S. Djebali, C. A. Davis, A. Merkel, A. Dobin, T. Lassmann et al., Landscape of transcription in human cells, Nature, vol.474, issue.7414, pp.101-108, 2012.
DOI : 10.1038/nature10006
URL : https://hal.archives-ouvertes.fr/hal-01216755

S. Geisler and J. Coller, RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts, Nature Reviews Molecular Cell Biology, vol.472, issue.11, pp.699-712, 2013.
DOI : 10.1038/nature09819
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852478/pdf

J. Harrow, A. Frankish, J. M. Gonzalez, E. Tapanari, M. Diekhans et al., GENCODE: The reference human genome annotation for The ENCODE Project, Genome Research, vol.22, issue.9, pp.1760-1774, 2012.
DOI : 10.1101/gr.135350.111

T. Mondal, S. Subhash, R. Vaid, S. Enroth, S. Uday et al., MEG3 long noncoding RNA regulates the TGF-?? pathway genes through formation of RNA???DNA triplex structures, Nature Communications, vol.19, p.7743, 2015.
DOI : 10.1006/meth.1999.0879

C. M. Clemson, J. N. Hutchinson, S. A. Sara, A. W. Ensminger, A. H. Fox et al., An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles, Molecular Cell, vol.33, issue.6, pp.717-726, 2009.
DOI : 10.1016/j.molcel.2009.01.026

O. Wapinski and H. Y. Chang, Long noncoding RNAs and human disease, Trends in Cell Biology, vol.21, issue.6, pp.354-361, 2011.
DOI : 10.1016/j.tcb.2011.04.001

R. C. Spitale, M. C. Tsai, and H. Y. Chang, RNA templating the epigenome, Epigenetics, vol.100, issue.5, pp.539-543, 2011.
DOI : 10.1146/annurev.biochem.75.103004.142710
URL : http://www.tandfonline.com/doi/pdf/10.4161/epi.6.5.15221?needAccess=true

M. C. Good, J. G. Zalatan, and W. A. Lim, Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information, Science, vol.20, issue.6, pp.680-686, 2011.
DOI : 10.1016/j.molcel.2005.10.030

T. Chujo, T. Yamazaki, and T. Hirose, Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1859, issue.1, pp.1859-139, 2015.
DOI : 10.1016/j.bbagrm.2015.05.007

M. Tsai, O. Manor, Y. Wan, N. Mosammaparast, J. K. Wang et al., Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes, Science, vol.458, issue.7235, pp.689-693, 2010.
DOI : 10.1038/nature07672

Y. Zhang, Q. He, Z. Hu, Y. Feng, L. Fan et al., Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer, Nature Structural & Molecular Biology, vol.103, issue.6, pp.1-12, 2016.
DOI : 10.1016/S0092-8674(00)00188-4

D. Cirillo, M. Blanco, A. Armaos, A. Buness, P. Avner et al., Quantitative predictions of protein interactions with long noncoding RNAs, Nature Methods, vol.12, issue.1, pp.5-6, 2016.
DOI : 10.1016/j.celrep.2015.06.067

B. M. Beckmann, A. Castello, and J. Medenbach, The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions. Pflügers Arch. -Eur, J. Physiol, vol.468, pp.1029-1040, 2016.

Y. Hao, W. Wu, H. Li, J. Yuan, J. Luo et al., NPInter v3.0: an upgraded database of noncoding RNA-associated interactions, Database, vol.2016, p.57, 2016.
DOI : 10.1093/database/baw057

F. Agostini, A. Zanzoni, P. Klus, D. Marchese, D. Cirillo et al., catRAPID omics: a web server for large-scale prediction of protein-RNA interactions, Bioinformatics, vol.29, issue.22, pp.2928-2930, 2013.
DOI : 10.1093/bioinformatics/btt495

G. Consortium, The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans, Science, vol.55, issue.4, pp.648-660, 2015.
DOI : 10.1016/j.biopsych.2003.10.013

