D. S. Johnson, A. Mortazavi, R. M. Myers, and B. Wold, Genome-wide mapping of in vivo protein-DNA interactions, Science, vol.316, pp.1497-1502, 2007.

H. S. Rhee and B. F. Pugh, Comprehensive Genome-wide Protein-DNA interactions detected at single nucleotide resolution, Cell, vol.147, pp.1408-1419, 2011.

A. Bartlett, R. C. O'malley, S. C. Huang, M. Galli, J. R. Nery et al., Mapping genome-wide transcription-factor binding sites using DAP-seq, Nat. Protoc, vol.12, pp.1659-1672, 2017.

A. Griffon, Q. Barbier, J. Dalino, J. Van-helden, S. Spicuglia et al., Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape, Nucleic Acids Res, vol.43, p.27, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01219379

T. Barrett, S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim et al., NCBI GEO: archive for functional genomics data sets--update, Nucleic Acids Res, vol.41, pp.991-995, 2012.

. Encode-project-consortium, An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, pp.57-74, 2012.

C. A. Davis, B. C. Hitz, C. A. Sloan, E. T. Chan, J. M. Davidson et al., The Encyclopedia of DNA elements (ENCODE): data portal update, Nucleic Acids Res, vol.46, pp.794-801, 2018.

J. Chèneby, M. Gheorghe, M. Artufel, A. Mathelier, and B. Ballester, ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments, Nucleic Acids Res, vol.46, pp.267-275, 2018.

B. Braschi, P. Denny, K. Gray, T. Jones, R. Seal et al., Genenames.org: the HGNC and VGNC resources in 2019, Nucleic Acids Res, vol.47, pp.786-792, 2019.

A. Chang, I. Schomburg, S. Placzek, L. Jeske, M. Ulbrich et al., BRENDA in 2015: exciting developments in its 25th year of existence, Nucleic Acids Res, vol.43, pp.439-446, 2015.

A. Bairoch, The Cellosaurus, a cell-line knowledge resource, J. Biomol. Tech. JBT, vol.29, pp.25-38, 2018.

P. J. Kersey, J. E. Allen, A. Allot, M. Barba, S. Boddu et al.,

, Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species, Nucleic Acids Res, vol.46, pp.802-808

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Genome Project Data Processing Subgroup, vol.25, pp.2078-2079, 1000.

Y. Zhang, T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson et al., Model-based analysis of ChIP-Seq (MACS), 2008.

, Genome Biol, vol.9, p.137

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 Res, vol.22, pp.1813-1831, 2012.

A. R. Quinlan, BEDTools: The Swiss-army tool for genome feature analysis, Curr. Protoc. Bioinforma, vol.47, 2014.

M. A. Mendoza-parra, M. M. Saleem, M. Blum, P. Cholley, and H. Gronemeyer, NGS-QC Generator: A quality control system for ChIP-Seq and related deep sequencing-generated datasets, Methods Mol. Biol, vol.1418, pp.243-265, 2016.

G. K. Marinov, A. Kundaje, P. J. Park, and B. J. Wold, Large-scale quality analysis of published ChIP-seq data, vol.3, pp.209-223, 2014.

D. Chen, W. Yan, L. Fu, and K. Kaufmann, Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana, Nat. Commun, vol.9, p.4534, 2018.

A. J. Bannister and T. Kouzarides, Regulation of chromatin by histone modifications, Cell Res, vol.21, pp.381-395, 2011.

S. Venkatesh and J. L. Workman, Histone exchange, chromatin structure and the regulation of transcription, Nat. Rev. Mol. Cell Biol, vol.16, pp.178-189, 2015.

T. Kouzarides, Chromatin modifications and their function, Cell, vol.128, pp.693-705, 2007.

. Roadmap-epigenomics-consortium, A. Kundaje, W. Meuleman, J. Ernst, M. Bilenky et al., Integrative analysis of 111 reference human epigenomes, Nature, vol.518, pp.317-330, 2015.

F. Cunningham, P. Achuthan, W. Akanni, J. Allen, M. R. Amode et al., Nucleic Acids Res, vol.47, pp.745-751, 2019.

M. Haeussler, A. S. Zweig, C. Tyner, M. L. Speir, K. R. Rosenbloom et al.,

, The UCSC Genome Browser database: 2019 update, Nucleic Acids Res, vol.47, pp.853-858

B. J. Raney, T. R. Dreszer, G. P. Barber, H. Clawson, P. A. Fujita et al., Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser, Bioinformatics, vol.30, pp.1003-1005, 2014.

O. Fornes, J. A. Castro-mondragon, A. Khan, R. Lee, . Van-der et al., JASPAR 2020: update of the open-access database of transcription factor binding profiles, Nucleic Acids Res, 2019.