. Tab, 7: Résultats pour les g` enes cibles des facteurs Rel/NF-?B dans la région, 2000.

S. Aerts, . Thijs, . Coessens, Y. Staes, . Moreau et al., Toucan: deciphering the cis-regulatory logic of coregulated genes, Nucleic Acids Research, vol.31, issue.6, pp.311753-64, 2003.
DOI : 10.1093/nar/gkg268

W. Ao, W. J. Gaudet, . Kent, S. Muttumu, and . Mango, Environmentally Induced Foregut Remodeling by PHA-4/FoxA and DAF-12/NHR, Science, vol.305, issue.5691, pp.3051743-3051749, 2004.
DOI : 10.1126/science.1102216

T. Bailey and C. Elkan, Unsupervised learning of multiple motifs in biopolymers using expectation maximization, Machine Learning, pp.51-80, 1995.
DOI : 10.1007/BF00993379

M. Beckstette, . Homann, S. Giegerich, and . Kurtz, Fast index based algorithms and software for matching position specific scoring matrices, BMC Bioinformatics, vol.7, issue.1, p.389, 2006.
DOI : 10.1186/1471-2105-7-389

P. Benos, M. Bulyk, and G. Stormo, Additivity in protein-DNA interactions: how good an approximation is it?, Nucleic Acids Research, vol.30, issue.20, pp.4442-51, 2002.
DOI : 10.1093/nar/gkf578

P. Benos, A. Lapedes, and G. Stormo, Is there a code for protein-DNA recognition? Probab(ilistical)ly?, BioEssays, vol.98, issue.5, pp.466-75, 2002.
DOI : 10.1002/bies.10073

O. Berg and P. Hippel, Selection of DNA binding sites by regulatory proteins, Journal of Molecular Biology, vol.193, issue.4, pp.723-50, 1987.
DOI : 10.1016/0022-2836(87)90354-8

D. Bernard, . Monte, C. Vandenbunder, and . Abbadie, The c-Rel transcription factor can both induce and inhibit apoptosis in the same cells via the upregulation of MnSOD, Oncogene, vol.21, issue.28
DOI : 10.1038/sj.onc.1205536

D. Boffelli, . Mcauliffe, K. Ovcharenko, . Lewis, . Ovcharenko et al., Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome, Science, vol.299, issue.5611, pp.2991391-2991395, 2003.
DOI : 10.1126/science.1081331

C. Bonferroni, Il calcolo delle assicurazioni su gruppi di teste, Studi in Onore del Professore Salvatore Ortu Carboni, pp.13-60, 1935.

N. Bray, L. Dubchak, and . Pachter, AVID: A Global Alignment Program, Genome Research, vol.13, issue.1, pp.97-102, 2003.
DOI : 10.1101/gr.789803

M. Brudno, C. Do, M. Cooper, . Kim, E. Davydov et al., LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA, Genome Research, vol.13, issue.4, pp.721-752, 2003.
DOI : 10.1101/gr.926603

M. Buck and J. Lieb, ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments, Genomics, vol.83, issue.3, pp.349-60, 2004.
DOI : 10.1016/j.ygeno.2003.11.004

K. Cartharius, . Frech, . Grote, . Klocke, . Haltmeier et al., MatInspector and beyond: promoter analysis based on transcription factor binding sites, Bioinformatics, vol.21, issue.13, pp.2933-2975, 2005.
DOI : 10.1093/bioinformatics/bti473

R. Chowdhary, R. Ali, . Albig, V. Doenecke, and . Bajic, Promoter modeling: the case study of mammalian histone promoters, Bioinformatics, vol.21, issue.11, pp.2623-2631, 2005.
DOI : 10.1093/bioinformatics/bti387

J. Claverie and S. Audic, The statistical significance of nucleotide position-weight matrix matches, Bioinformatics, vol.12, issue.5, pp.431-440, 1996.
DOI : 10.1093/bioinformatics/12.5.431

E. Gavin, G. Crooks, J. Hon, . Chandonia, E. Steven et al., WebLogo : a sequence logo generator, Genome Res, vol.14, issue.6, pp.1188-90, 2004.

