E. P. Consortium, An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, issue.7414, pp.57-74, 2012.

F. Consortium, . Rp, . Clst, A. R. Forrest, H. Kawaji et al., A promoter-level mammalian expression atlas, Nature, vol.507, issue.7493, pp.462-70, 2014.

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.507, issue.7493, pp.455-61, 2014.
DOI : 10.1038/nature12787

URL : http://europepmc.org/articles/pmc5215096?pdf=render

R. Epigenomics, C. Kundaje, A. Meuleman, W. Ernst, J. Bilenky et al., Integrative analysis of 111 reference human epigenomes, Nature, vol.518, issue.7539, pp.317-347, 2015.

L. Ettwiller, B. Paten, M. Ramialison, E. Birney, and J. Wittbrodt, Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation, Nat Methods, vol.4, issue.7, pp.563-568, 2007.
DOI : 10.1038/nmeth1061

Y. Haudry, M. Ramialison, P. B. Wittbrodt, J. Ettwiller, and L. , Using Trawler_ standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation, Nat Protoc, vol.5, issue.2, pp.323-357, 2010.
DOI : 10.1038/nprot.2009.158

O. Corradin and P. C. Scacheri, Enhancer variants: evaluating functions in common disease, Genome medicine, vol.6, issue.10, p.85, 2014.
DOI : 10.1186/s13073-014-0085-3

URL : https://genomemedicine.biomedcentral.com/track/pdf/10.1186/s13073-014-0085-3

F. Spitz and E. E. Furlong, Transcription factors: from enhancer binding to developmental control, Nat Rev Genet, vol.13, issue.9, pp.613-639, 2012.
DOI : 10.1038/nrg3207

D. S. Johnson, A. Mortazavi, R. M. Myers, and B. Wold, Genome-wide mapping of in vivo protein-DNA interactions, Science, vol.316, issue.5830, pp.1497-502, 2007.

B. Van-steensel, J. Delrow, and S. Henikoff, Chromatin profiling using targeted DNA adenine methyltransferase, Nat Genet, vol.27, issue.3, pp.304-312, 2001.

R. Bouveret, A. J. Waardenberg, N. Schonrock, M. Ramialison, T. Doan et al., NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets, elife, vol.6, 2015.

J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, and W. J. Greenleaf, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nat Methods, vol.10, issue.12, pp.1213-1221, 2013.

X. Zhou, D. Li, B. Zhang, R. F. Lowdon, N. B. Rockweiler et al., Epigenomic annotation of genetic variants using the roadmap epigenome browser, Nat Biotechnol, vol.33, issue.4, pp.345-351, 2015.

C. E. Romanoski, C. K. Glass, H. G. Stunnenberg, L. Wilson, and G. Almouzni, Epigenomics: roadmap for regulation, Nature, vol.518, issue.7539, pp.314-320, 2015.

D. M. Budden, D. G. Hurley, and E. J. Crampin, Predictive modelling of gene expression from transcriptional regulatory elements, Brief Bioinform, vol.16, issue.4, pp.616-644, 2015.
DOI : 10.1093/bib/bbu034

URL : https://academic.oup.com/bib/article-pdf/16/4/616/1003334/bbu034.pdf

K. Suryamohan and M. S. Halfon, Identifying transcriptional cis-regulatory modules in animal genomes, Wiley Interdiscip Rev Dev Biol, vol.4, issue.2, pp.59-84, 2015.
DOI : 10.1002/wdev.168

URL : http://europepmc.org/articles/pmc4339228?pdf=render

L. Kuttippurathu, M. Hsing, Y. Liu, B. Schmidt, D. L. Maskell et al., CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments, Bioinformatics, vol.27, issue.5, pp.715-722, 2011.
DOI : 10.1093/bioinformatics/btq707

URL : https://academic.oup.com/bioinformatics/article-pdf/27/5/715/16901759/btq707.pdf

P. Machanick and T. L. Bailey, MEME-ChIP: motif analysis of large DNA datasets, Bioinformatics, vol.27, issue.12, pp.1696-1703, 2011.
DOI : 10.1093/bioinformatics/btr189

URL : https://academic.oup.com/bioinformatics/article-pdf/27/12/1696/17123312/btr189.pdf

A. A. Sharov and M. S. Ko, Exhaustive search for over-represented DNA sequence motifs with CisFinder, DNA Res, vol.16, issue.5, pp.261-73, 2009.
DOI : 10.1093/dnares/dsp014

URL : https://academic.oup.com/dnaresearch/article-pdf/16/5/261/1165499/dsp014.pdf

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 Res, vol.40, issue.4, p.31, 2012.
DOI : 10.1093/nar/gkr1104

URL : https://hal.archives-ouvertes.fr/hal-01624284

F. Zambelli, G. Pesole, and G. Pavesi, PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments, Nucleic Acids Res, vol.41, pp.535-578, 2013.
DOI : 10.1093/nar/gkt448

URL : https://academic.oup.com/nar/article-pdf/41/W1/W535/16943601/gkt448.pdf

J. Zhou and O. G. Troyanskaya, Predicting effects of noncoding variants with deep learning-based sequence model, Nat Methods, vol.12, issue.10, pp.931-935, 2015.

