A. Etudes-du-transcriptome-des-patientes, 186 2.1. Hypothèses de travail et étude du profil d'expression du syndrome d'Aicardi186 2.2. Analyse des résultats d'expression : les consensus établis, p.186

G. Annotations, Relations entre gène candidat et maladies

]. J. Aicardi, J. Levebre, and A. , Lerique-Koechlin, A new syndrome: spasms in flexion, callosal agenesis, ocular abnormalities, Electroencephalogr. Clin. Neurophysiol, vol.19, pp.609-610, 1965.

J. Aicardi, Aicardi syndrome, Brain and Development, vol.27, issue.3, pp.164-171, 2005.
DOI : 10.1016/j.braindev.2003.11.011

V. R. Sutton, B. J. Hopkins, T. N. Eble, N. Gambhir, R. A. Lewis et al., Van den Veyver, Facial and physical features of Aicardi syndrome: infants to teenagers, Am. J. Med. Genet, pp.138-254, 2005.

J. A. Molina, F. Mateos, M. Merino, J. L. Epifanio, and M. Gorrono, Aicardi syndrome in two sisters, The Journal of Pediatrics, vol.115, issue.2, p.115, 1989.
DOI : 10.1016/S0022-3476(89)80085-X

I. J. Hopkins, I. Humphrey, C. G. Keith, M. Susman, G. C. Webb et al., The Aicardi Syndrome in a 47, XXY Male, Journal of Paediatrics and Child Health, vol.26, issue.4, pp.15-278, 1979.
DOI : 10.1111/j.1440-1754.1979.tb01246.x

J. Aicardi, Aicardi syndrome: old and new findings, Int. Pediatr, vol.14, pp.5-8, 1999.

S. K. Prakash, R. Paylor, S. Jenna, N. Lamarche-vane, D. L. Armstrong et al., Functional analysis of ARHGAP6, a novel GTPase-activating protein for RhoA, Human Molecular Genetics, vol.9, issue.4, pp.477-488, 2000.
DOI : 10.1093/hmg/9.4.477

M. Bauters, H. Van-esch, P. Marynen, and G. , Froyen, X chromosome array-CGH for the identification of novel Xlinked mental retardation genes, Eur. J. Med. Genet, pp.48-263, 2005.

H. Van-esch, M. Bauters, J. Ignatius, M. Jansen, M. Raynaud et al., Duplication of the MECP2 Region Is a Frequent Cause of Severe Mental Retardation and Progressive Neurological Symptoms in Males, The American Journal of Human Genetics, vol.77, issue.3, p.77, 2005.
DOI : 10.1086/444549

J. R. Vermeesch, C. Melotte, G. Froyen, S. Van-vooren, B. Dutta et al., Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis, Journal of Histochemistry & Cytochemistry, vol.36, issue.3, pp.53-413, 2005.
DOI : 10.1086/379977

. Wechsler, Intelligence Scale for Children-Revised (WISC-R), 1974.

R. Stevenson, Splitting and lumping in the nosology of XLMR. American journal of medical genetics, pp.174-182, 2000.

H. Leonard and X. Wen, The epidemiology of mental retardation: challenges and opportunities in the new millennium. Mental retardation and developmental disabilities research reviews, pp.117-134, 2002.

J. Mclaren and S. Bryson, Review of recent epidemiological studies of mental retardation: prevalence, associated disorders, and etiology, Am J Ment Retard, vol.92, issue.3, pp.243-254, 1987.

B. Hagberg and M. Kyllerman, Epidemiology of mental retardation???A Swedish survey, Brain and Development, vol.5, issue.5, pp.441-449, 1983.
DOI : 10.1016/S0387-7604(83)80072-2

J. Flint and S. Knight, The use of telomere probes to investigate submicroscopic rearrangements associated with mental retardation. Current opinion in genetics & development, pp.310-316, 2003.

J. Chelly, M. Khelfaoui, F. Francis, B. Cherif, and T. Bienvenu, Genetics and pathophysiology of mental retardation, European Journal of Human Genetics, vol.45, issue.Spec No. 1, pp.701-713, 2006.
DOI : 10.1016/j.neuron.2005.01.038

H. Ropers, B. Hamel, A. Brouwer, H. Yntema, T. Kleefstra et al., X-linked mental retardation Nature reviews Mutation frequencies of X-linked mental retardation genes in families from the EuroMRX consortium. Human mutation, pp.46-57207, 2005.

R. Lehrke, Theory of X-linkage of major intellectual traits American journal of mental deficiency, pp.611-619, 1972.

J. Fishburn, G. Turner, A. Daniel, and R. Brookwell, The diagnosis and frequency of Xlinked conditions in a cohort of moderately retarded males with affected brothers. American journal of medical genetics, pp.713-724, 1983.

D. Herbst and J. Miller, Nonspecific X-linked mental retardation II: the frequency in British Columbia American journal of medical genetics, pp.461-469, 1980.

F. Raymond, X linked mental retardation: a clinical guide, Journal of Medical Genetics, vol.43, issue.3, pp.193-200, 2006.
DOI : 10.1136/jmg.2005.033043

J. Mandel and J. Chelly, Monogenic X-linked mental retardation: Is it as frequent as currently estimated? The paradox of the ARX (Aristaless X) mutations, European Journal of Human Genetics, vol.37, issue.9, pp.689-693, 2004.
DOI : 10.1136/jmg.37.12.e45

G. Neri, F. Gurrieri, A. Gal, and H. Lubs, XLMR genes: update 1990 American journal of medical genetics, pp.186-189, 1991.

P. Chiurazzi, E. Tabolacci, and G. Neri, X-linked mental retardation (XLMR): from clinical conditions to cloned genes. Critical reviews in clinical laboratory sciences, pp.117-158, 2004.

Y. Yu, S. Tsai, C. Hong, T. Chen, and C. Yang, Association Analysis for MAOA Gene Polymorphism with Long-Latency Auditory Evoked Potentials in Healthy Females, Neuropsychobiology, vol.18, issue.4, pp.288-291, 2004.
DOI : 10.1038/sj.mp.4000246

A. Caspi, J. Mcclay, T. Moffitt, J. Mill, J. Martin et al., Role of Genotype in the Cycle of Violence in Maltreated Children, Science, vol.297, issue.5582, pp.297851-854, 2002.
DOI : 10.1126/science.1072290

H. Ropers, X-linked mental retardation, Nature Reviews Genetics, vol.119, issue.1, pp.260-269, 2006.
DOI : 10.1002/ajmg.a.20195

URL : https://hal.archives-ouvertes.fr/hal-00187942

F. Laumonnier, P. Cuthbert, and S. Grant, The role of neuronal complexes in human X-linked brain diseases American journal of human genetics, pp.205-220, 2007.

S. Mcbride, C. Choi, Y. Wang, D. Liebelt, E. Braunstein et al., Pharmacological Rescue of Synaptic Plasticity, Courtship Behavior, and Mushroom Body Defects in a Drosophila Model of Fragile X Syndrome, Neuron, vol.45, issue.5, pp.45753-764, 2005.
DOI : 10.1016/j.neuron.2005.01.038

J. Aicardi and J. Chevrie, Rousselie F: [Spasma-in-flexion syndrome, callosal agenesis, chorioretinal abnormalities]. Archives francaises de pediatrie, pp.1103-1120, 1969.

A. Donnenfeld, R. Packer, E. Zackai, C. Chee, B. Sellinger et al., Clinical, cytogenetic, and pedigree findings in 18 cases of Aicardi syndrome. American journal of medical genetics, pp.461-467, 1989.

A. Menezes, D. Macgregor, and J. Buncic, Aicardi syndrome: Natural history and possible predictors of severity, Pediatric Neurology, vol.11, issue.4, pp.313-318, 1994.
DOI : 10.1016/0887-8994(94)90008-6

V. Sutton, B. Hopkins, T. Eble, N. Gambhir, and R. Lewis, Van den Veyver IB: Facial and physical features of Aicardi syndrome: infants to teenagers, Am J Med Genet A, vol.138, issue.3, pp.254-258, 2005.

