B: TAD enrichment within groups of genes whose expression is accurately predicted by our model. The enrichment for each TAD (containing more than 10 genes) in each gene group accurately predicted by our model (i.e. groups with mean error < mean errors of the 1st quartile) was evaluated using an hypergeometric test. The fraction of groups with enriched TADs (pvalue < 0.05) is represented, Trends in genetics: TIG, issue.8, pp.31426-433, 2015. ,
3D genome organization in health and disease: emerging opportunities in cancer translational medicine, Nucleus, vol.950, issue.20, pp.382-393, 2015. ,
DOI : 10.1016/j.cell.2013.12.001
URL : http://europepmc.org/articles/pmc4915485?pdf=render
Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization, Genes, vol.1, issue.3, pp.734-750, 2015. ,
DOI : 10.1073/pnas.0402724101
URL : https://hal.archives-ouvertes.fr/hal-01264317
On TADs and LADs: Spatial Control Over Gene Expression, Trends in Genetics, vol.32, issue.8, p.27312344, 2016. ,
DOI : 10.1016/j.tig.2016.05.004
CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation, Annual Review of Genomics and Human Genetics, vol.17, issue.1, pp.17-43, 2016. ,
DOI : 10.1146/annurev-genom-083115-022339
Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.148, issue.7398, pp.376-380, 2012. ,
DOI : 10.1016/j.cell.2012.01.010
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
Genome-Wide Mapping of in Vivo Protein-DNA Interactions, Science, vol.272, issue.3, pp.1497-1502, 2007. ,
DOI : 10.1074/jbc.272.3.1929
Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins, Cell, vol.147, issue.6, pp.1270-1282, 2011. ,
DOI : 10.1016/j.cell.2011.10.053
URL : https://doi.org/10.1016/j.cell.2011.10.053
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins, Nature Biotechnology, vol.18, issue.7, pp.667-670, 2009. ,
DOI : 10.1126/science.1136800
Applied bioinformatics for the identification of regulatory elements, Nature Reviews Genetics, vol.14, issue.4, pp.276-287, 2004. ,
DOI : 10.1093/bioinformatics/18.9.1272
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man, Cell, vol.140, issue.5, pp.744-752, 2010. ,
DOI : 10.1016/j.cell.2010.01.044
A census of human RNA-binding proteins, Nature Reviews Genetics, vol.7, issue.12, pp.829-845, 2014. ,
DOI : 10.1038/nrm1964
An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, issue.7414, pp.57-74, 2012. ,
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data, Genome Biology, vol.16, issue.Suppl 1, pp.82-27139377, 2016. ,
DOI : 10.1038/nrg2905
URL : http://doi.org/10.1186/s13059-016-0925-0
Understanding transcriptional regulation by integrative analysis of transcription factor binding data, Genome Research, vol.22, issue.9, pp.1658-1667, 2012. ,
DOI : 10.1101/gr.136838.111
Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia, PLoS Computational Biology, vol.30, issue.10, pp.1003908-25340776, 2014. ,
DOI : 10.1371/journal.pcbi.1003908.s008
Inference of transcriptional regulation in cancers, Proceedings of the National Academy of Sciences, vol.2012, issue.7415, pp.7731-7736, 2015. ,
DOI : 10.1007/978-1-4614-7138-7
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction, Nucleic Acids Research, vol.217, issue.1, pp.54-66, 2017. ,
DOI : 10.1186/gb-2008-9-9-r137
URL : https://academic.oup.com/nar/article-pdf/45/1/54/9249383/gkw1061.pdf
Do short, frequent DNA sequence motifs mould the epigenome?, Nature Reviews Molecular Cell Biology, vol.480, issue.4, pp.257-262, 2016. ,
DOI : 10.1093/nar/gku1305
Identification of Genetic Variants That Affect Histone Modifications in Human Cells, Science, vol.9, issue.4, pp.747-749, 2013. ,
DOI : 10.1371/journal.pgen.1003486
Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription, Science, vol.10, issue.21, pp.744-747, 2013. ,
DOI : 10.1101/gad.10.21.2657
Extensive Variation in Chromatin States Across Humans, Science, vol.3, issue.11, pp.750-752, 2013. ,
DOI : 10.1371/journal.pgen.0030161
URL : http://europepmc.org/articles/pmc4075767?pdf=render
Predicting the human epigenome from DNA motifs, Nature Methods, vol.33, issue.3, pp.265-272, 2015. ,
DOI : 10.2307/2282967
URL : http://europepmc.org/articles/pmc4344378?pdf=render
Predicting effects of noncoding variants with deep learning???based sequence model, Nature Methods, vol.12, issue.10, pp.931-934, 2015. ,
DOI : 10.1371/journal.pcbi.1001025
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein, BMC Bioinformatics, vol.6, issue.1, pp.59-15773999, 2005. ,
DOI : 10.1186/1471-2105-6-59
The Swiss-Army Tool for Genome Feature Analysis, Curr Protoc Bioinformatics, vol.47, pp.1-34, 2014. ,
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles, Nucleic Acids Research, vol.44, issue.D1, pp.110-115, 2016. ,
DOI : 10.1093/bioinformatics/btq475
URL : https://hal.archives-ouvertes.fr/hal-01281181
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding, Bioinformatics, vol.32, issue.8, pp.1211-1213, 2016. ,
DOI : 10.1073/pnas.1422023112
URL : https://academic.oup.com/bioinformatics/article-pdf/32/8/1211/16921293/btv735.pdf
