212
URL : https://www.nature.com/articles/nature11212.pdf

W. De-laat and D. Duboule, Topology of mammalian developmental enhancers and their regulatory landscapes, Nature, vol.502, pp.499-506, 2013.

X. Liu, Y. Zhang, Y. Chen, M. Li, F. Zhou et al., Situ Capture of Chromatin Interactions by Biotinylated dCas9, vol.170, pp.1028-1043, 2017.
DOI : 10.1016/j.cell.2017.08.003

I. V. Kulakovskiy, I. E. Vorontsov, I. S. Yevshin, A. V. Soboleva, A. S. Kasianov et al., HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models, Nucleic Acids Res, vol.44, pp.116-125, 2016.

. R-core-team, R: A language and environment for statistical computing. R Found Stat Comput

G. Warnes, B. Bolker, L. Bonebakker, R. Gentleman, W. Liaw et al., gplots: Various R Programming Tools for Plotting Data

J. A. Castro-mondragon, S. Jaeger, D. Thieffry, M. Thomas-chollier, and J. Van-helden, RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections, Nucleic Acids Res, vol.45, p.119, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01624366

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