T. Rosser, M. Acosta, and R. Packer, Aicardi syndrome: spectrum of disease and long-term prognosis in 77 females, Pediatric Neurology, vol.27, issue.5, pp.343-346, 2002.
DOI : 10.1016/S0887-8994(02)00450-2

J. Aicardi, Aicardi syndrome, Brain and Development, vol.27, issue.3, pp.164-171, 2005.
DOI : 10.1016/j.braindev.2003.11.011

A. Menezes, R. Enzenauer, and J. Buncic, Aicardi syndrome--the elusive mild case., British Journal of Ophthalmology, vol.78, issue.6
DOI : 10.1136/bjo.78.6.494

V. Chau, G. Karvelas, P. Jacob, and L. Carmant, Early treatment of Aicardi syndrome with vigabatrin can improve outcome, Neurology, vol.63, issue.9, pp.1756-1757, 2004.
DOI : 10.1212/01.WNL.0000143070.66093.D3

S. Grosso, G. Lasorella, A. Russo, P. Galluzzi, G. Morgese et al., Aicardi syndrome with favorable outcome: Case report and review, Brain and Development, vol.29, issue.7, pp.443-446, 2007.
DOI : 10.1016/j.braindev.2006.11.011

J. Aicardi, Aicardi syndrome: Old and new findings, Int Pediatr, vol.14, pp.5-8, 1999.

M. Yacoub, N. Missaoui, B. Tabarli, M. Ghorbel, K. Tlili et al., Syndrome d???Aicardi d?????volution favorable, Aicardi syndrome with favorable outcome, pp.530-532, 2003.
DOI : 10.1016/S0929-693X(03)00095-2

S. Carney, M. Brodsky, W. Good, C. Glasier, M. Greibel et al., Aicardi syndrome: More than meets the eye, Survey of Ophthalmology, vol.37, issue.6, pp.419-424, 1993.
DOI : 10.1016/0039-6257(93)90139-X

E. Mcpherson and S. Jones, Cleft lip and palate in Aicardi syndrome American journal of medical genetics, pp.318-319, 1990.

W. Umansky, J. Neidich, and S. Schendel, The association of cleft lip and palate with Aicardi syndrome. Plastic and reconstructive surgery, pp.595-597, 1994.

R. Trifiletti, G. Incorpora, A. Polizzi, M. Cocuzza, E. Bolan et al., Aicardi syndrome with multiple tumors: a case report with literature review, Brain and Development, vol.17, issue.4, pp.283-285457, 1995.
DOI : 10.1016/0387-7604(95)00045-D

A. Matlary, T. Prescott, B. Tvedt, K. Lindberg, A. Server et al., Aicardi syndrome in a girl with mild developmental delay, absence of epilepsy and normal EEG, Clinical Dysmorphology, vol.13, issue.4, pp.257-260, 2004.
DOI : 10.1097/00019605-200410000-00012

S. Lee, K. Kim, S. Cho, and S. Lee, An Atypical Case of Aicardi Syndrome with Favorable Outcome, Korean Journal of Ophthalmology, vol.18, issue.1, pp.79-83, 2004.
DOI : 10.3341/kjo.2004.18.1.79

P. Vinas, J. , M. Gonzalez, M. , G. Ribes et al., Callosal agenesis, chorioretinal lacunae, absence of infantile spasms, and normal development: Aicardi syndrome without epilepsy? Developmental medicine and child neurology Role of ocular involvement in the prediction of visual development and clinical prognosis in Aicardi syndrome. The British journal of ophthalmology, pp.419-420805, 1996.

J. Molina, F. Mateos, M. Merino, J. Epifanio, and M. Gorrono, Aicardi syndrome in two sisters. The Journal of pediatrics, pp.282-283, 1989.

D. Taggard and A. Menezes, Three Choroid Plexus Papillomas in a Patient with Aicardi Syndrome, Pediatric Neurosurgery, vol.33, issue.4, pp.219-223, 2000.
DOI : 10.1159/000055956

I. Hopkins, I. Humphrey, C. Keith, M. Susman, G. Webb et al., The Aicardi Syndrome in a 47, XXY Male, Journal of Paediatrics and Child Health, vol.26, issue.4, pp.278-280, 1979.
DOI : 10.1111/j.1440-1754.1979.tb01246.x

H. Hoag, S. Taylor, A. Duncan, and M. Khalifa, Evidence that skewed X inactivation is not needed for the phenotypic expression of Aicardi syndrome. Human genetics, pp.3-4459, 1997.

M. Lyon, Sex chromatin and gene action in the mammalian X-chromosome

M. Barr and . Hj, A quantitative study of certain morphological changes in spinal motor neurons during axon reaction, The Journal of Comparative Neurology, vol.23, issue.2, pp.93-121, 1948.
DOI : 10.1113/jphysiol.1898.sp000717

C. Brown, W. Robinson, C. Brown, R. Lafreniere, V. Powers et al., Localization of the X inactivation centre on the human X chromosome in Xq13 Brown SD: XIST and the mapping of the X chromosome inactivation centre Requirement for Xist in X chromosome inactivation, 55. Panning B, Dausman J, Jaenisch R: X chromosome inactivation is mediated by Xist RNA stabilization, pp.353-36382, 1991.

N. Xu, C. Tsai, and J. Lee, Transient Homologous Chromosome Pairing Marks the Onset of X Inactivation, Science, vol.311, issue.5764, pp.3111149-1152, 2006.
DOI : 10.1126/science.1122984

C. Bacher, M. Guggiari, B. Brors, S. Augui, P. Clerc et al., Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation, Nature Cell Biology, vol.379, issue.3, pp.293-299, 2006.
DOI : 10.1038/379131a0

L. Carrel and H. Willard, Counting on Xist, Nature Genetics, vol.4, issue.3, pp.211-212, 1998.
DOI : 10.1007/BF00364788

R. Wettke-schafer and G. Kantner, X-linked dominant inherited diseases with lethality in hemizygous males. Human genetics, pp.1-23, 1983.

B. Migeon, J. Axelman, J. De-beur, S. Valle, D. Mitchell et al., Selection against lethal alleles in females heterozygous for incontinentia pigmenti, American journal of human genetics, vol.44, issue.1, pp.100-106, 1989.

P. Wieacker, J. Zimmer, and H. Ropers, X inactivation patterns in two syndromes with probable X-linked dominant, male lethal inheritance, Clinical Genetics, vol.28, issue.3, pp.238-242, 1985.
DOI : 10.1111/j.1399-0004.1985.tb00392.x

J. Neidich, R. Nussbaum, R. Packer, B. Emanuel, and J. Puck, Heterogeneity of clinical severity and molecular lesions in Aicardi syndrome. The Journal of pediatrics, pp.911-917, 1990.

F. Collins, Positional cloning: Let's not call it reverse anymore, Nature Genetics, vol.88, issue.1, pp.3-6, 1992.
DOI : 10.1038/355637a0

J. Weissenbach, G. Gyapay, C. Dib, A. Vignal, J. Morissette et al., A second-generation linkage map of the human genome, Nature, vol.359, issue.6398, pp.359794-801, 1992.
DOI : 10.1038/359794a0

H. Ropers, O. Zuffardi, E. Bianchi, L. Tiepolo, J. Neidich et al., Agenesis of corpus callosum, ocular, and skeletal anomalies (X-linked dominant Aicardi's syndrome) in a girl with balanced X/3 translocation. Human genetics Heterogeneity in clinical severity and molecular lesions in Aicardi syndrome, American journal of human genetics, vol.61, issue.66A91, pp.364-368, 1982.

A. Donnenfeld, J. Graham, J. Packer, R. Aquino, R. Berg et al., Microphthalmia and chorioretinal lesions in a girl with an Xp22.2-pter deletion and partial 3p trisomy: clinical observations relevant to Aicardi syndrome gene localization American journal of medical genetics, pp.182-186, 1990.

K. Naritomi, Y. Izumikawa, S. Nagataki, Y. Fukushima, K. Wakui et al., Combined Goltz and Aicardi syndromes in a terminal Xp deletion: are they a contiguous gene syndrome? American journal of medical genetics Van den Veyver IB: Microphthalmia with linear skin defects (MLS), Aicardi, and Goltz syndromes: are they related X-linked dominant male-lethal disorders? Cytogenetic and genome researchX;Y) females with linear skin defects and congenital microphthalmia: a new syndrome at Xp22.3, XX,t( Journal of medical, vol.43, issue.271, pp.839-843289, 1990.

I. Temple, J. Hurst, S. Hing, L. Butler, and M. Baraitser, De novo deletion of Xp22.2-pter in a female with linear skin lesions of the face and neck, microphthalmia, and anterior chamber eye anomalies., Journal of Medical Genetics, vol.27, issue.1, pp.56-58, 1990.
DOI : 10.1136/jmg.27.1.56

R. Happle, O. Daniels, and R. Koopman, MIDAS syndrome (microphthalmia, dermal aplasia, and sclerocornea): an X-linked phenotype distinct from Goltz syndrome. American journal of medical genetics, pp.710-713, 1993.

