The RNA Polymerase II Machinery, Cell, vol.108, issue.4, pp.453-463, 2002. ,
DOI : 10.1016/S0092-8674(02)00646-3
Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs, Genes & Development, vol.15, issue.19, pp.2515-2519, 2001. ,
DOI : 10.1101/gad.924301
DNA binding sites: representation and discovery, Bioinformatics, vol.16, issue.1, pp.16-23, 2000. ,
DOI : 10.1093/bioinformatics/16.1.16
DNAse footprinting : a simple method for the detection of protein-DNA binding specificity, Nucleic Acids Research, vol.5, issue.9, pp.3157-3170, 1978. ,
A new method for sequencing DNA, Proceedings of the National Academy of Sciences of the United States of America, vol.74, issue.2, pp.560-564, 1977. ,
SELEX???A (r)evolutionary method to generate high-affinity nucleic acid ligands, Biomolecular Engineering, vol.24, issue.4, pp.381-403, 2003. ,
DOI : 10.1016/j.bioeng.2007.06.001
In vitro DNA-binding profile of transcription factors: methods and new insights, Journal of Endocrinology, vol.210, issue.1, pp.15-27, 2005. ,
DOI : 10.1530/JOE-11-0010
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors, Nature Biotechnology, vol.18, issue.8, pp.988-994, 2005. ,
DOI : 10.1007/BF00291041
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system, Nature Protocols, vol.14, issue.1, pp.30-45, 2005. ,
DOI : 10.1038/nprot.2006.6
Discovering DNA regulatory elements with bacteria, Nature Biotechnology, vol.270, issue.8, pp.942-944, 2005. ,
DOI : 10.1101/gr.2584104
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments, Genomics, vol.83, issue.3, pp.349-360, 2004. ,
DOI : 10.1016/j.ygeno.2003.11.004
Sequence-specific DNA-binding activities of the gap proteins encoded by hunchback and Kr??ppel in Drosophila, Nature, vol.341, issue.6240, pp.331-335, 1989. ,
DOI : 10.1038/341331a0
Signal search analysis: a new method to localize and characterize functionally important DNA sequences, Nucleic Acids Research, vol.12, issue.1Part1, pp.287-305, 1984. ,
DOI : 10.1093/nar/12.1Part1.287
Computer methods to locate signals in nucleic acid sequences, Nucleic Acids Research, vol.12, issue.1Part2, 1984. ,
DOI : 10.1093/nar/12.1Part2.505
DNA Binding Specificity of Different STAT Proteins. COMPARISON OF IN VITRO SPECIFICITY WITH NATURAL TARGET SITES, Journal of Biological Chemistry, vol.276, issue.9, pp.6675-88, 2001. ,
DOI : 10.1074/jbc.M001748200
Critical comparison of consensus methods for molecular sequences, Nucleic Acids Research, vol.20, issue.6, pp.1093-1099, 1992. ,
WebLogo: A Sequence Logo Generator, Genome Research, vol.14, issue.6, pp.1188-1190, 2004. ,
DOI : 10.1101/gr.849004
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419797
Sequence logos : a new way to display consensus sequences, Nucleic Acids Research, vol.18, issue.20, pp.6097-6100, 1990. ,
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences, Bioinformatics, vol.15, issue.78, pp.563-577, 1999. ,
MEME SUITE: tools for motif discovery and searching, Nucleic Acids Research, vol.37, issue.Web Server, pp.202-208, 2009. ,
DOI : 10.1093/nar/gkp335
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
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling, Bioinformatics, vol.25, issue.20, pp.2715-2722, 2009. ,
DOI : 10.1093/bioinformatics/btp490
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes, Journal of Computational Biology, vol.9, issue.2, pp.447-464, 2002. ,
DOI : 10.1089/10665270252935566
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules, Nature Protocols, vol.281, issue.10, pp.1578-88, 2008. ,
DOI : 10.1038/nprot.2008.97
Développement et évaluation de méthodes bioinformatiques pour la détection de s ´ quences cis-régulatrices impliquées dans le développement de la drosophile. Catalogue des theses electroniques de l ULB, p.19, 2009. ,
Applied bioinformatics for the identification of regulatory elements, Nature Reviews Genetics, vol.14, issue.4, pp.276-87, 2004. ,
DOI : 10.1093/bioinformatics/18.9.1272
rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites, Genome Research, vol.12, issue.5, pp.832-839, 2002. ,
DOI : 10.1101/gr.225502
Cluster-Buster: finding dense clusters of motifs in DNA sequences, Nucleic Acids Research, vol.31, issue.13, pp.313666-3668, 2003. ,