J. H. Li, S. Liu, H. Zhou, L. H. Qu, and J. H. Yang, starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein???RNA interaction networks from large-scale CLIP-Seq data, Nucleic Acids Research, vol.42, issue.D1, pp.92-97, 2014.
DOI : 10.1093/nar/gkt1248

E. L. Huttlin, L. Ting, R. J. Bruckner, F. Gebreab, M. P. Gygi et al., The BioPlex Network: A Systematic Exploration of the Human Interactome, Cell, vol.162, issue.2, pp.425-440, 2015.
DOI : 10.1016/j.cell.2015.06.043

C. Wan, B. Borgeson, S. Phanse, F. Tu, K. Drew et al., Panorama of ancient metazoan macromolecular complexes, Nature, vol.347, issue.7569, pp.339-344, 2015.
DOI : 10.1016/j.devcel.2011.03.015
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036527/pdf

A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-kaltenbach et al., CORUM: the comprehensive resource of mammalian protein complexes???2009, Nucleic Acids Research, vol.38, issue.suppl_1, pp.497-501, 2009.
DOI : 10.1093/nar/gkp914

P. C. Havugimana, G. T. Hart, T. Nepusz, H. Yang, A. L. Turinsky et al., A Census of Human Soluble Protein Complexes, Cell, vol.150, issue.5, pp.1068-1081, 2012.
DOI : 10.1016/j.cell.2012.08.011

C. E. Chapple, B. Robisson, L. Spinelli, C. Guien, E. Becker et al., Extreme multifunctional proteins identified from a human protein interaction network, Nature Communications, vol.31, p.7412, 2015.
DOI : 10.1093/nar/gkg545
URL : https://hal.archives-ouvertes.fr/hal-01407399

M. Bellucci, F. Agostini, M. Masin, and G. G. Tartaglia, Predicting protein associations with long noncoding RNAs, Nature Methods, vol.8, issue.6, pp.444-445, 2011.
DOI : 10.1126/science.1192002

F. Agostini, D. Cirillo, B. Bolognesi, and G. G. Tartaglia, X-inactivation: quantitative predictions of protein interactions in the Xist network, Nucleic Acids Research, vol.41, issue.1, pp.1-9, 2013.
DOI : 10.1093/nar/gks968

A. E. Kornienko, C. P. Dotter, P. M. Guenzl, H. Gisslinger, B. Gisslinger et al., Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans, Genome Biology, vol.30, issue.1, p.14, 2016.
DOI : 10.1093/nar/30.1.207
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-016-0873-8?site=genomebiology.biomedcentral.com

S. Lee, F. Kopp, T. C. Chang, A. Sataluri, B. Chen et al., Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins, Cell, vol.164, issue.1-2, pp.69-80, 2015.
DOI : 10.1016/j.cell.2015.12.017
URL : https://doi.org/10.1016/j.cell.2015.12.017

A. Minajigi, J. E. Froberg, C. Wei, H. Sunwoo, B. Kesner et al., A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation, Science, vol.521, issue.10, p.2276, 2015.
DOI : 10.1038/nature14443
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4845908/pdf

M. Ballarino, V. Cazzella, D. D-'andrea, L. Grassi, L. Bisceglie et al., Overlapping lncRNA Transcript Controls Myoblast Differentiation, Molecular and Cellular Biology, vol.35, issue.4, pp.728-736, 2015.
DOI : 10.1128/MCB.01394-14
URL : http://mcb.asm.org/content/35/4/728.full.pdf

R. J. Kelm, J. G. Cogan, P. K. Elder, A. R. Strauch, and M. J. Getz, Molecular Interactions between Single-stranded DNA-binding Proteins Associated with an Essential MCAT Element in the Mouse Smooth Muscle ??-Actin Promoter, Journal of Biological Chemistry, vol.17, issue.20, pp.14238-14245, 1999.
DOI : 10.1016/0378-1119(94)90167-8

D. Cirillo, F. Agostini, and G. G. Tartaglia, Predictions of protein-RNA interactions, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.35, issue.suppl 1, pp.161-175, 2013.
DOI : 10.1016/0092-8674(83)90117-4