M. Morleo, T. Pramparo, L. Perone, G. Gregato, L. Caignec et al., Microphthalmia with linear skin defects (MLS) syndrome: Clinical, cytogenetic, and molecular characterization of 11 cases, American Journal of Medical Genetics Part A, vol.138, issue.2, pp.190-198, 2005.
DOI : 10.1001/archopht.1994.01090180151050

S. Prakash, T. Cormier, A. Mccall, J. Garcia, R. Sierra et al., Van Den Veyver IB: Loss of holocytochrome c-type synthetase causes the male lethality of X-linked dominant microphthalmia with linear skin defects (MLS) syndrome. Human molecular genetics, pp.113237-3248, 2002.

K. Nielsen, M. Anvret, O. Flodmark, P. Furuskog, and K. Bohman-valis, Aicardi syndrome: early neuroradiological manifestations and results of DNA studies in one patient American journal of medical genetics DD: Presence of filamin in the astrocytic inclusions of Aicardi syndrome, Pediatric neurology, vol.38, issue.301, pp.65-687, 1991.

V. Curwen, E. Eyras, T. Andrews, L. Clarke, E. Mongin et al., The Ensembl Automatic Gene Annotation System, Genome Research, vol.14, issue.5, pp.942-950, 2004.
DOI : 10.1101/gr.1858004

X. Wang, R. Sutton, V. , O. Peraza-llanes, J. Yu et al., Mutations in X-linked PORCN, a putative regulator of Wnt signaling, cause focal dermal hypoplasia, Nature Genetics, vol.9, issue.7, pp.39836-838, 2007.
DOI : 10.1111/j.1600-0560.1982.tb01063.x

K. Grzeschik, D. Bornholdt, F. Oeffner, A. Konig, D. C. Boente et al., Deficiency of PORCN, a regulator of Wnt signaling, is associated with focal dermal hypoplasia, Nature Genetics, vol.11, issue.7, pp.39833-835, 2007.
DOI : 10.1002/ajmg.10456

D. Pinkel, R. Segraves, D. Sudar, S. Clark, I. Poole et al., High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays, Nature Genetics, vol.26, issue.2, pp.207-211, 1998.
DOI : 10.1016/0888-7543(95)80092-Z

D. Pinkel and D. Albertson, Comparative genomic hybridization. Annual review of genomics and human genetics, pp.331-354, 2005.

J. Schoumans, B. Anderlid, E. Blennow, B. Teh, M. Nordenskjold et al., The performance of CGH array for the detection of cryptic constitutional chromosome imbalances Journal of medical genetics Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances, Genes, chromosomes & cancer, vol.41, issue.204, pp.198-202399, 1997.

D. Pinkel and D. Albertson, Array comparative genomic hybridization and its applications in cancer, Nature Genetics, vol.95, issue.6s, pp.11-17, 2005.
DOI : 10.1038/ng1408

D. Albertson, Profiling breast cancer by array CGH. Breast cancer research and treatment, pp.289-298, 2003.
DOI : 10.1023/a:1023025506386

F. Jehee, C. Rosenberg, A. Krepischi-santos, F. Kok, J. Knijnenburg et al., An Xq22.3 duplication detected by comparative genomic hybridization microarray (Array-CGH) defines a new locus (FGS5) for FG syndrome, American Journal of Medical Genetics Part A, vol.58, issue.3, pp.221-226, 2005.
DOI : 10.1002/ajmg.a.30991

C. Bruder, C. Hirvela, I. Tapia-paez, I. Fransson, R. Segraves et al., High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH. Human molecular genetics Chromosome 22 tiling-path array-CGH analysis identifies germ-line-and tumor-specific aberrations in patients with glioblastoma multiforme al: A tiling resolution DNA microarray with complete coverage of the human genome, Genes, chromosomes & cancer Nat Genet, vol.10, issue.363, pp.271-282161, 2001.

J. Pollack, C. Perou, A. Alizadeh, M. Eisen, A. Pergamenschikov et al., Genome-wide analysis of DNA copy-number changes using cDNA microarrays, Nat Genet, vol.23, issue.1, pp.41-46, 1999.

P. Dhami, A. Coffey, S. Abbs, J. Vermeesch, J. Dumanski et al., Exon Array CGH: Detection of Copy-Number Changes at the Resolution of Individual Exons in the Human Genome, The American Journal of Human Genetics, vol.76, issue.5, pp.76750-762, 2005.
DOI : 10.1086/429588

B. Carvalho, E. Ouwerkerk, G. Meijer, and B. Ylstra, High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides, Journal of Clinical Pathology, vol.57, issue.6, pp.644-646, 2004.
DOI : 10.1136/jcp.2003.013029

J. Pollack, T. Sorlie, C. Perou, C. Rees, S. Jeffrey et al., Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors, Proceedings of the National Academy of Sciences, vol.340, issue.26, pp.9912963-12968, 2002.
DOI : 10.1042/0264-6021:3400621

G. Bignell, J. Huang, J. Greshock, S. Watt, A. Butler et al., High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays, Genome Research, vol.14, issue.2, pp.287-295, 2004.
DOI : 10.1101/gr.2012304

T. Okamoto, T. Suzuki, and N. Yamamoto, Microarray fabrication with covalent attachment of DNA using Bubble Jet technology, Nature Biotechnology, vol.7, issue.4, pp.438-441, 2000.
DOI : 10.1248/cpb.29.1130

T. Hughes, M. Mao, A. Jones, J. Burchard, M. Marton et al., Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer, Nature Biotechnology, vol.24, issue.7, pp.342-347, 2001.
DOI : 10.1126/science.278.5338.680

J. Bailey, Z. Gu, R. Clark, K. Reinert, R. Samonte et al., Recent Segmental Duplications in the Human Genome, Science, vol.297, issue.5583, pp.2971003-1007, 2002.
DOI : 10.1126/science.1072047

L. Armengol, M. Pujana, J. Cheung, S. Scherer, and X. Estivill, Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements, Human Molecular Genetics, vol.12, issue.17, pp.122201-2208, 2003.
DOI : 10.1093/hmg/ddg223

J. Bailey, R. Baertsch, W. Kent, D. Haussler, and E. Eichler, Hotspots of mammalian chromosomal evolution, Genome Biology, vol.5, issue.4, p.23, 2004.
DOI : 10.1186/gb-2004-5-4-r23

A. Iafrate, L. Feuk, M. Rivera, M. Listewnik, P. Donahoe et al., Detection of large-scale variation in the human genome, Nature Genetics, vol.36, issue.9, pp.949-951, 2004.
DOI : 10.1038/ng1307

S. Mccarroll, T. Hadnott, G. Perry, P. Sabeti, M. Zody et al., Common deletion polymorphisms in the human genome, Nature Genetics, vol.21, issue.1, pp.86-92, 2006.
DOI : 10.1042/bj3000271

J. Sebat, B. Lakshmi, J. Troge, A. J. Young, J. Lundin et al., Large-Scale Copy Number Polymorphism in the Human Genome, Science, vol.305, issue.5683, pp.305525-528, 2004.
DOI : 10.1126/science.1098918

B. De-vries, R. Pfundt, M. Leisink, D. Koolen, L. Vissers et al., Diagnostic Genome Profiling in Mental Retardation, The American Journal of Human Genetics, vol.77, issue.4, pp.606-616, 2005.
DOI : 10.1086/491719

J. Freeman, G. Perry, L. Feuk, R. Redon, S. Mccarroll et al., Copy number variation: New insights in genome diversity, Genome Research, vol.16, issue.8, pp.16949-961, 2006.
DOI : 10.1101/gr.3677206

E. Tuzun, A. Sharp, J. Bailey, R. Kaul, V. Morrison et al., Fine-scale structural variation of the human genome, Nature Genetics, vol.5, issue.Suppl, pp.37727-732, 2005.
DOI : 10.1097/00008571-199510000-00010

P. Aldred, E. Hollox, and J. Armour, Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3. Human molecular genetics, pp.2045-2052, 2005.

A. Sharp, Z. Cheng, and E. Eichler, Structural variation of the human genome. Annual review of genomics and human genetics, pp.407-442, 2006.

D. Kleinjan and V. Van-heyningen, Position effect in human genetic disease. Human molecular genetics, pp.1611-1618, 1998.