B. Alipanahi, A. Delong, M. T. Weirauch, and B. J. Frey, Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning, Nat Biotech, vol.33, issue.8, pp.831-839, 2015.

E. Afgan, D. Baker, M. Van-den-beek, D. Blankenberg, D. Bouvier et al., The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update, Nucleic Acids Res, vol.44, issue.W1, pp.3-10, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01360125

G. Ambrosini, R. Dreos, S. Kumar, and P. Bucher, The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data, BMC Genomics, vol.17, issue.1, p.938, 2016.

B. L. Aken, S. Ayling, D. Barrell, L. Clarke, V. Curwen et al., The Ensembl gene annotation system, Database (Oxford), 2016.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-843, 2010.

J. D. Fleming, G. Pavesi, P. Benatti, C. Imbriano, R. Mantovani et al., NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growthcontrolling transcription factors, Genome Res, vol.23, issue.8, pp.1195-209, 2013.

T. Vavouri and B. Lehner, Human genes with CpG island promoters have a distinct transcription-associated chromatin organization, Genome Biol, vol.13, issue.11, p.110, 2012.

R. J. Kinsella, A. Kahari, S. Haider, J. Zamora, G. Proctor et al., Ensembl BioMarts: a hub for data retrieval across taxonomic space, Database (Oxford), p.30, 2011.

M. A. Hume, L. A. Barrera, S. S. Gisselbrecht, and M. L. Bulyk, UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions, Nucleic Acids Res, vol.43, pp.117-139, 2015.

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 Res, vol.42, pp.142-149, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00943558

I. V. Kulakovskiy, Y. A. Medvedeva, U. Schaefer, A. S. Kasianov, I. E. Vorontsov et al., HOCOMOCO: a comprehensive collection of human transcription factor binding sites models, Nucleic Acids Res, vol.41, pp.195-202, 2013.

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, issue.D1, pp.116-141, 2016.

W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle et al., The human genome browser at UCSC, Genome Res, vol.12, issue.6, pp.996-1006, 2002.

M. Thomas-chollier, E. Darbo, C. Herrmann, M. Defrance, D. Thieffry et al., A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs, Nat Protoc, vol.7, issue.8, pp.1551-68, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01624286

T. L. Bailey, DREME: motif discovery in transcription factor ChIP-seq data, Bioinformatics, vol.27, issue.12, pp.1653-1662, 2011.

C. T. Harbison, D. B. Gordon, T. I. Lee, N. J. Rinaldi, K. D. Macisaac et al., Transcriptional regulatory code of a eukaryotic genome, Nature, vol.431, issue.7004, pp.99-104, 2004.

S. Mahony and P. V. Benos, STAMP: a web tool for exploring DNA-binding motif similarities, Nucleic Acids Res, vol.35, pp.253-261, 2007.

R. Sulahian, J. Chen, Z. Arany, U. Jadhav, S. Peng et al., SOX15 governs transcription in human stratified epithelia and a subset of esophageal adenocarcinomas, Cell Mol Gastroenterol Hepatol, vol.1, issue.6, pp.598-609, 2015.

A. Woolfe, M. Goodson, D. K. Goode, P. Snell, G. K. Mcewen et al., Highly conserved non-coding sequences are associated with vertebrate development, PLoS Biol, vol.3, issue.1, p.7, 2005.

W. J. Kent, A. S. Zweig, G. Barber, A. S. Hinrichs, and D. Karolchik, BigWig and BigBed: enabling browsing of large distributed datasets, Bioinformatics, vol.26, issue.17, pp.2204-2211, 2010.

P. S. Linsley, J. Schelter, J. Burchard, M. Kibukawa, M. M. Martin et al., Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression, Mol Cell Biol, vol.27, issue.6, pp.2240-52, 2007.

J. Konig, K. Zarnack, N. M. Luscombe, and J. Ule, Protein-RNA interactions: new genomic technologies and perspectives, Nat Rev Genet, vol.13, issue.2, pp.77-83, 2012.

M. Ramialison, R. Reinhardt, T. Henrich, B. Wittbrodt, T. Kellner et al., Cis-regulatory properties of medaka synexpression groups, Development, vol.139, issue.5, pp.917-945, 2012.

T. Houles, G. Rodier, L. Cam, L. Sardet, C. Kirsh et al., Description of an optimized ChIP-seq analysis pipeline dedicated to genome wide identification of E4F1 binding sites in primary and transformed MEFs, Genom Data, vol.5, pp.368-70, 2015.

W. Huang, P. Perez-garcia, A. Pokhilko, A. J. Millar, I. Antoshechkin et al., Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator, Science, vol.336, issue.6077, pp.75-84, 2012.

L. Skalska, R. Stojnic, J. Li, B. Fischer, G. Cerda-moya et al., Chromatin signatures at notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation, EMBO J, vol.34, issue.14, pp.1889-904, 2015.

C. L. Winata, I. Kondrychyn, V. Kumar, K. G. Srinivasan, Y. Orlov et al., Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish, PLoS Genet, vol.9, issue.10, p.1003852, 2013.