E. Becker, B. Robisson, C. E. Chapple, A. Guénoche, and C. Brun, Multifunctional proteins revealed by overlapping clustering in protein interaction network, Bioinformatics, vol.28, issue.1, pp.84-90, 2012.
DOI : 10.1093/bioinformatics/btr621
URL : https://hal.archives-ouvertes.fr/hal-00877694

C. Brun, F. Chevenet, D. Martin, J. Wojcik, A. Guénoche et al., Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network, Genome Biology, vol.5, issue.1, p.6, 2003.
DOI : 10.1186/gb-2003-5-1-r6
URL : https://hal.archives-ouvertes.fr/hal-00311029

C. Davidovich, L. Zheng, K. J. Goodrich, and T. R. Cech, Promiscuous RNA binding by Polycomb repressive complex 2, Nature Structural & Molecular Biology, vol.57, issue.11, pp.1250-1257, 2013.
DOI : 10.1093/nar/gkm226
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823624/pdf

N. Mukherjee, L. Calviello, A. Hirsekorn, S. De-pretis, M. Pelizzola et al., Integrative classification of human coding and noncoding genes through RNA metabolism profiles, Nature Structural & Molecular Biology, vol.8, issue.1, pp.86-96, 2017.
DOI : 10.1371/journal.pgen.1002433

C. Hon, J. Ramilowski, J. Harshbarger, N. Bertin, O. Rackham et al., An atlas of human long non-coding RNAs with accurate 5??? ends, Nature, vol.2016, issue.7644, pp.199-204, 2017.
DOI : 10.1093/database/baw105
URL : https://hal.archives-ouvertes.fr/hal-01607778

S. J. Liu, S. J. Liu, M. A. Horlbeck, S. W. Cho, H. S. Birk et al., CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells, Science, vol.2, issue.6320, pp.355-7111, 2017.
DOI : 10.1093/nar/gkw257

S. Ning, J. Zhang, P. Wang, H. Zhi, J. Wang et al., Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers, Nucleic Acids Research, vol.44, issue.D1, pp.980-985, 2016.
DOI : 10.1093/nar/gkv1094

G. Chen, Z. Wang, D. Wang, C. Qiu, M. Liu et al., LncRNADisease: a database for long-non-coding RNA-associated diseases, Nucleic Acids Research, vol.41, issue.D1, pp.983-986, 2013.
DOI : 10.1093/nar/gks1099
URL : https://academic.oup.com/nar/article-pdf/41/D1/D983/3618811/gks1099.pdf

A. Necsulea, M. Soumillon, M. Warnefors, A. Liechti, T. Daish et al., The evolution of lncRNA repertoires and expression patterns in tetrapods, Nature, vol.39, issue.7485, pp.635-640, 2014.
DOI : 10.1093/nar/gkq1027

M. A. Smith, T. Gesell, P. F. Stadler, and J. S. Mattick, Widespread purifying selection on RNA structure in mammals, Nucleic Acids Research, vol.41, issue.17, pp.8220-8236, 2013.
DOI : 10.1093/nar/gkt596
URL : https://academic.oup.com/nar/article-pdf/41/17/8220/16948081/gkt596.pdf

B. Gulko, M. J. Hubisz, I. Gronau, and A. Siepel, A method for calculating probabilities of fitness consequences for point mutations across the human genome, Nature Genetics, vol.158, issue.3, pp.276-283, 2015.
DOI : 10.1101/gr.135350.111

A. Hamosh, A. F. Scott, J. S. Amberger, C. A. Bocchini, and V. A. Mckusick, Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders, Nucleic Acids Research, vol.33, issue.Database issue, pp.514-517, 2005.
DOI : 10.1093/nar/gki033

P. M. Tørring, M. J. Larsen, A. D. Kjeldsen, L. B. Ousager, Q. Tan et al., Long Non-Coding RNA Expression Profiles in Hereditary Haemorrhagic Telangiectasia, PLoS ONE, vol.16, issue.3, p.90272, 2014.
DOI : 10.1371/journal.pone.0090272.s011