M. Johnson, L. Viggiano, J. Bailey, M. Abdul-rauf, G. Goodwin et al., Positive selection of a gene family during the emergence of humans and African apes, Nature, vol.3, issue.6855, pp.413514-519, 2001.
DOI : 10.1016/B978-1-4832-3211-9.50009-7

C. Paulding, M. Ruvolo, and D. Haber, The Tre2 (USP6) oncogene is a hominoid-specific gene, Proceedings of the National Academy of Sciences, vol.408, issue.6810, pp.2507-2511, 2003.
DOI : 10.1038/35042526

J. Beckmann, X. Estivill, and S. Antonarakis, Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability, Nature Reviews Genetics, vol.39, issue.8, pp.639-646, 2007.
DOI : 10.1186/1479-7364-2-6-383

B. Emanuel and T. Shaikh, Segmental duplications: an 'expanding' role in genomic instability and disease, Nature Reviews Genetics, vol.67, issue.10, pp.791-800, 2001.
DOI : 10.1002/(SICI)1096-8628(19980123)75:3<288::AID-AJMG12>3.0.CO;2-L

A. Sharp, D. Locke, S. Mcgrath, Z. Cheng, J. Bailey et al., Segmental Duplications and Copy-Number Variation in the Human Genome, The American Journal of Human Genetics, vol.77, issue.1, pp.78-88, 2005.
DOI : 10.1086/431652

X. Zhang, A. Snijders, R. Segraves, X. Zhang, A. Niebuhr et al., High-Resolution Mapping of Genotype-Phenotype Relationships in Cri du Chat Syndrome Using Array Comparative Genomic Hybridization, The American Journal of Human Genetics, vol.76, issue.2, pp.312-326, 2005.
DOI : 10.1086/427762

R. Redon, S. Ishikawa, K. Fitch, L. Feuk, G. Perry et al., Global variation in copy number in the human genome, Nature, vol.38, issue.7118, pp.444444-454, 2006.
DOI : 10.1126/science.1117196

D. Locke, R. Segraves, R. Nicholls, S. Schwartz, D. Pinkel et al., BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications, Journal of Medical Genetics, vol.41, issue.3, pp.41175-182, 2004.
DOI : 10.1136/jmg.2003.013813

K. Shianna and H. Willard, Human genomics: In search of normality, Nature, vol.444, issue.7118, pp.428-429, 2006.
DOI : 10.1126/science.1101160

N. Carter, Methods and strategies for analyzing copy number variation using DNA microarrays, Nature Genetics, vol.5, issue.7s, p.16, 2007.
DOI : 10.1017/S0001566000006607

J. Bueno-filho, S. Gilmour, and G. Rosa, Design of Microarray Experiments for Genetical Genomics Studies, Genetics, vol.174, issue.2, pp.945-957, 2006.
DOI : 10.1534/genetics.106.057281

L. Vissers, C. Van-ravenswaaij, R. Admiraal, J. Hurst, B. De-vries et al., Mutations in a new member of the chromodomain gene family cause CHARGE syndrome, Nature Genetics, vol.63, issue.9, pp.955-957, 2004.
DOI : 10.1086/302122

N. Solomon, S. Ross, T. Morgan, J. Belsky, F. Hol et al., Array comparative genomic hybridisation analysis of boys with X linked hypopituitarism identifies a 3.9 Mb duplicated critical region at Xq27 containing SOX3, Journal of medical genetics, issue.9, pp.41669-678, 2004.

B. Dave and W. Sanger, Role of cytogenetics and molecular cytogenetics in the diagnosis of genetic imbalances. Seminars in pediatric neurology, pp.2-6, 2007.

C. Shaw-smith, R. Redon, L. Rickman, M. Rio, L. Willatt et al., Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features, Journal of Medical Genetics, vol.41, issue.4, pp.241-248, 2004.
DOI : 10.1136/jmg.2003.017731

S. Murthy, A. Nygren, E. Shakankiry, H. Schouten, J. et al., Detection of a novel familial deletion of four genes between BP1 and BP2 of the Prader-Willi/Angelman syndrome critical region by oligo-array CGH in a child with neurological disorder and speech impairment, Cytogenetic and Genome Research, vol.73, issue.1-2, pp.135-140, 2007.
DOI : 10.1086/379977

H. Van-esch, A. Jansen, M. Bauters, G. Froyen, and J. Fryns, Encephalopathy and bilateral cataract in a boy with an interstitial deletion of Xp22 comprising the CDKL5 and NHS genes, American Journal of Medical Genetics Part A, vol.75, issue.4, pp.364-369, 2007.
DOI : 10.1002/ajmg.a.31572

G. Toruner, D. Streck, M. Schwalb, and J. Dermody, An oligonucleotide based array-CGH system for detection of genome wide copy number changes including subtelomeric regions for genetic evaluation of mental retardation, American Journal of Medical Genetics Part A, vol.115, issue.8, pp.143824-829, 2007.
DOI : 10.1002/ajmg.a.31656

L. Vissers, P. Stankiewicz, S. Yatsenko, E. Crawford, H. Creswick et al., Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies Human genetics, 2007.

D. Lugtenberg, H. Yntema, M. Banning, A. Oudakker, H. Firth et al., ZNF674: A New Kr??ppel-Associated Box???Containing Zinc-Finger Gene Involved in Nonsyndromic X-Linked Mental Retardation, The American Journal of Human Genetics, vol.78, issue.2, pp.265-278, 2006.
DOI : 10.1086/500306

T. Golub, D. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek et al., Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring, Science, vol.286, issue.5439, pp.286531-537, 1999.
DOI : 10.1126/science.286.5439.531

M. Van-de-vijver, Y. He, . Van-'t, L. Veer, H. Dai et al., A Gene-Expression Signature as a Predictor of Survival in Breast Cancer, New England Journal of Medicine, vol.347, issue.25, pp.3471999-2009, 2002.
DOI : 10.1056/NEJMoa021967

T. Sorlie, C. Perou, R. Tibshirani, T. Aas, S. Geisler et al., Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications, Proceedings of the National Academy of Sciences, vol.179, issue.1, pp.9810869-10874, 2001.
DOI : 10.1002/(SICI)1096-9896(199605)179:1<31::AID-PATH523>3.0.CO;2-O

A. Alizadeh and L. Staudt, Genomic-scale gene expression profiling of normal and malignant immune cells, Current Opinion in Immunology, vol.12, issue.2, pp.219-225, 2000.
DOI : 10.1016/S0952-7915(99)00078-3

A. Alizadeh, M. Eisen, R. Davis, C. Ma, I. Lossos et al., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling, Nature, vol.303, issue.6769, pp.403503-511, 2000.
DOI : 10.1016/S0076-6879(99)03014-1

G. Churchill, Fundamentals of experimental design for cDNA microarrays, Nature Genetics, vol.32, issue.Supp, pp.490-495, 2002.
DOI : 10.1038/ng1031

Y. Yang and T. Speed, Design issues for cDNA microarray experiments, Nature Reviews Genetics, vol.33, issue.8, pp.579-588, 2002.
DOI : 10.1073/pnas.231625398

P. Pavlidis, Q. Li, and W. Noble, The effect of replication on gene expression microarray experiments, Bioinformatics, vol.19, issue.13, pp.1620-1627, 2003.
DOI : 10.1093/bioinformatics/btg227

M. Lee, F. Kuo, G. Whitmore, and J. Sklar, Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations, Proceedings of the National Academy of Sciences, vol.95, issue.25, pp.979834-9839, 2000.
DOI : 10.1073/pnas.95.25.14863

D. Allison, X. Cui, G. Page, and M. Sabripour, Microarray data analysis: from disarray to consolidation and consensus, Nature Reviews Genetics, vol.12, issue.Suppl. 2, pp.55-65, 2006.
DOI : 10.1089/cmb.2005.12.482

Y. Leung and D. Cavalieri, Fundamentals of cDNA microarray data analysis, Trends in Genetics, vol.19, issue.11, pp.649-659, 2003.
DOI : 10.1016/j.tig.2003.09.015

K. Dobbin, J. Shih, and R. Simon, Questions and Answers on Design of Dual-Label Microarrays for Identifying Differentially Expressed Genes, JNCI Journal of the National Cancer Institute, vol.94, issue.13, pp.951362-1369, 2003.
DOI : 10.1093/jnci/94.13.990

R. Miller, A. Galecki, and R. Shmookler-reis, Interpretation, design, and analysis of gene array expression experiments. The journals of gerontology, pp.52-57, 2001.