DOI : 10.1093/nar/gkg540
Computational identification of developmental enhancers : conservation and function of transcription factor bindingsite clusters in Drosophila melanogaster and Drosophila pseudoobscura, Genome Biology, vol.5, issue.9, pp.61-95, 2004. ,
DOI : 10.1186/gb-2004-5-9-r61
REGULATORY MODULES, Biocomputing 2005, pp.519-549, 2005. ,
DOI : 10.1142/9789812702456_0049
Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors, Nucleic Acids Research, vol.31, issue.13, pp.3589-3592, 2003. ,
DOI : 10.1093/nar/gkg544
TFBScluster: a resource for the characterization of transcriptional regulatory networks, Bioinformatics, vol.21, issue.13, pp.3058-3067, 2005. ,
DOI : 10.1093/bioinformatics/bti461
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome, Proceedings of the National Academy of Sciences, vol.99, issue.2, pp.757-62, 2002. ,
DOI : 10.1073/pnas.231608898
Computational methods for the detection of cis-regulatory modules, Briefings in Bioinformatics, vol.10, issue.5, pp.509-533, 2009. ,
DOI : 10.1093/bib/bbp025
Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences, The 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp.68-72, 1920. ,
DOI : 10.1109/IEMBS.2004.1403814
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, Nucleic Acids Research, vol.38, issue.Database, pp.105-115, 1920. ,
DOI : 10.1093/nar/gkp950
FlyFactorSurvey : a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system, Nucleic acids research, vol.39, issue.66, pp.111-118, 1920. ,
Motif discovery and motif finding from genome-mapped DNase footprint data Nucleic acids research, Bioinformatics, issue.18, pp.252318-252343, 1920. ,
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation, Genome Biology, vol.8, issue.10, p.207, 1921. ,
DOI : 10.1186/gb-2007-8-10-r207
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences, Nucleic Acids Research, vol.37, issue.Database, pp.54-60, 1921. ,
DOI : 10.1093/nar/gkn783
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster, Bioinformatics, vol.21, issue.8, pp.1747-1749, 2004. ,
DOI : 10.1093/bioinformatics/bti173
Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster, PLoS Computational Biology, vol.13, issue.1, pp.7-82, 2007. ,
DOI : 10.1371/journal.pcbi.0030007.st001
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila, Nucleic Acids Research, vol.36, issue.Database, pp.594-602, 1921. ,
DOI : 10.1093/nar/gkm876
Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites, Cell, vol.133, issue.7, pp.1277-89, 2008. ,
DOI : 10.1016/j.cell.2008.05.023
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system, Nucleic Acids Research, vol.36, issue.8, pp.2547-60, 2008. ,
DOI : 10.1093/nar/gkn048
Largescale turnover of functional transcription factor binding sites in Drosophila, PLoS computational biology, vol.2, issue.10, p.130, 1921. ,
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm, PLoS Biology, vol.22, issue.2, pp.27-34, 2008. ,
DOI : 10.1371/journal.pbio.0060027.st004
A novel mediator between activator proteins and the RNA polymerase II transcription apparatus, Cell, vol.61, issue.7, pp.611209-611224, 1920. ,
DOI : 10.1016/0092-8674(90)90685-8
Mediator complexes and eukaryotic transcription regulation: An overview, Biochimie, vol.89, issue.12, pp.1439-1485, 1922. ,
DOI : 10.1016/j.biochi.2007.08.002
Establishment of cell fate during early Drosophila embryogenesis requires transcriptional Mediator subunit dMED31, Developmental Biology, vol.313, issue.2, pp.802-815, 1922. ,
DOI : 10.1016/j.ydbio.2007.11.019
Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature, issue.6648, pp.389251-60, 1922. ,
Crucial Roles for Chromatin Dynamics in Cellular Memory, Journal of Biochemistry, vol.141, issue.5, pp.615-624, 1922. ,
DOI : 10.1093/jb/mvm092
A gene complex controlling segmentation in Drosophila, Nature, vol.58, issue.5688, pp.565-570, 1923. ,
DOI : 10.1038/265211a0
Mutations affecting segment number and polarity in Drosophila, Nature, vol.52, issue.5785, pp.795-801, 1923. ,
DOI : 10.1038/287795a0
The maternal-to-zygotic transition: a play in two acts, Development, vol.136, issue.18, pp.3033-3075, 2009. ,
DOI : 10.1242/dev.033183
