J. M. Johnson, S. Edwards, D. Shoemaker, and E. E. Schadt, Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments, Trends in Genetics, vol.21, issue.2, pp.93-102, 2005.
DOI : 10.1016/j.tig.2004.12.009

A. T. Willingham and T. R. Gingeras, TUF Love for ???Junk??? DNA, Cell, vol.125, issue.7, pp.1215-1220, 2006.
DOI : 10.1016/j.cell.2006.06.009

URL : http://doi.org/10.1016/j.cell.2006.06.009

M. B. Gerstein, C. Bruce, J. S. Rozowsky, D. Zheng, J. Du et al., What is a gene, post-ENCODE? History and updated definition, Genome Research, vol.17, issue.6, pp.669-681, 2007.
DOI : 10.1101/gr.6339607

P. Kapranov, J. Cheng, S. Dike, D. A. Nix, R. Duttagupta et al., RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription, Science, vol.316, issue.5830, pp.1484-1488, 2007.
DOI : 10.1126/science.1138341

V. A. Moran, R. J. Perera, and A. M. Khalil, Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs, Nucleic Acids Research, vol.40, issue.14, pp.6391-6400, 2012.
DOI : 10.1093/nar/gks296

M. B. Clark, P. P. Amaral, F. J. Schlesinger, M. E. Dinger, R. J. Taft et al., The Reality of Pervasive Transcription, PLoS Biology, vol.25, issue.7, p.1000625, 2011.
DOI : 10.1371/journal.pbio.1000625.s008

P. Kapranov, G. St-laurent, T. Raz, F. Ozsolak, C. P. Reynolds et al., The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA, BMC Biology, vol.8, issue.1, p.149, 2010.
DOI : 10.1186/1741-7007-8-149

T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali et al., The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression, Genome Research, vol.22, issue.9, pp.1775-1789, 2012.
DOI : 10.1101/gr.132159.111

URL : https://hal.archives-ouvertes.fr/hal-01205054

M. N. Cabili, C. Trapnell, L. Goff, M. Koziol, B. Tazon-vega et al., Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses, Genes & Development, vol.25, issue.18, pp.1915-1927, 2011.
DOI : 10.1101/gad.17446611

J. L. Rinn, M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu et al., Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs, Cell, vol.129, issue.7, pp.1311-1323, 2007.
DOI : 10.1016/j.cell.2007.05.022

M. Guttman, I. Amit, M. Garber, C. French, M. F. Lin et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, vol.322, issue.7235, pp.223-227, 2009.
DOI : 10.1038/nature07672

T. R. Mercer, M. E. Dinger, and J. S. Mattick, Long non-coding RNAs: insights into functions, Nature Reviews Genetics, vol.72, issue.3, pp.155-159, 2009.
DOI : 10.1038/nrg2521

C. P. Ponting, P. L. Oliver, and W. Reik, Evolution and Functions of Long Noncoding RNAs, Cell, vol.136, issue.4, pp.629-641, 2009.
DOI : 10.1016/j.cell.2009.02.006

V. Verk, M. C. Hickman, R. Pieterse, C. M. Van-wees, and S. C. , RNA-Seq: revelation of the messengers, Trends in Plant Science, vol.18, issue.4, pp.175-179, 2013.
DOI : 10.1016/j.tplants.2013.02.001

P. Kapranov and G. S. Laurent, Genomic 'dark matter': implications for understanding human disease mechanisms, diagnostics, and cures, Front. Genet, vol.3, p.95, 2012.
DOI : 10.3389/fgene.2012.00095

URL : http://doi.org/10.3389/fgene.2012.00095

M. S. Kowalczyk, D. R. Higgs, and T. R. Gingeras, Molecular biology: RNA discrimination, Nature, vol.465, issue.7385, pp.310-311, 2012.
DOI : 10.1038/482310a

S. Laurent, G. Savva, Y. A. Kapranov, and P. , Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape, Frontiers in Genetics, vol.3, p.57, 2012.
DOI : 10.3389/fgene.2012.00057