M. Dekker, Handbook of fungal biotechnology, 2003.

R. Dubin, . Eddy, G. Krogh, and . Mitchison, Biological sequence analysis, 1998.

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-63, 1998.
DOI : 10.1093/bioinformatics/14.9.755

S. Eddy, A Model of the Statistical Power of Comparative Genome Sequence Analysis, PLoS Biology, vol.13, issue.1, p.10, 2005.
DOI : 10.1371/journal.pbio.0030010.g004

C. Fondrat and A. Kalogeropoulos, Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III, Current Genetics, vol.6, issue.5, pp.396-406, 1994.
DOI : 10.1007/BF00351777

M. Fried, Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay, Electrophoresis, vol.20, issue.5-6, pp.366-76, 1989.
DOI : 10.1002/elps.1150100515

M. Frith, Y. Fu, J. Yu, . Chen, Z. Hansen et al., Detection of functional DNA motifs via statistical over-representation, Nucleic Acids Research, vol.32, issue.4, pp.1372-81, 2004.
DOI : 10.1093/nar/gkh299

D. Galas and A. Schmitz, DNAase footprinting a simple method for the detection of protein-DNA binding specificity, Nucleic Acids Research, vol.5, issue.9, pp.3157-70, 1978.
DOI : 10.1093/nar/5.9.3157

N. Gershenzon, G. Stormo, and I. Ioshikhes, Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites, Nucleic Acids Research, vol.33, issue.7, pp.2290-301, 2005.
DOI : 10.1093/nar/gki519

K. Gosselin, H. Touzet, and C. Abbadie, NF-kappaB target genes

J. Gralla and J. Collado-vides, Organization and function of transcriptional regulatory elements, Cellular and Molecular Biology, 1996.

R. Hardison, Conserved noncoding sequences are reliable guides to regulatory elements, Trends in Genetics, vol.16, issue.9, pp.369-72, 2000.
DOI : 10.1016/S0168-9525(00)02081-3

G. Hertz, G. W. Hartzell, and G. Stormo, Identification of consensus patterns in unaligned DNA sequences known to be functionally related, Bioinformatics, vol.6, issue.2, pp.81-92, 1990.
DOI : 10.1093/bioinformatics/6.2.81

G. Hertz and G. Stormo, Identifying DNA and protein patterns with statistically significant alignments of multiple sequences, Bioinformatics, vol.15, issue.7, pp.563-77, 1999.
DOI : 10.1093/bioinformatics/15.7.563

J. Heumann, A. Lapedes, G. Stormo, J. Hiscott, . Marois et al., Neural networks for determining protein specificity and multiple alignment of binding sites Characterization of a functional NF-kappaB site in the human interleukin 1 beta promoter : evidence for a positive autoregulatory loop, Proc Int Conf Intell Syst Mol Biol Mol Cell Biol, vol.233, issue.13, pp.1553-0833188, 1993.

S. Sui, J. Mortimer, D. J. Arenillas, C. J. Brumm, . Walsh et al., oPOSSUM : identification of over-represented transcription factor binding sites in co-expressed genes, Nucleic Acids Res, issue.10, pp.333154-64, 2005.

C. Horak and M. Snyder, ChIP-chip: A genomic approach for identifying transcription factor binding sites, Methods Enzymol, vol.350, pp.76-6879469, 2002.
DOI : 10.1016/S0076-6879(02)50979-4

H. Huang, M. Kao, J. Zhou, W. Liu, and . Wong, Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification, Journal of Computational Biology, vol.11, issue.1, pp.1-14, 2004.
DOI : 10.1089/106652704773416858

T. Hubbard, . Barker, . Birney, . Cameron, . Chen et al., The Ensembl genome database project, Nucleic Acids Research, vol.30, issue.1, pp.38-41, 2002.
DOI : 10.1093/nar/30.1.38

J. Hughes, P. Estep, G. Tavazoie, and . Church, Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae, Journal of Molecular Biology, vol.296, issue.5, pp.1205-1219, 2000.
DOI : 10.1006/jmbi.2000.3519

D. Karolchik, . Baertsch, T. Diekhans, . Furey, Y. Hinrichs et al., The UCSC Genome Browser Database, Nucleic Acids Research, vol.31, issue.1, pp.3151-3155, 2003.
DOI : 10.1093/nar/gkg129

W. Krivan and W. Wasserman, A Predictive Model for Regulatory Sequences Directing Liver-Specific Transcription, Genome Research, vol.11, issue.9, pp.1559-66, 2001.
DOI : 10.1101/gr.180601