Onset of the DNA Replication Checkpoint in the Early Drosophila Embryo, Genetics, vol.175, issue.2, pp.567-84, 2007. ,
DOI : 10.1534/genetics.106.065219
An essential role for the RNA-binding protein Smaug during the Drosophila maternal-to-zygotic transition, Development, vol.136, issue.6, pp.923-955, 1924. ,
DOI : 10.1242/dev.031815
URL : https://hal.archives-ouvertes.fr/hal-00363874
smaug protein represses translation of unlocalized nanos mRNA in the Drosophila embryo., Genes & Development, vol.10, issue.20, pp.2600-2609, 1926. ,
DOI : 10.1101/gad.10.20.2600
A Gradient of JAK Pathway Activity Patterns the Anterior-Posterior Axis of the Follicular Epithelium, Developmental Cell, vol.4, issue.2, pp.167-77, 1928. ,
DOI : 10.1016/S1534-5807(02)00412-4
The centrosome-nucleus complex and microtubule organization in the Drosophila oocyte, Development, vol.133, issue.1, pp.129-168, 1928. ,
DOI : 10.1242/dev.02179
URL : https://hal.archives-ouvertes.fr/hal-00015465
Patterning: JAK-STAT Signalling in the Drosophila Follicular Epithelium, Current Biology, vol.13, issue.10, pp.388-90, 1928. ,
DOI : 10.1016/S0960-9822(03)00317-8
Bicoid associates with the 5'-cap-bound complex of caudal mRNA and represses translation, Genes & Development, vol.16, issue.19, pp.2576-82, 2002. ,
DOI : 10.1101/gad.240002
Developmental control of nuclear morphogenesis and anchoring by charleston, identified in a functional genomic screen of Drosophila cellularisation, Development, vol.67, issue.45, pp.30711-30734, 1929. ,
Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo, PLoS Biology, vol.3, issue.5, pp.117-152, 2007. ,
DOI : 10.1371/journal.pbio.0050117.st009
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis, Molecular Systems Biology, vol.298, issue.3, pp.72-101, 2007. ,
DOI : 10.1038/msb4100112
Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function, Cell, vol.131, issue.1, pp.174-187, 2007. ,
DOI : 10.1016/j.cell.2007.08.003
Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition, Development, vol.136, issue.12, pp.2101-2111, 1929. ,
DOI : 10.1242/dev.034421
SMAUG Is a Major Regulator of Maternal mRNA Destabilization in Drosophila and Its Translation Is Activated by the PAN GU Kinase, Developmental Cell, vol.12, issue.1, pp.143-155, 2007. ,
DOI : 10.1016/j.devcel.2006.10.005
Genome-wide analysis of mRNA decay patterns during early Drosophila development, Genome Biology, vol.11, issue.9, pp.93-125, 2010. ,
DOI : 10.1186/gb-2010-11-9-r93
Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila, Current Biology, vol.18, issue.7, pp.501-507, 2008. ,
DOI : 10.1016/j.cub.2008.02.081
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster, Proceedings of the National Academy of Sciences, vol.103, issue.12, pp.4487-92, 2006. ,
DOI : 10.1073/pnas.0509260103
Zygotic degradation of two maternal Cdc25 mRNAs terminates Drosophila's early cell cycle program ,
Genetic control of cell division patterns in the Drosophila embryo, Cell, vol.57, issue.32, pp.177-87, 1989. ,
Activation of transcription in Drosophila embryos is a gradual process mediated by the nucleocytoplasmic ratio, Genes & development, vol.10, issue.67, pp.1131-1173, 1932. ,
DNAreplication checkpoint control at the Drosophila midblastula transition The Drosophila evenskipped promoter is transcribed in a stage-specific manner in vitro and contains multiple, overlapping factor-binding sites, Nature Molecular and cellular biology, vol.388, issue.66378, pp.93-100, 1990. ,
Graded dorsal and differential gene regulation in the Drosophila embryo, Cold Spring Harbor perspectives in biology, vol.1, issue.4, pp.836-870, 2009. ,
The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription, Development, vol.133, issue.34, pp.1967-77, 2006. ,
The zincfinger protein Zelda is a key activator of the early zygotic genome in Drosophila, Nature, vol.34, issue.7220, pp.456400-456403, 2008. ,
STAT Is an Essential Activator of the Zygotic Genome in the Early
Drosophila Embryo, PLoS Genetics, vol.110, issue.5, p.1002086, 1934. ,
DOI : 10.1371/journal.pgen.1002086.s013
Robust estimators for expression analysis, Bioinformatics, vol.18, issue.12, pp.1585-1592, 2002. ,
DOI : 10.1093/bioinformatics/18.12.1585