P. Baldi and A. Long, A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes, Bioinformatics, vol.17, issue.6, pp.509-519, 2001.
DOI : 10.1093/bioinformatics/17.6.509

M. Kerr, M. Martin, and G. Churchill, Analysis of Variance for Gene Expression Microarray Data, Journal of Computational Biology, vol.7, issue.6, pp.819-837, 2000.
DOI : 10.1089/10665270050514954

S. Draghici, O. Kulaeva, B. Hoff, A. Petrov, S. Shams et al., Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays, Bioinformatics, vol.19, issue.11, pp.191348-1359, 2003.
DOI : 10.1093/bioinformatics/btg165

N. Mah, A. Thelin, T. Lu, S. Nikolaus, T. Kuhbacher et al., A comparison of oligonucleotide and cDNA-based microarray systems, Physiological Genomics, vol.16, issue.3, pp.361-370, 2004.
DOI : 10.1093/nar/30.10.e48

Y. Moreau, S. Aerts, D. Moor, B. , D. Strooper et al., Comparison and meta-analysis of microarray data: from the bench to the computer desk, Trends in Genetics, vol.19, issue.10, pp.570-577, 2003.
DOI : 10.1016/j.tig.2003.08.006

S. Draghici, P. Khatri, A. Eklund, and Z. Szallasi, Reliability and reproducibility issues in DNA microarray measurements, Trends in Genetics, vol.22, issue.2, pp.101-109, 2006.
DOI : 10.1016/j.tig.2005.12.005

C. Lock, G. Hermans, R. Pedotti, A. Brendolan, E. Schadt et al., Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis, Nature Medicine, vol.158, issue.5, pp.500-508, 2002.
DOI : 10.1126/science.1325670

S. Dhanasekaran, T. Barrette, D. Ghosh, R. Shah, S. Varambally et al., Delineation of prognostic biomarkers in prostate cancer, Nature, vol.6, issue.6849, pp.412822-826, 2001.
DOI : 10.1002/pros.2990110405

. Van-'t, L. Veer, H. Dai, M. Van-de-vijver, Y. He et al., Gene expression profiling predicts clinical outcome of breast cancer, Nature, issue.6871, pp.415530-536, 2002.

M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor et al., Molecular classification of cutaneous malignant melanoma by gene expression profiling, Nature, issue.6795, pp.406536-540, 2000.

A. Young, M. Amin, C. Moreno, S. Lim, C. Cohen et al., Expression Profiling of Renal Epithelial Neoplasms, The American Journal of Pathology, vol.158, issue.5, pp.1639-1651, 2001.
DOI : 10.1016/S0002-9440(10)64120-X

A. Abdullah-sayani, J. Bueno-de-mesquita, and M. Van-de-vijver, Technology Insight: tuning into the genetic orchestra using microarrays--limitations of DNA microarrays in clinical practice. Nature clinical practice, pp.501-516, 2006.

R. Simon, M. Radmacher, and K. Dobbin, Design of studies using DNA microarrays, Genetic Epidemiology, vol.8, issue.1, pp.21-36, 2002.
DOI : 10.1089/106652701753307520

G. Peyman, A. Kazi, M. Riazi-esfahani, E. Aydin, M. Kivilcim et al., The Effect of Combinations of Flurbiprofen, Low Molecular Weight Heparin, and Doxycycline on the Inhibition of Corneal Neovascularization, Cornea, vol.25, issue.5, pp.582-585, 2006.
DOI : 10.1097/01.ico.0000220767.73660.3a

J. Quackenbush and . Genomics, GENOMICS: Microarrays--Guilt by Association, Science, vol.302, issue.5643, pp.240-241, 2003.
DOI : 10.1126/science.1090887

R. Balasubramanian, T. Laframboise, D. Scholtens, and R. Gentleman, A graph-theoretic approach to testing associations between disparate sources of functional genomics data, Bioinformatics, vol.20, issue.18, pp.3353-3362, 2004.
DOI : 10.1093/bioinformatics/bth405

C. Giallourakis, C. Henson, M. Reich, X. Xie, and V. Mootha, Disease gene discovery through integrative genomics. Annual review of genomics and human genetics, pp.381-406, 2005.

V. Mootha, P. Lepage, K. Miller, J. Bunkenborg, M. Reich et al., Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics, Proceedings of the National Academy of Sciences, vol.14, issue.16, pp.605-610, 2003.
DOI : 10.1046/j.1432-1327.1998.2550156.x

H. Meng, I. Vera, C. N. Wang, X. Wang, S. Ingram-drake et al., Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics, Proceedings of the National Academy of Sciences, vol.173, issue.2, pp.1044530-4535, 2007.
DOI : 10.1534/genetics.106.057455

H. Bilofsky, C. Burks, J. Fickett, W. Goad, F. Lewitter et al., The GenBank genetic sequence databank. Nucleic acids research, pp.1-4, 1986.

G. Hamm and G. Cameron, The EMBL data library. Nucleic acids research, pp.5-9, 1986.

D. George, W. Barker, and L. Hunt, The protein identification resource (PIR) Nucleic acids research, pp.11-15, 1986.

M. Galperin, The Molecular Biology Database Collection: 2007 update. Nucleic acids research, pp.3-4, 2007.

D. Maglott, J. Ostell, K. Pruitt, and T. Tatusova, Entrez Gene: gene-centered information at NCBI. Nucleic acids research, pp.26-31, 2007.

J. Blake, J. Eppig, C. Bult, J. Kadin, and J. Richardson, MGD: the Mouse Genome Database, Nucleic Acids Research, vol.31, issue.1, pp.562-567, 2006.
DOI : 10.1093/nar/gkg047

J. Sprague, L. Bayraktaroglu, D. Clements, T. Conlin, D. Fashena et al., The Zebrafish Information Network: the zebrafish model organism database, Nucleic Acids Research, vol.34, issue.90001, pp.34-581, 2006.
DOI : 10.1093/nar/gkj086

J. Hirschman, R. Balakrishnan, K. Christie, M. Costanzo, S. Dwight et al., Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome, Nucleic Acids Research, vol.34, issue.90001, pp.34-442, 2006.
DOI : 10.1093/nar/gkj117

R. Tatusov, N. Fedorova, J. Jackson, A. Jacobs, B. Kiryutin et al., The COG database: an updated version includes eukaryotes, BMC Bioinformatics, vol.4, issue.1, p.41, 2003.
DOI : 10.1186/1471-2105-4-41

M. Crosby, J. Goodman, V. Strelets, P. Zhang, and W. Gelbart, FlyBase: genomes by the dozen. Nucleic acids research, pp.486-491, 2007.

V. Mckusick, Mendelian Inheritance in Man and its online version, OMIM. American journal of human genetics, pp.588-604, 2007.

C. Stoeckert, J. Causton, H. Ball, and C. , Microarray databases: standards and ontologies, Nature Genetics, vol.32, issue.Supp, pp.469-473, 2002.
DOI : 10.1038/ng1028

M. Ashburner, C. Ball, J. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000.
DOI : 10.1091/mbc.9.12.3273

E. Camon, D. Barrell, V. Lee, E. Dimmer, and R. Apweiler, The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase, silico biology, pp.5-6, 2004.

P. Khatri and S. Draghici, Ontological analysis of gene expression data: current tools, limitations, and open problems, Bioinformatics, vol.5, issue.4, pp.3587-3595, 2005.
DOI : 10.1186/1471-2105-5-16

C. Pasquier, F. Girardot, J. De-fombelle, K. , and C. R. , THEA: ontology-driven analysis of microarray data, Bioinformatics, vol.20, issue.16, pp.2636-2643, 2004.
DOI : 10.1093/bioinformatics/bth295

URL : https://hal.archives-ouvertes.fr/hal-00170450

B. Zeeberg, W. Feng, G. Wang, M. Wang, A. Fojo et al., GoMiner: a resource for biological interpretation of genomic and proteomic data, Genome Biology, vol.4, issue.4, p.28, 2003.
DOI : 10.1186/gb-2003-4-4-r28

B. Zeeberg, H. Qin, S. Narasimhan, M. Sunshine, H. Cao et al., High-Throughput GoMiner, an 'industrialstrength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID), BMC Bioinformatics, vol.6, issue.1, p.168, 2005.
DOI : 10.1186/1471-2105-6-168

S. Draghici, P. Khatri, P. Bhavsar, A. Shah, S. Krawetz et al., Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate, Nucleic Acids Research, vol.31, issue.13, pp.313775-3781, 2003.
DOI : 10.1093/nar/gkg624

F. Al-shahrour, R. Diaz-uriarte, and J. Dopazo, FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes, Bioinformatics, vol.20, issue.4, pp.578-580, 2004.
DOI : 10.1093/bioinformatics/btg455

T. Dryja, T. Mcgee, E. Reichel, L. Hahn, G. Cowley et al., A point mutation of the rhodopsin gene in one form of retinitis pigmentosa, Nature, vol.343, issue.6256, pp.343364-366, 1990.
DOI : 10.1038/343364a0

G. Jimenez-sanchez, B. Childs, and D. Valle, Human disease genes, Nature, vol.56, issue.6822, pp.853-855, 2001.
DOI : 10.1002/ajmg.1320560404

N. Lopez-bigas, B. Blencowe, and C. Ouzounis, Highly consistent patterns for inherited human diseases at the molecular level, Bioinformatics, vol.3, issue.Suppl. 2, pp.269-277, 2006.
DOI : 10.1186/jbiol16

N. Lopez-bigas and C. Ouzounis, Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic acids research, pp.3108-3114, 2004.