N. Philippe, A. Boureux, L. Bre´heíinbre´heíin, J. Tarhio, T. Commes et al., Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity, Nucleic Acids Research, vol.37, issue.15, pp.104-104, 2009.
DOI : 10.1093/nar/gkp492

URL : https://hal.archives-ouvertes.fr/hal-00452377

N. Philippe, M. Salson, T. Commes, and E. Rivals, CRAC: an integrated approach to the analysis of RNA-seq reads, Genome Biology, vol.14, issue.3, 2013.
DOI : 10.1371/journal.pone.0012271

URL : https://hal.archives-ouvertes.fr/inserm-00850972

P. Flicek, M. R. Amode, D. Barrell, K. Beal, S. Brent et al., Ensembl 2012, Nucleic Acids Research, vol.40, issue.D1, pp.84-90, 2012.
DOI : 10.1093/nar/gkr991

URL : http://doi.org/10.1093/nar/gkr991

E. Rivals, A. Boureux, M. Lejeune, F. Ottones, O. P. Pe´rezpe´rez et al., Transcriptome annotation using tandem SAGE tags, Nucleic Acids Research, vol.35, issue.17, pp.108-108, 2007.
DOI : 10.1093/nar/gkm495

URL : https://hal.archives-ouvertes.fr/lirmm-00203923

D. W. Huang, B. T. Sherman, and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, vol.99, issue.1, pp.44-57, 2009.
DOI : 10.1038/nprot.2008.211

M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein, Cluster analysis and display of genome-wide expression patterns, Proc. Natl Acad. Sci. USA, pp.14863-14868, 1998.
DOI : 10.1073/pnas.95.25.14863

S. Assou, D. Cerecedo, S. Tondeur, V. Pantesco, O. Hovatta et al., A gene expression signature shared by human mature oocytes and embryonic stem cells, BMC Genomics, vol.10, issue.1, p.10, 2009.
DOI : 10.1186/1471-2164-10-10

URL : https://hal.archives-ouvertes.fr/inserm-00369777

Q. Bai, S. Assou, D. Haouzi, J. Ramirez, C. Monzo et al., Dissecting the First Transcriptional Divergence During Human Embryonic Development, Stem Cell Reviews and Reports, vol.22, issue.Suppl A, pp.150-162, 2012.
DOI : 10.1007/s12015-011-9301-3

URL : https://hal.archives-ouvertes.fr/inserm-00664573

K. J. Livak and T. D. Schmittgen, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods, pp.402-408, 2001.

J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer, Substantial biases in ultra-short read data sets from high-throughput DNA sequencing, Nucleic Acids Research, vol.36, issue.16, p.105, 2008.
DOI : 10.1093/nar/gkn425

A. S. Morrissy, R. D. Morin, A. Delaney, T. Zeng, H. Mcdonald et al., Nextgeneration tag sequencing for cancer gene expression profiling, 2009.
DOI : 10.1101/gr.094482.109

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765282

T. Raz, P. Kapranov, D. Lipson, S. Letovsky, P. M. Milos et al., Protocol Dependence of Sequencing-Based Gene Expression Measurements, PLoS ONE, vol.5, issue.5, p.19287, 2011.
DOI : 10.1371/journal.pone.0019287.s008

D. Piquemal, T. Commes, L. Manchon, M. Lejeune, C. Ferraz et al., Transcriptome Analysis of Monocytic Leukemia Cell Differentiation, Genomics, vol.80, issue.3, pp.361-371, 2002.
DOI : 10.1006/geno.2002.6836

M. E. Dinger, D. K. Gascoigne, and J. S. Mattick, The evolution of RNAs with multiple functions, Biochimie, vol.93, issue.11, pp.2013-2018, 2011.
DOI : 10.1016/j.biochi.2011.07.018

Z. Zhang, A. Pang, and M. Gerstein, Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human, BMC Evolutionary Biology, vol.7, issue.Suppl 1, p.14, 2007.
DOI : 10.1186/1471-2148-7-S1-S14