S. Dupuis-girod, S. Bailly, and H. Plauchu, Hereditary hemorrhagic telangiectasia: from molecular biology to patient care, Journal of Thrombosis and Haemostasis, vol.30, issue.3 Pt 1, pp.1447-1456, 2010.
DOI : 10.1159/000110632

C. J. Gallione, G. M. Repetto, E. Legius, A. K. Rustgi, S. L. Schelley et al., A combined syndrome of juvenile polyposis and hereditary haemorrhagic telangiectasia associated with mutations in MADH4 (SMAD4), The Lancet, vol.363, issue.9412, pp.852-859, 2004.
DOI : 10.1016/S0140-6736(04)15732-2

D. Yin, Z. Liu, E. Zhang, R. Kong, Z. Zhang et al., Decreased expression of long noncoding RNA MEG3 affects cell proliferation and predicts a poor prognosis in patients with colorectal cancer, Tumor Biology, vol.8, issue.6, pp.4851-4859, 2015.
DOI : 10.1097/PAT.0000000000000125

M. Zhang, W. Wang, T. Li, X. Yu, Y. Zhu et al., Long noncoding RNA SNHG1 predicts a poor prognosis and promotes hepatocellular carcinoma tumorigenesis, Biomedicine & Pharmacotherapy, vol.80, pp.73-79, 2016.
DOI : 10.1016/j.biopha.2016.02.036

J. You, N. Fang, J. Gu, Y. Zhang, X. Li et al., Noncoding RNA small nucleolar RNA host gene 1 promote cell proliferation in nonsmall cell lung cancer, Indian Journal of Cancer, vol.51, issue.7, pp.99-102, 2014.
DOI : 10.4103/0019-509X.154092

T. Luedde and R. F. Schwabe, NF-??B in the liver???linking injury, fibrosis and hepatocellular carcinoma, Nature Reviews Gastroenterology & Hepatology, vol.53, issue.2, pp.108-118, 2011.
DOI : 10.1016/j.jhep.2010.02.027

Y. Wu and B. P. Zhou, TNF-??/NF-??B/Snail pathway in cancer cell migration and invasion, British Journal of Cancer, vol.29, issue.4, pp.639-644, 2010.
DOI : 10.1038/ncb1173
URL : http://www.nature.com/bjc/journal/v102/n4/pdf/6605530a.pdf

H. Zhang, D. Zhou, M. Ying, M. Chen, P. Chen et al., Expression of Long Non-Coding RNA (lncRNA) Small Nucleolar RNA Host Gene 1 (SNHG1) Exacerbates Hepatocellular Carcinoma Through Suppressing miR-195, Medical Science Monitor, vol.22, pp.4820-4829, 2016.
DOI : 10.12659/MSM.898574

J. Ding, S. Huang, Y. Wang, Q. Tian, R. Zha et al., Genome-wide screening reveals that miR-195 targets the TNF-??/NF-??B pathway by down-regulating I??B kinase alpha and TAB3 in hepatocellular carcinoma, Hepatology, vol.400, issue.2, pp.654-666, 2013.
DOI : 10.1016/j.bbrc.2010.08.046

K. Venkatesan, J. Rual, A. Vazquez, U. Stelzl, I. Lemmens et al., An empirical framework for binary interactome mapping, Nature Methods, vol.6, issue.1, pp.83-90, 2009.
DOI : 10.1038/nprot.2006.14
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872561/pdf

K. C. Wang and H. Y. Chang, Molecular Mechanisms of Long Noncoding RNAs, Molecular Cell, vol.43, issue.6, pp.904-914, 2012.
DOI : 10.1016/j.molcel.2011.08.018

J. Li, L. Han, P. Roebuck, L. Diao, L. Liu et al., TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer, Cancer Research, vol.75, issue.18, pp.3728-3737, 2015.
DOI : 10.1158/0008-5472.CAN-15-0273

Z. Zhao, J. Bai, A. Wu, Y. Wang, J. Zhang et al., Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data, Database: J. Biol. databases Curation, pp.1-7, 2015.