E. Adie, R. Adams, K. Evans, D. Porteous, and B. Pickard, Speeding disease gene discovery by sequence based candidate prioritization, BMC Bioinformatics, vol.6, issue.1, p.55, 2005.
DOI : 10.1186/1471-2105-6-55

Z. Tu, L. Wang, M. Xu, X. Zhou, T. Chen et al., Further understanding human disease genes by comparing with housekeeping genes and other genes, BMC Genomics, vol.7, issue.1, p.31, 2006.
DOI : 10.1186/1471-2164-7-31

J. Xu and Y. Li, Discovering disease-genes by topological features in human protein???protein interaction network, Bioinformatics, vol.23, issue.22, pp.2800-2805, 2006.
DOI : 10.1007/s00246-001-0097-9

M. Oti, B. Snel, M. Huynen, and H. Brunner, Predicting disease genes using protein-protein interactions, Journal of Medical Genetics, vol.43, issue.8, pp.691-698, 2006.
DOI : 10.1136/jmg.2006.041376

B. Calvo, N. Lopez-bigas, S. Furney, P. Larranaga, and J. Lozano, A partially supervised classification approach to dominant and recessive human disease gene prediction. Computer methods and programs in biomedicine, pp.229-237, 2007.

J. Chelly and J. Mandel, Monogenic causes of X-linked mental retardation, Nature Reviews Genetics, vol.21, issue.9, pp.669-680, 2001.
DOI : 10.1016/S0896-6273(00)80651-0

J. Freudenberg and P. Propping, A similarity-based method for genome-wide prediction of disease-relevant human genes, Bioinformatics, vol.18, issue.Suppl 2, pp.110-115, 2002.
DOI : 10.1093/bioinformatics/18.suppl_2.S110

F. Turner, D. Clutterbuck, and C. Semple, POCUS: mining genomic sequence annotation to predict disease genes, Genome Biology, vol.4, issue.11, p.75, 2003.
DOI : 10.1186/gb-2003-4-11-r75

C. Perez-iratxeta, P. Bork, and M. Andrade, Association of genes to genetically inherited diseases using data mining, Nature Genetics, vol.25, issue.3, pp.316-319, 2002.
DOI : 10.1093/nar/25.17.3389

C. Perez-iratxeta, M. Wjst, P. Bork, and M. Andrade, G2D: a tool for mining genes associated with disease, BMC Genetics, vol.6, issue.1, p.45, 2005.
DOI : 10.1186/1471-2156-6-45

M. Masseroli, D. Martucci, F. Pinciroli, and . Gfinder, Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. Nucleic acids research, pp.293-300, 2004.

M. Masseroli, O. Galati, and F. Pinciroli, GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic acids research, pp.717-723, 2005.

E. Adie, R. Adams, K. Evans, D. Porteous, and B. Pickard, SUSPECTS: enabling fast and effective prioritization of positional candidates, Bioinformatics, vol.11, issue.1, pp.773-774, 2006.
DOI : 10.1038/sj.ejhg.5200918

S. Rossi, D. Masotti, C. Nardini, E. Bonora, G. Romeo et al., TOM: a web-based integrated approach for identification of candidate disease genes, Nucleic Acids Research, vol.34, issue.Web Server, pp.285-292, 2006.
DOI : 10.1093/nar/gkl340

S. Aerts, D. Lambrechts, S. Maity, V. Loo, P. Coessens et al., Gene prioritization through genomic data fusion, Nature Biotechnology, vol.352, issue.Suppl 2, pp.537-544, 2006.
DOI : 10.1056/NEJMoa042765

R. George, J. Liu, L. Feng, R. Bryson-richardson, D. Fatkin et al., Analysis of protein sequence and interaction data for candidate disease gene prediction, Nucleic Acids Research, vol.16, issue.19, pp.34-130, 2006.
DOI : 10.1101/gr.4526006

J. Chiang, J. Shin, H. Liu, and C. Chin, GeneLibrarian: an effective geneinformation summarization and visualization system, BMC Bioinformatics, vol.7, issue.1, p.392, 2006.
DOI : 10.1186/1471-2105-7-392

A. Franke, A. Wollstein, M. Teuber, M. Wittig, T. Lu et al., GENOMIZER: an integrated analysis system for genome-wide association data, Human Mutation, vol.76, issue.6, pp.27583-588, 2006.
DOI : 10.1002/humu.20306

H. Sun, H. Fang, T. Chen, R. Perkins, and W. Tong, GOFFA: Gene Ontology For Functional Analysis ??? A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data, BMC Bioinformatics, vol.7, issue.Suppl 2, p.23, 2006.
DOI : 10.1186/1471-2105-7-S2-S23

M. Van-driel, K. Cuelenaere, P. Kemmeren, J. Leunissen, H. Brunner et al., GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases, Nucleic Acids Research, vol.33, issue.Web Server, pp.758-761, 2005.
DOI : 10.1093/nar/gki435

W. Kent, F. Hsu, D. Karolchik, R. Kuhn, H. Clawson et al., Exploring relationships and mining data with the UCSC Gene Sorter, Genome Research, vol.15, issue.5, pp.737-741, 2005.
DOI : 10.1101/gr.3694705

N. Tiffin, J. Kelso, A. Powell, H. Pan, V. Bajic et al., Integration of text-and data-mining using ontologies successfully selects disease gene candidates. Nucleic acids research, pp.1544-1552, 2005.

C. Philippe, Cartographie physique du chromosome X humain. Nancy: Institut National Polytechnique de Lorraine, 1994.

L. Rainen, U. Oelmueller, S. Jurgensen, R. Wyrich, C. Ballas et al., Stabilization of mRNA expression in whole blood samples, Clinical chemistry, issue.11, pp.481883-1890, 2002.

V. Chai, A. Vassilakos, Y. Lee, J. Wright, and A. Young, Optimization of the PAXgene??? blood RNA extraction system for gene expression analysis of clinical samples, Journal of Clinical Laboratory Analysis, vol.48, issue.5, pp.182-188, 2005.
DOI : 10.1002/jcla.20075

M. Bauters, V. Esch, H. Marynen, P. Froyen, and G. , X chromosome array-CGH for the identification of novel X-linked mental retardation genes. European journal of medical genetics, pp.263-275, 2005.

R. Nadon and J. Shoemaker, Statistical issues with microarrays: processing and analysis, Trends in Genetics, vol.18, issue.5, pp.265-271, 2002.
DOI : 10.1016/S0168-9525(02)02665-3

D. Kreil and R. Russell, Tutorial section: There is no silver bullet -- a guide to low-level data transforms and normalisation methods for microarray data, Briefings in Bioinformatics, vol.6, issue.1, pp.86-97, 2005.
DOI : 10.1093/bib/6.1.86

J. Quackenbush, Microarray data normalization and transformation, Nature Genetics, vol.32, issue.Supp, pp.496-501, 2002.
DOI : 10.1038/ng1032

R. Allen, H. Zoghbi, A. Moseley, H. Rosenblatt, and J. Belmont, Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgenreceptor gene correlates with X chromosome inactivation, American journal of human genetics, issue.6, pp.511229-1239, 1992.

J. Zhang, L. Feuk, G. Duggan, R. Khaja, and S. Scherer, Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenetic and genome research, pp.3-4205, 2006.

