P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith et al., The transcriptional landscape of the mammalian genome, Science, vol.309, pp.1559-1563, 2005.

J. M. Claverie, Fewer Genes, More Noncoding RNA, Science, vol.309, issue.5740, pp.1529-1530, 2005.
DOI : 10.1126/science.1116800

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese et al., Database resources of the National Center for Biotechnology Information, Database resources of the National Center for Biotechnology Information, pp.173-180, 2006.
DOI : 10.1093/nar/gkj158

P. Bertone, V. Stolc, T. E. Royce, J. S. Rozowsky, A. E. Urban et al., Global Identification of Human Transcribed Sequences with Genome Tiling Arrays, Science, vol.306, issue.5705, pp.2242-2246, 2004.
DOI : 10.1126/science.1103388

J. Cheng, P. Kapranov, J. Drenkow, S. Dike, S. Brubaker et al., Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution, Science, vol.308, issue.5725, pp.1149-1154, 2005.
DOI : 10.1126/science.1108625

B. Virlon, L. Cheval, J. M. Buhler, E. Billon, A. Doucet et al., Serial microanalysis of renal transcriptomes, Proc. Natl Acad. Sci. USA, pp.15286-15291, 1999.
DOI : 10.1073/pnas.96.26.15286

V. E. Velculescu, L. Zhang, B. Vogelstein, and K. W. Kinzler, Serial Analysis of Gene Expression, Science, vol.270, issue.5235, pp.484-487, 1995.
DOI : 10.1126/science.270.5235.484

S. Saha, A. B. Sparks, C. Rago, V. Akmaev, C. J. Wang et al., Using the transcriptome to annotate the genome, Nature Biotechnology, vol.20, issue.5, pp.508-512, 2002.
DOI : 10.1038/nbt0502-508

M. Margulies, M. Egholm, W. E. Altman, S. Attiya, J. S. Bader et al., Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, pp.376-380, 2005.
DOI : 10.1016/0888-7543(88)90007-9

J. Shendure, R. D. Mitra, C. Varma, and G. M. Church, Advanced sequencing technologies: methods and goals, Nature Reviews Genetics, vol.11, issue.5, pp.335-344, 2004.
DOI : 10.1016/S0014-5793(02)03275-1

K. L. Nielsen, A. L. Hogh, and J. Emmersen, DeepSAGE???digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples, Nucleic Acids Research, vol.34, issue.19, p.133, 2006.
DOI : 10.1093/nar/gkl714

Q. Que´re´, R. Manchon, L. Pierrat, F. Ludewig, U. Nesch et al., Rapid and Accurate Pyrosequencing of Serial Analysis of Gene Expression Ditags, pp.2-8, 2007.

J. Jurka, V. V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany et al., Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and Genome Research, vol.110, issue.1-4, pp.462-467, 2005.
DOI : 10.1159/000084979

C. H. Woelk, F. Ottones, C. R. Plotkin, P. Du, C. D. Royer et al., Interferon Gene Expression following HIV Type 1 Infection of Monocyte-Derived Macrophages, AIDS Research and Human Retroviruses, vol.20, issue.11, pp.1210-1222, 2004.
DOI : 10.1089/aid.2004.20.1210

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

Q. Que´re´, R. Manchon, L. Lejeune, M. Cle´mentcle´ment, O. Pierrat et al., Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression, Nucleic Acids Research, vol.32, issue.20, p.163, 2004.
DOI : 10.1093/nar/gnh161

J. Tarhio and H. Peltola, String matching in the DNA alphabet. Software: Practice and Experience, pp.851-861, 1997.

R. N. Horspool, Practical fast searching in strings. Software: Practice and Experience, pp.501-506, 1980.

J. L. Rinn, G. Euskirchen, P. Bertone, R. Martone, N. M. Luscombe et al., The transcriptional activity of human Chromosome 22, Genes & Development, vol.17, issue.4, pp.529-540, 2003.
DOI : 10.1101/gad.1055203

A. P. Silva, J. E. De-souza, P. A. Galante, G. J. Riggins, D. Souza et al., The impact of SNPs on the interpretation of SAGE and MPSS experimental data, Nucleic Acids Research, vol.32, issue.20, pp.6104-6110, 2004.
DOI : 10.1093/nar/gkh937

M. Semon and L. Duret, Evidence that functional transcription units cover at least half of the human genome, Trends in Genetics, vol.20, issue.5, pp.229-232, 2004.
DOI : 10.1016/j.tig.2004.03.001
URL : https://hal.archives-ouvertes.fr/hal-00427647

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

P. Bertone, M. Gerstein, and M. Snyder, Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery, Chromosome Research, vol.13, issue.3, pp.259-274, 2005.
DOI : 10.1007/s10577-005-2165-0

T. C. Mockler, S. Chan, A. Sundaresan, H. Chen, S. E. Jacobsen et al., Applications of DNA tiling arrays for whole-genome analysis, Genomics, vol.85, issue.1, pp.1-15, 2005.
DOI : 10.1016/j.ygeno.2004.10.005

J. M. Cummins, Y. He, R. J. Leary, R. Pagliarini, L. A. Diaz et al., The colorectal microRNAome, Proc. Natl Acad. Sci. USA, pp.3687-3692, 2006.
DOI : 10.1073/pnas.0511155103
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450142

A. Huttenhofer and J. Vogel, Experimental approaches to identify non-coding RNAs, Nucleic Acids Research, vol.34, issue.2, pp.635-646, 2006.
DOI : 10.1093/nar/gkj469
URL : http://doi.org/10.1093/nar/gkj469

P. Ng, C. L. Wei, W. K. Sung, K. P. Chiu, L. Lipovich et al., Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation, Nature Methods, vol.30, issue.2, pp.105-111, 2005.
DOI : 10.1038/326292a0

S. Brenner, M. Johnson, J. Bridgham, G. Golda, D. H. Lloyd et al., Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays, Nature Biotechnology, vol.311, issue.6, pp.630-634, 2000.
DOI : 10.1038/76469

X. Ge, Q. Wu, Y. C. Jung, J. Chen, and S. M. Wang, A large quantity of novel human antisense transcripts detected by LongSAGE, Bioinformatics, vol.22, issue.20, pp.2475-2479, 2006.
DOI : 10.1093/bioinformatics/btl429

P. Bertone, V. Trifonov, J. S. Rozowsky, F. Schubert, O. Emanuelsson et al., Design optimization methods for genomic DNA tiling arrays, Genome Research, vol.16, issue.2, pp.271-281, 2006.
DOI : 10.1101/gr.4452906

J. Chen, S. Lee, G. Zhou, and S. M. Wang, High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3? complementary DNAs, Genes, Chromosomes and Cancer, vol.276, issue.3, pp.252-261, 2002.
DOI : 10.1002/gcc.10017