J. Laity, P. Lee, and . Wright, Zinc finger proteins: new insights into structural and functional diversity, Current Opinion in Structural Biology, vol.11, issue.1, pp.39-46, 2001.
DOI : 10.1016/S0959-440X(00)00167-6

C. Lawrence, S. Altschul, M. Boguski, J. Liu, A. Neuwald et al., Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Science, vol.262, issue.5131, pp.262208-262222, 1993.
DOI : 10.1126/science.8211139

C. Lawrence and A. Reilly, An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences, Proteins: Structure, Function, and Genetics, vol.240, issue.1, pp.41-51, 1990.
DOI : 10.1002/prot.340070105

B. Lenhard, . Sandelin, . Mendoza, . Engstrom, W. Jareborg et al., Identification of conserved regulatory elements by comparative genome analysis, Journal of Biology, vol.2, issue.2, p.13, 2003.
DOI : 10.1186/1475-4924-2-13

M. Lescot, . Dehais, . Thijs, Y. Marchal, Y. Moreau et al., PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences, Nucleic Acids Research, vol.30, issue.1, pp.325-332, 2002.
DOI : 10.1093/nar/30.1.325

M. Li, L. Ma, and . Wang, Finding similar regions in many strings, Proceedings of the thirty-first annual ACM symposium on Theory of computing , STOC '99, pp.473-482, 1999.
DOI : 10.1145/301250.301376

S. Li, P. Michael, J. Czubryt, R. Mcanally, . Bassel-duby et al., Requirement for serum response factor for skeletal muscle growth and maturation revealed by tissue-specific gene deletion in mice, Proceedings of the National Academy of Sciences, vol.15, issue.3, pp.27-84241082, 2005.
DOI : 10.1096/fj.00-026com

A. Liefooghe, J. Touzet, and . Varré, Large Scale Matching for Position Weight Matrices, Combinatorial Pattern Matching, 2006.
DOI : 10.1007/11780441_36

URL : https://hal.archives-ouvertes.fr/inria-00270270

G. Loots, . Ovcharenko, . Pachter, E. Dubchak, and . Rubin, rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites, Genome Research, vol.12, issue.5, pp.832-841, 2002.
DOI : 10.1101/gr.225502

L. Marsan and M. Sagot, Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification, Journal of Computational Biology, vol.7, issue.3-4, pp.3-4345, 2000.
DOI : 10.1089/106652700750050826

A. Moses, D. Chiang, E. Kellis, M. Lander, and . Eisen, Position specific variation in the rate of evolution in transcription factor binding sites, BMC Evol Biol, vol.3, pp.1471-214819, 2003.

C. Muller, Transcription factors: global and detailed views, Current Opinion in Structural Biology, vol.11, issue.1, pp.26-32, 2001.
DOI : 10.1016/S0959-440X(00)00163-9

L. Narlikar and A. Hartemink, Sequence features of DNA binding sites reveal structural class of associated transcription factor, Bioinformatics, vol.22, issue.2, pp.157-63, 2006.
DOI : 10.1093/bioinformatics/bti731

S. Needleman and C. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-53, 1970.
DOI : 10.1016/0022-2836(70)90057-4

A. Neuwald, J. Liu, and C. Lawrence, Gibbs motif sampling: Detection of bacterial outer membrane protein repeats, Protein Science, vol.17, issue.8, pp.1618-1650, 1995.
DOI : 10.1002/pro.5560040820

G. Nuel, LD-SPatt: Large Deviations Statistics for Patterns on Markov Chains, Journal of Computational Biology, vol.11, issue.6, pp.1023-1056, 2004.
DOI : 10.1089/cmb.2004.11.1023

URL : https://hal.archives-ouvertes.fr/hal-00271507

J. Oeltjen, T. Malley, D. Muzny, . Miller, J. Gibbs et al., Largescale comparative sequence analysis of the human and murine bruton's tyrosine kinase loci reveals conserved regulatory domains, Genome Res, vol.7, issue.4, pp.315-344, 1997.