M. Morley, C. Molony, T. Weber, J. Devlin, K. Ewens et al., Genetic analysis of genome-wide variation in human gene expression, Nature, vol.2, issue.7001, pp.430743-747, 2004.
DOI : 10.1159/000072312

D. Mutch, A. Berger, R. Mansourian, A. Rytz, and M. Roberts, The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data, BMC Bioinformatics, vol.3, issue.1, p.17, 2002.
DOI : 10.1186/1471-2105-3-17

M. Doherty, I. Glass, C. Bennett, P. Cotter, N. Watson et al., An Xp; Yq Translocation Causing a Novel Contiguous Gene Syndrome in Brothers with Generalized Epilepsy, Ichthyosis, and Attention Deficits, Epilepsia, vol.42, issue.12, pp.441529-1535, 2003.
DOI : 10.1038/sj.ejhg.5200402

C. Garcia, H. Blair, M. Seager, A. Coulthard, S. Tennant et al., Identification of a mutation in synapsin I, a synaptic vesicle protein, in a family with epilepsy, Journal of Medical Genetics, vol.41, issue.3, pp.41183-186, 2004.
DOI : 10.1136/jmg.2003.013680

D. Martin, C. Brun, R. E. Mouren, P. Thieffry, D. Jacq et al., GOToolBox: functional analysis of gene datasets based on Gene Ontology, Genome Biology, vol.5, issue.12, p.101, 2004.
DOI : 10.1186/gb-2004-5-12-r101

URL : https://hal.archives-ouvertes.fr/inserm-00095249

F. Jehee, D. Bertola, K. Yelavarthi, A. Krepischi-santos, C. Kim et al., An 11q11-q13.3 duplication, including FGF3 and FGF4 genes, in a patient with syndromic multiple craniosynostoses, Am J Med Genet A, issue.16, pp.1431912-1918, 2007.

N. Maas, T. Van-de-putte, C. Melotte, A. Francis, C. Schrander-stumpel et al., The C20orf133 gene is disrupted in a patient with Kabuki syndrome, Journal of medical genetics, 2007.

B. Thienpont, T. De-ravel, V. Esch, H. , V. Schoubroeck et al., Partial duplications of the ATRX gene cause the ATR-X syndrome, European Journal of Human Genetics, vol.51, issue.10, 2007.
DOI : 10.1159/000094223

G. Froyen, V. Esch, H. Bauters, M. Hollanders, K. Frints et al., Detection of genomic copy number changes in patients with idiopathic mental retardation by high-resolution X-array-CGH: important role for increased gene dosage of XLMR genes Human mutation, 2007.

B. Thienpont, L. Mertens, T. De-ravel, B. Eyskens, D. Boshoff et al., Submicroscopic chromosomal imbalances detected by array-CGH are a frequent cause of congenital heart defects in selected patients, European Heart Journal, vol.28, issue.22, 2007.
DOI : 10.1093/eurheartj/ehl560

D. Castermans, J. Vermeesch, J. Fryns, J. Steyaert, W. Van-de-ven et al., Identification and characterization of the TRIP8 and REEP3 genes on chromosome 10q21.3 as novel candidate genes for autism, European Journal of Human Genetics, vol.54, issue.4, pp.422-431, 2007.
DOI : 10.1002/ajmg.c.30078

A. Wozniak, R. Sciot, L. Guillou, P. Pauwels, B. Wasag et al., Array CGH analysis in primary gastrointestinal stromal tumors: Cytogenetic profile correlates with anatomic site and tumor aggressiveness, irrespective of mutational status, Genes, Chromosomes and Cancer, vol.53, issue.3, pp.261-276, 2007.
DOI : 10.1016/S0002-9440(10)64623-8

J. Friedman, A. Baross, A. Delaney, A. A. Arbour, L. Armstrong et al., Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation, The American Journal of Human Genetics, vol.79, issue.3, pp.79500-513, 2006.
DOI : 10.1086/507471

J. Vermeesch, H. Fiegler, N. De-leeuw, K. Szuhai, J. Schoumans et al., Guidelines for molecular karyotyping in constitutional genetic diagnosis, European Journal of Human Genetics, vol.17, issue.11, 2007.
DOI : 10.1111/j.1399-0004.2007.00756.x

J. Vermeesch, C. Melotte, G. Froyen, S. Van-vooren, B. Dutta et al., Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis, Journal of Histochemistry & Cytochemistry, vol.36, issue.3, pp.413-422, 2005.
DOI : 10.1086/379977

J. Lupski, R. De-oca-luna, S. Slaugenhaupt, L. Pentao, V. Guzzetta et al., DNA duplication associated with Charcot-Marie-Tooth disease type 1A, Cell, vol.66, issue.2, pp.219-232, 1991.
DOI : 10.1016/0092-8674(91)90613-4

B. Menten, N. Maas, B. Thienpont, K. Buysse, J. Vandesompele et al., Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports, Journal of Medical Genetics, vol.43, issue.8, pp.43625-633, 2006.
DOI : 10.1136/jmg.2005.039453

L. Vissers, J. Veltman, A. Van-kessel, and H. Brunner, Identification of disease genes by whole genome CGH arrays. Human molecular genetics, pp.215-223, 2005.

D. Lugtenberg, A. De-brouwer, T. Kleefstra, A. Oudakker, S. Frints et al., Chromosomal copy number changes in patients with non-syndromic X linked mental retardation detected by array CGH, Journal of Medical Genetics, vol.43, issue.4, pp.362-370, 2006.
DOI : 10.1136/jmg.2005.036178

H. Ropers, M. Hoeltzenbein, V. Kalscheuer, H. Yntema, B. Hamel et al., Nonsyndromic X-linked mental retardation: where are the missing mutations?, Trends in Genetics, vol.19, issue.6, pp.316-320, 2003.
DOI : 10.1016/S0168-9525(03)00113-6

J. Veltman, H. Yntema, D. Lugtenberg, H. Arts, S. Briault et al., High resolution profiling of X chromosomal aberrations by array comparative genomic hybridisation, Journal of Medical Genetics, vol.41, issue.6, pp.41425-432, 2004.
DOI : 10.1136/jmg.2004.018531

S. Yilmaz, H. Fontaine, K. Brochet, M. Gregoire, M. Devignes et al., Screening of subtle copy number changes in Aicardi syndrome patients with a high resolution X chromosome array-CGH. European journal of medical genetics, 2007.

A. Gargiulo, R. Auricchio, M. Barone, G. Cotugno, W. Reardon et al., Filamin A Is Mutated in X-Linked Chronic Idiopathic Intestinal Pseudo-Obstruction with Central Nervous System Involvement, The American Journal of Human Genetics, vol.80, issue.4, pp.751-758, 2007.
DOI : 10.1086/513321

V. Sheen, P. Dixon, J. Fox, S. Hong, L. Kinton et al., Mutations in the X-linked filamin 1 gene cause periventricular nodular heterotopia in males as well as in females, Human Molecular Genetics, vol.10, issue.17, pp.101775-1783, 2001.
DOI : 10.1093/hmg/10.17.1775

Y. Tang, D. Gilbert, T. Glauser, A. Hershey, and F. Sharp, Blood Gene Expression Profiling of Neurologic Diseases, Archives of Neurology, vol.62, issue.2, pp.210-215, 2005.
DOI : 10.1001/archneur.62.2.210

A. Hershey, Y. Tang, S. Powers, M. Kabbouche, D. Gilbert et al., Genomic Abnormalities in Patients With Migraine and Chronic Migraine: Preliminary Blood Gene Expression Suggests Platelet Abnormalities, Headache: The Journal of Head and Face Pain, vol.54, issue.2, pp.44994-1004, 2004.
DOI : 10.1016/S0140-6736(96)90669-8

D. Moore, H. Li, N. Jeffries, V. Wright, R. Cooper et al., Using Peripheral Blood Mononuclear Cells to Determine a Gene Expression Profile of Acute Ischemic Stroke: A Pilot Investigation, Circulation, vol.111, issue.2, pp.212-221, 2005.
DOI : 10.1161/01.CIR.0000152105.79665.C6

A. Achiron, M. Gurevich, N. Friedman, N. Kaminski, and M. Mandel, Blood transcriptional signatures of multiple sclerosis: Unique gene expression of disease activity, Annals of Neurology, vol.21, issue.3, pp.410-417, 2004.
DOI : 10.4049/jimmunol.168.6.2618

F. Sharp, H. Xu, L. Lit, W. Walker, M. Apperson et al., The Future of Genomic Profiling of Neurological Diseases Using Blood, Archives of Neurology, vol.63, issue.11, pp.631529-1536, 2006.
DOI : 10.1001/archneur.63.11.1529

L. Steinman and S. Zamvil, Transcriptional analysis of targets in multiple sclerosis, Nature Reviews Immunology, vol.3, issue.6, pp.483-492, 2003.
DOI : 10.1038/nri1108