DAVID-WS: a stateful web service to facilitate gene/protein list analysis, Bioinformatics, vol.8, issue.1, pp.1805-1806, 2012. ,
DOI : 10.1186/1471-2105-8-426
URL : https://academic.oup.com/bioinformatics/article-pdf/28/13/1805/641736/bts251.pdf
Regression shrinkage and selection via the lasso, Journal of the Royal Statistical Society Series B (Methodological), pp.267-288, 1996. ,
DOI : 10.1111/j.1467-9868.2011.00771.x
R: A Language and Environment for Statistical Computing Available from: http:// www.R-project.org ,
Classification and Regression Trees, 1984. ,
Random Forests, Machine Learning, vol.45, issue.1, pp.5-321010933404324, 2001. ,
DOI : 10.1023/A:1010933404324
Stability selection, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.7, issue.4, pp.417-473, 2010. ,
DOI : 10.1186/1471-2105-9-307
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9868.2010.00740.x/pdf
: Extended Inference with Lasso and Elastic-Net Regularized Cox and Generalized Linear Models, Journal of Statistical Software, vol.62, issue.5, 2015. ,
DOI : 10.18637/jss.v062.i05
URL : https://doi.org/10.18637/jss.v062.i05
Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the royal statistical society Series B (Methodological), pp.289-300, 1995. ,
Metazoan promoters: emerging characteristics and insights into transcriptional regulation, Nature Reviews Genetics, vol.107, issue.4, pp.233-245, 2012. ,
DOI : 10.1073/pnas.1000967107
High-throughput functional comparison of promoter and enhancer activities, Genome Research, vol.26, issue.8, 2016. ,
DOI : 10.1101/gr.204834.116
A widespread role of the motif environment in transcription factor binding across diverse protein families, Genome Research, vol.25, issue.9, pp.1268-1280, 2015. ,
DOI : 10.1101/gr.184671.114
Maps of context-dependent putative regulatory regions and genomic signal interactions, Nucleic Acids Research, vol.1823, p.27625394, 2016. ,
DOI : 10.1101/gr.092759.109
A compendium of RNA-binding motifs for decoding gene regulation, Nature, vol.35, issue.7457, pp.172-177, 2013. ,
DOI : 10.1093/nar/gkm272
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure, RNA, vol.16, issue.6, pp.1096-1107, 2010. ,
DOI : 10.1261/rna.2017210
Sequence-specific binding of single-stranded RNA: is there a code for recognition?, Nucleic Acids Research, vol.98, issue.17, pp.4943-4959, 2006. ,
DOI : 10.1073/pnas.181342398
CLIP-based prediction of mammalian microRNA binding sites, Nucleic Acids Research, vol.19, issue.3, p.23703212, 2013. ,
DOI : 10.1038/nsmb.2230
Codon influence on protein expression in E. coli correlates with mRNA levels, Nature, vol.177, issue.582, pp.358-363, 2016. ,
DOI : 10.1128/jb.177.14.4121-4130.1995
Codon identity regulates mRNA stability and translation efficiency during the maternal???to???zygotic transition, The EMBO Journal, vol.35, issue.19, 2016. ,
DOI : 10.15252/embj.201694699
Codon Optimality Is a Major Determinant of mRNA Stability, Cell, vol.160, issue.6, pp.1111-1124, 2015. ,
DOI : 10.1016/j.cell.2015.02.029
The Function of Introns, Frontiers in Genetics, vol.3, pp.55-22518112, 2012. ,
DOI : 10.3389/fgene.2012.00055
Intron-Mediated Regulation of Gene Expression, Curr Top Microbiol Immunol, vol.326, pp.277-290, 2008. ,
DOI : 10.1007/978-3-540-76776-3_15
TT-seq maps the human transient transcriptome, Science, vol.51, issue.6290, pp.1225-1228, 2016. ,
DOI : 10.1073/pnas.95.4.1460
Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region, Immunity, vol.45, issue.3, pp.497-512, 2016. ,
DOI : 10.1016/j.immuni.2016.08.012
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data, Bioinformatics, vol.31, issue.24, pp.3938-3945, 2015. ,
Classification and Regression Trees, 1984. ,
The human transcriptome across tissues and individuals, Science, vol.18, issue.1, pp.660-665, 2015. ,
DOI : 10.1128/MCB.18.1.566
URL : http://science.sciencemag.org/content/sci/348/6235/660.full.pdf
A promoter-level mammalian expression atlas, Nature, vol.507, issue.7493, pp.462-470, 2014. ,
Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, vol.135, issue.7398, pp.381-385, 2012. ,
DOI : 10.1016/j.cell.2008.08.031
Chromosomal Contact Permits Transcription between Coregulated Genes, Cell, vol.155, issue.3, pp.606-620, 2013. ,
DOI : 10.1016/j.cell.2013.09.051
URL : https://doi.org/10.1016/j.cell.2013.09.051
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome, Science, vol.27, issue.2, pp.289-293, 2009. ,
DOI : 10.1038/nbt.1523
An Isochore Framework Underlies Chromatin Architecture):e0168023. https, PLoS ONE, vol.12, issue.1, p.28060840, 2017. ,
DOI : 10.1371/journal.pone.0168023
URL : http://doi.org/10.1371/journal.pone.0168023
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization, BMC Bioinformatics, vol.18, issue.1, pp.218-28420341, 2017. ,
DOI : 10.1093/nar/18.20.6097
Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks, BioRxiv, 2016. ,
DOI : 10.1101/085241
Sequence Recognition in the Pairing of DNA Duplexes, Physical Review Letters, vol.89, issue.16, pp.3666-3669, 2001. ,
DOI : 10.1073/pnas.89.14.6492