C. Pabo and R. Sauer, Transcription Factors: Structural Families and Principles of DNA Recognition, Annual Review of Biochemistry, vol.61, issue.1, pp.66-41541053, 1992.
DOI : 10.1146/annurev.bi.61.070192.005201

G. Pavesi, G. Mauri, and . Pesole, An algorithm for finding signals of unknown length in DNA sequences, Bioinformatics, vol.17, issue.Suppl 1, pp.1367-4803, 2001.
DOI : 10.1093/bioinformatics/17.suppl_1.S207

G. Pavesi, . Mereghetti, G. Mauri, and . Pesole, Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes, Nucleic Acids Research, vol.32, issue.Web Server, pp.199-203, 2004.
DOI : 10.1093/nar/gkh465

E. Perez-rueda, J. Gralla, and J. Collado-vides, Genomic position analyses and the transcription machinery, Journal of Molecular Biology, vol.275, issue.2, pp.165-70, 1998.
DOI : 10.1006/jmbi.1997.1465

J. Pickands, Statistical inference using extreme order statistics. The Annals of Statistics, 1975.

J. Ponjavic, C. Lenhard, . Kai, . Kawai, Y. Carninci et al., Transcriptional and structural impact of tata-initiation site spacing in mammalian core promoters The Eukaryotic Promoter Database, EPD : new entry types and links to gene expression data, Genome Biol Nucleic Acids Res, vol.764, issue.301, pp.78322-78326, 2002.

K. Pruitt, D. Tatusova, and . Maglott, NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Research, vol.33, issue.Database issue, pp.501-505, 2005.
DOI : 10.1093/nar/gki025

K. Quandt, H. Frech, . Karas, T. Wingender, and . Werner, Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data, Nucleic Acids Research, vol.23, issue.23, pp.4878-84, 1995.
DOI : 10.1093/nar/23.23.4878

M. Régnier and A. Denise, Rare events and conditional events on random strings, Discrete Mathematics and Theoretical Computer Science, vol.6, issue.2, pp.191-214, 2004.

G. Reinert and S. Schbath, Compound Poisson and Poisson Process Approximations for Occurrences of Multiple Words in Markov Chains, Journal of Computational Biology, vol.5, issue.2, pp.223-53, 1998.
DOI : 10.1089/cmb.1998.5.223

G. Reinert, M. Schbath, and . Waterman, Probabilistic and Statistical Properties of Words: An Overview, Journal of Computational Biology, vol.7, issue.1-2, pp.1-46, 2000.
DOI : 10.1089/10665270050081360

B. Ren, J. J. Robert, . Wyrick, E. Aparicio, . Jennings et al., Genomewide location and function of DNA binding proteins, Science, issue.5500, pp.2902306-2902315, 2000.

M. Sagot, Spelling approximate repeated or common motifs using a suffix tree, Lecture Notes in Computer Science, vol.1380, pp.111-138, 1998.
DOI : 10.1007/BFb0054337

URL : https://hal.archives-ouvertes.fr/hal-00428511

A. Sandelin, . Alkema, W. Engstrom, B. Wasserman, and . Lenhard, JASPAR: an open-access database for eukaryotic transcription factor binding profiles, Nucleic Acids Research, vol.32, issue.90001, pp.91-95, 2004.
DOI : 10.1093/nar/gkh012

A. Sandelin, W. Wasserman, and B. Lenhard, ConSite: web-based prediction of regulatory elements using cross-species comparison, Nucleic Acids Research, vol.32, issue.Web Server, pp.249-52, 2004.
DOI : 10.1093/nar/gkh372

T. Schneider and R. Stephens, Sequence logos: a new way to display consensus sequences, Nucleic Acids Research, vol.18, issue.20, pp.6097-100, 1990.
DOI : 10.1093/nar/18.20.6097

T. Schneider, G. Stormo, A. Gold, and . Ehrenfeucht, Information content of binding sites on nucleotide sequences, Journal of Molecular Biology, vol.188, issue.3, pp.415-446, 1986.
DOI : 10.1016/0022-2836(86)90165-8

R. Sharan, . Ovcharenko, R. Ben-hur, and . Karp, CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments, Bioinformatics, vol.19, issue.Suppl 1, p.19
DOI : 10.1093/bioinformatics/btg1039

A. Sidow, Sequence First. Ask Questions Later., Cell, vol.111, issue.1, pp.13-19, 2002.
DOI : 10.1016/S0092-8674(02)01003-6