F. Borovecki, L. Lovrecic, J. Zhou, H. Jeong, F. Then et al., Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease, Proceedings of the National Academy of Sciences, vol.22, issue.8, pp.10211023-11028, 2005.
DOI : 10.1016/j.tibtech.2004.06.005

A. Whitney, M. Diehn, S. Popper, A. Alizadeh, J. Boldrick et al., Individuality and variation in gene expression patterns in human blood, Proceedings of the National Academy of Sciences, vol.18, issue.2, pp.1896-1901, 2003.
DOI : 10.1038/ng0298-91

J. Melke, G. Botros, H. Chaste, P. Betancur, C. Nygren et al., Abnormal melatonin synthesis in autism spectrum disorders, Molecular Psychiatry, vol.280, issue.1, 2007.
DOI : 10.1002/mrdd.20023

URL : https://hal.archives-ouvertes.fr/inserm-00166901

Y. Tang, A. Lu, R. Ran, B. Aronow, E. Schorry et al., Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1, Molecular Brain Research, vol.132, issue.2, pp.155-167, 2004.
DOI : 10.1016/j.molbrainres.2003.10.014

K. Storch, O. Lipan, I. Leykin, N. Viswanathan, F. Davis et al., Extensive and divergent circadian gene expression in liver and heart, Nature, vol.107, issue.6884, pp.41778-83, 2002.
DOI : 10.1016/S0092-8674(01)00545-1

S. Panda, M. Antoch, B. Miller, A. Su, A. Schook et al., Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock, Cell, vol.109, issue.3, pp.307-320, 2002.
DOI : 10.1016/S0092-8674(02)00722-5

D. Arion, M. Sabatini, T. Unger, J. Pastor, L. Alonso-nanclares et al., Correlation of transcriptome profile with electrical activity in temporal lobe epilepsy, Neurobiology of Disease, vol.22, issue.2, pp.374-387, 2006.
DOI : 10.1016/j.nbd.2005.12.012

N. Gurvich, M. Berman, B. Wittner, R. Gentleman, P. Klein et al., Association of valproate-induced teratogenesis with histone deacetylase inhibition in vivo, The FASEB Journal, vol.19, issue.9, pp.1166-1168, 2005.
DOI : 10.1096/fj.04-3425fje

S. Milutinovic, D. 'alessio, A. Detich, N. Szyf, and M. , Valproate induces widespread epigenetic reprogramming which involves demethylation of specific genes, Carcinogenesis, vol.104, issue.3, pp.560-571, 2007.
DOI : 10.1016/S0092-8674(01)00196-9

N. Bahi-buisson and J. Chelly, des Portes V: [Update on the genetics of X-linked mental retardation]. Revue neurologique, pp.952-963, 2006.

B. Hendrich and W. Bickmore, Human diseases with underlying defects in chromatin structure and modification. Human molecular genetics, pp.2233-2242, 2001.

C. Perez-iratxeta, P. Bork, and M. Andrade-navarro, Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic acids research, pp.212-216, 2007.

S. @bullet-yilmaz, H. Fontaine, K. Brochet, M. Grégoire, M. Devignes et al., Les articles sont présentés dans la session résultats de ce manuscrit, Liste des publications Les travaux de thèse ont fait l'objet des deux publications ci?dessous Screening of subtle copy number changes in Aicardi Syndrome Patients with a high resolution X?chromosome array?CGH

S. @bullet-yilmaz, P. Jonveaux, C. Bicep, L. Pierron, M. Smaïl?tabbone et al., A Database Approach for Candidate Gene Retrieval based on semantic Data Integration and Expert View Definition

R. E. Amir, P. Fang, Z. Yu, D. G. Glaze, A. K. Percy et al., Van den Veyver, Mutations in exon 1 of MECP2 are a rare cause of Rett syndrome, J. Med. Genet, pp.42-57, 2005.

V. Bourdon, C. Philippe, O. Labrune, D. Amsallem, C. Arnould et al., A detailed analysis of the MECP2 gene: prevalence of recurrent mutations and gross DNA rearrangements in Rett syndrome patients, Human Genetics, vol.108, issue.1, pp.43-50, 2001.
DOI : 10.1007/s004390000422

V. Bourdon, C. Philippe, D. Martin, A. Verloes, A. Grandemenge et al., MECP2 mutations or polymorphisms in mentally retarded boys: diagnostic implications, Mol. Diagn, vol.7, pp.3-7, 2003.

F. Casilli, Z. C. Di-rocco, S. Gad, I. Tournier, D. Stoppa-lyonnet et al., Rapid detection of novelBRCA1 rearrangements in high-risk breast-ovarian cancer families using multiplex PCR of short fluorescent fragments, Human Mutation, vol.33, issue.3, pp.218-226, 2002.
DOI : 10.1136/jmg.33.7.550

M. D. Esposito, N. A. Quaderi, A. Ciccodicola, P. Bruni, T. Esposito et al., Isolation, physical mapping, and Northern analysis of the X-linked human gene encoding methyl CpG-binding protein, MECP2, Mammalian Genome, vol.12, issue.7, pp.533-535, 1996.
DOI : 10.1038/ng0296-205

J. C. Evans, H. L. Archer, S. D. Whatley, A. Kerr, A. Clarke et al., Variation in exon 1 coding region and promoter of MECP2 in Rett syndrome and controls, European Journal of Human Genetics, vol.65, issue.1, pp.13-124, 2005.
DOI : 10.1086/302690

B. Hagberg, F. Hanefeld, A. Percy, and O. Skjeldal, An update on clinically applicable diagnostic criteria in Rett syndrome, European Journal of Paediatric Neurology, vol.6, issue.5, pp.293-297, 2001.
DOI : 10.1053/ejpn.2002.0612

M. Krawczak and D. N. Cooper, Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment, Human Genetics, vol.86, issue.5, pp.425-441, 1991.
DOI : 10.1007/BF00194629

S. Kriaucionis and A. Bird, The major form of MeCP2 has a novel N-terminus generated by alternative splicing, Nucleic Acids Research, vol.32, issue.5, pp.1818-1823, 2004.
DOI : 10.1093/nar/gkh349

G. Miltenberger-miltenyi and F. Laccone, Mutations and polymorphisms in the human methyl CpG-binding protein MECP2, Human Mutation, vol.17, issue.2, pp.107-115, 2003.
DOI : 10.1177/088307380201700105

G. N. Mnatzakanian, H. Lohi, I. Munteanu, S. E. Alfred, T. Yamada et al., A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome, Nat. Genet, pp.36-339, 2004.

C. Philippe, L. Villard, N. De-roux, M. Raynaud, J. P. Bonnefont et al., Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update, European Journal of Medical Genetics, vol.49, issue.1
DOI : 10.1016/j.ejmg.2005.04.003

K. Ravn, J. B. Nielsen, and M. Schwartz, Mutations found within exon 1 of MECP2 in Danish patients with Rett syndrome, Clin. Genet, vol.67, pp.532-533, 2005.

K. Reichwald, J. Thiesen, T. Wiehe, J. Weitzel, W. A. Poustka et al., Comparative sequence analysis of the MECP2-locus in human and mouse reveals new transcribed regions, Mammalian Genome, vol.11, issue.3, pp.182-190, 2000.
DOI : 10.1007/s003350010035

A. Saxena, D. De-lagarde, H. Leonard, S. Williamson, V. Vasudevan et al., Lost in translation: translational interference from a recurrent mutation in exon 1 of MECP2, Journal of Medical Genetics, vol.43, issue.6, 2005.
DOI : 10.1136/jmg.2005.036244

L. S. Weaving, C. J. Ellaway, J. Gecz, and J. Christodoulou, Rett syndrome: clinical review and genetic update, Journal of Medical Genetics, vol.42, issue.1, pp.42-43, 2005.
DOI : 10.1136/jmg.2004.027730

@. Liste-des-posters-avec-comité-de-lecture, S. Yilmaz, H. Fontaine, K. Brochet, M. Grégoire et al., Screening of subtle copy number changes in Aicardi Syndrome Patients with a high resolution X?chromosome array?CGH European Human genetics conference, 2007.

. Approches-génétiques-du-syndrome-d-'aicardi, Assises de génétique humaine et médicale, Médecine Sciences, pp.22-124, 2006.

. Génétique-du-syndrome-d-'aicardi, Gene signature symposium, Applied Biosystem, vol.27, 2005.

. Génétique-du-syndrome-d-'aicardi, Journée de recherche clinique du CHU de Nancy, 2005.