X. Chen, Y. Hao, Y. Cui, Z. Fan, S. He et al., LncVar: a database of genetic variation associated with long non-coding genes, Bioinformatics, vol.33, issue.1, pp.112-118, 2017.
DOI : 10.1093/bioinformatics/btw581

C. Park, N. Yu, I. Choi, W. Kim, and S. Lee, lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs, Bioinformatics, vol.30, issue.17, pp.2480-2485, 2014.
DOI : 10.1093/bioinformatics/btu325

A. Zanzoni, D. Marchese, F. Agostini, B. Bolognesi, D. Cirillo et al., Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein, Nucleic Acids Research, vol.41, issue.22, pp.9987-9998, 2013.
DOI : 10.1093/nar/gkt794

J. West, C. Davis, H. Sunwoo, M. Simon, R. Sadreyev et al., The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites, Molecular Cell, vol.55, issue.5, pp.791-802, 2014.
DOI : 10.1016/j.molcel.2014.07.012
URL : https://doi.org/10.1016/j.molcel.2014.07.012

A. Cerase, G. Pintacuda, A. Tattermusch, and P. Avner, Xist localization and function: new insights from multiple levels, Genome Biology, vol.141, issue.1, p.166, 2015.
DOI : 10.1016/j.cell.2010.04.042
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-015-0733-y?site=genomebiology.biomedcentral.com

Y. Zhao, H. Li, S. Fang, Y. Kang, Y. Hao et al., NONCODE 2016: an informative and valuable data source of long non-coding RNAs, Nucleic Acids Research, vol.44, issue.D1, pp.203-208, 2016.
DOI : 10.1093/nar/gkv1252

K. Kashi, L. Henderson, A. Bonetti, and P. Carninci, Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1859, issue.1, pp.3-15, 2015.
DOI : 10.1016/j.bbagrm.2015.10.010

T. Trimarchi, E. Bilal, P. Ntziachristos, G. Fabbri, R. Dalla-favera et al., Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia, Cell, vol.158, issue.3, pp.593-606, 2014.
DOI : 10.1016/j.cell.2014.05.049

X. Yu, Y. Zhang, T. Li, Z. Ma, H. Jia et al., Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD, Nature Communications, vol.8, p.14016, 2017.
DOI : 10.1038/nmeth.2019
URL : http://www.nature.com/articles/ncomms14016.pdf

O. Leary, V. B. Hain, S. Maugg, D. Smida, J. Azimzadeh et al., Long non-coding RNA PARTICLE bridges histone and DNA methylation, Sci. Rep, vol.7, p.1790, 2017.

C. Li, S. Wang, Z. Xing, A. Lin, K. Liang et al., A ROR1???HER3???lncRNA signalling axis modulates the Hippo???YAP pathway to regulate bone metastasis, Nature Cell Biology, vol.3, issue.2, pp.106-119, 2017.
DOI : 10.1007/s12253-015-9955-2

A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert et al., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. U.S.A, pp.15545-15550, 2005.

X. C. Quek, D. W. Thomson, J. L. Maag, N. Bartonicek, B. Signal et al., lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs, 2015) lncRNAdb v2.0: Expanding the reference database for functional long noncoding RNAs, pp.168-173
DOI : 10.1093/nar/gku988

S. Orchard, M. Ammari, B. Aranda, L. Breuza, L. Briganti et al., The MIntAct project???IntAct as a common curation platform for 11 molecular interaction databases, Nucleic Acids Research, vol.42, issue.D1, pp.358-363, 2014.
DOI : 10.1093/nar/gkt1115

R. Lorenz, S. H. Bernhart, C. Oner-zu-siederdissen, H. Tafer, C. Flamm et al., ViennaRNA Package 2.0, Algorithms for Molecular Biology, vol.6, issue.1, p.26, 2011.
DOI : 10.1016/0005-2795(75)90109-9
URL : https://almob.biomedcentral.com/track/pdf/10.1186/1748-7188-6-26?site=almob.biomedcentral.com