S. Sinha and M. Tompa, Discovery of novel transcription factor binding sites by statistical overrepresentation, Nucleic Acids Research, vol.30, issue.24, pp.5549-60, 2002.
DOI : 10.1093/nar/gkf669

S. Sinha and M. Tompa, YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation, Nucleic Acids Research, vol.31, issue.13, pp.313586-313594, 2003.
DOI : 10.1093/nar/gkg618

R. Staden, Computer methods to locate signals in nucleic acid sequences, Nucleic Acids Research, vol.12, issue.1Part2, pp.505-524, 1984.
DOI : 10.1093/nar/12.1Part2.505

G. Stormo, [22] Probing information content of DNA-binding sites, Methods Enzymol, vol.208, pp.76-6879458, 1991.
DOI : 10.1016/0076-6879(91)08024-C

G. Stormo, DNA binding sites: representation and discovery, Bioinformatics, vol.16, issue.1, pp.16-23, 2000.
DOI : 10.1093/bioinformatics/16.1.16

G. Stormo and D. Fields, Specificity, free energy and information content in protein???DNA interactions, Trends in Biochemical Sciences, vol.23, issue.3, pp.109-122, 1998.
DOI : 10.1016/S0968-0004(98)01187-6

Y. Suzuki, . Tsunoda, . Sese, J. Taira, H. Mizushima-sugano et al., Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes, Genome Research, vol.11, issue.5, pp.677-84, 2001.
DOI : 10.1101/gr.GR-1640R

G. Thijs, . Lescot, . Marchal, . Rombauts, . De-moor et al., A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling, Bioinformatics, vol.17, issue.12, pp.171113-171135, 2001.
DOI : 10.1093/bioinformatics/17.12.1113

M. Tompa, T. Li, G. Bailey, . Church, . De-moor et al., Assessing computational tools for the discovery of transcription factor binding sites, Nature Biotechnology, vol.5, issue.1, pp.137-144, 2005.
DOI : 10.1002/prot.10556

T. Tsunoda and T. Takagi, Automatic extraction of position specific cooccurrence of transcription factor bindings on promoters, Pac Symp Biocomput, pp.252-63, 1998.

J. Van-helden, J. Andre, and . Collado-vides, Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies

J. Van-helden, A. Rios, and J. Collado-vides, Discovering regulatory elements in non-coding sequences by analysis of spaced dyads, Nucleic Acids Research, vol.28, issue.8, pp.1808-1826, 2000.
DOI : 10.1093/nar/28.8.1808

J. Walter and M. Biggin, Measurement ofin VivoDNA Binding by Sequence-Specific Transcription Factors Using UV Cross-Linking, Methods, vol.11, issue.2, pp.215-239, 1997.
DOI : 10.1006/meth.1996.0408

W. Wasserman and J. Fickett, Identification of regulatory regions which confer muscle-specific gene expression, Journal of Molecular Biology, vol.278, issue.1, pp.167-81, 1998.
DOI : 10.1006/jmbi.1998.1700

W. Wasserman, . Palumbo, J. Thompson, C. Fickett, and . Lawrence, Human-mouse genome comparisons to locate regulatory sites, Nature Genetics, vol.266, issue.2, pp.225-233, 2000.
DOI : 10.1038/79965

A. Weinmann and P. Farnham, Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation, Methods, vol.26, issue.1, pp.37-47, 2002.
DOI : 10.1016/S1046-2023(02)00006-3

E. Wingender, . Chen, . Hehl, . Karas, . Liebich et al., TRANSFAC: an integrated system for gene expression regulation, Nucleic Acids Research, vol.28, issue.1, pp.316-325, 2000.
DOI : 10.1093/nar/28.1.316

C. Yuh, E. Bolouri, and . Davidson, Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene, Science, vol.279, issue.5358, pp.2791896-902, 1998.
DOI : 10.1126/science.279.5358.1896

Z. Zhang and M. Gerstein, Of mice and men : phylogenetic footprinting aids the discovery of regulatory elements, Journal of Biology, vol.2, issue.2, p.11, 2003.
DOI : 10.1186/1475-4924-2-11

J. Zheng, Z. Wu, and . Sun, An approach to identify over-represented cis-elements in related sequences, Nucleic Acids Research, vol.31, issue.7, pp.311995-2005, 2003.
DOI : 10.1093/nar/gkg287