Summaries of Affymetrix GeneChip probe level data, Nucleic Acids Research, vol.31, issue.4, pp.15-40, 2003. ,
DOI : 10.1093/nar/gng015
The utility of MAS5 expression summary and detection call algorithms, BMC Bioinformatics, vol.8, issue.1, pp.273-313, 2007. ,
DOI : 10.1186/1471-2105-8-273
Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, vol.4, issue.2, pp.249-64, 2003. ,
DOI : 10.1093/biostatistics/4.2.249
Stochastic models inspired by hybridization theory for short oligonucleotide arrays, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.882-93, 2005. ,
DOI : 10.1145/974614.974628
Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons, Nucleic Acids Research, vol.34, issue.2, pp.8-40, 2006. ,
DOI : 10.1093/nar/gnj010
R : A language and environment for statistical computing, pp.3-900051, 2008. ,
MeV: MultiExperiment Viewer, Biomedical Informatics for Cancer Research, pp.267-277, 2010. ,
DOI : 10.1007/978-1-4419-5714-6_15
Network Analysis Tools: from biological networks to clusters and pathways, Nature Protocols, vol.28, issue.10, pp.1616-1645, 2008. ,
DOI : 10.1038/nprot.2008.100
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition, PLoS Genetics, vol.40, issue.10, pp.1002266-114, 2011. ,
DOI : 10.1371/journal.pgen.1002266.s008
Activation properties of GAGA transcription factor, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1779, issue.5, pp.312-319, 2008. ,
DOI : 10.1016/j.bbagrm.2008.02.005
Chromatin: Ga-ga over GAGA factor, Current Biology, vol.5, issue.3, pp.238-279, 1995. ,
DOI : 10.1016/S0960-9822(95)00048-0
Drosophila FACT contributes to Hox gene expression through physical and functional interactions with GAGA factor, Genes & Development, vol.17, issue.13, pp.1605-1621, 2003. ,
DOI : 10.1101/gad.1086803
Anything else but GAGA : a nonhistone protein complex reshapes chromatin structure. Trends in genetics : TIG, pp.15-22, 2004. ,
FlyBase High Throughput Expression Pattern Data Beta Version, p.114, 2010. ,
The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation, Nucleic Acids Research, vol.30, issue.20, pp.4406-4419, 2002. ,
DOI : 10.1093/nar/gkf570
Isolation and characterization of cDNA for DREF, a promoter-activating factor for Drosophila DNA replication-related genes, The Journal of biological chemistry, issue.7, pp.2713930-2713937, 1996. ,
Evidence for an antagonistic relationship between the boundary element-associated factor BEAF and the transcription factor DREF, Chromosoma, vol.108, issue.6, pp.375-383, 1999. ,
DOI : 10.1007/s004120050389
Functional Classification Tool : a novel biological module-centric algorithm to functionally analyze large gene lists, Genome biology, vol.8, issue.9, pp.183-69, 2007. ,
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature protocols, vol.4, issue.1, pp.44-57, 2009. ,
GOToolBox : functional analysis of gene datasets based on Gene Ontology Identifying biological themes within lists of genes with EASE, Genome Biology, vol.5, issue.12, pp.101-70, 2003. ,
DOI : 10.1186/gb-2004-5-12-r101
Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification, PLoS Biology, vol.102, issue.7, pp.1000435-73, 2010. ,
DOI : 10.1371/journal.pbio.1000435.s024
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses, Genome Biology, vol.8, issue.6, pp.101-73, 2007. ,
DOI : 10.1186/gb-2007-8-6-r101
Repression by suppressor of hairless and activation by Notch are required to define a single row of singleminded expressing cells in the Drosophila embryo, Genes & development, vol.14, issue.76, pp.377-88, 2000. ,
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl, Bioinformatics, vol.25, issue.20, pp.252739-252779, 2009. ,
DOI : 10.1093/bioinformatics/btp519
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences, Nature Protocols, vol.3, issue.10, pp.1589-603, 2008. ,
DOI : 10.1038/nprot.2008.98
Modulation of heat shock gene expression by the TAC1 chromatin-modifying complex, Nature Cell Biology, vol.19, issue.2, pp.162-169, 2004. ,
DOI : 10.1038/35020506
Transcriptional Coregulators in Development, Science, vol.284, issue.5414, pp.606-609, 1985. ,
DOI : 10.1126/science.284.5414.606
The acetyltransferase activity of Drosophila CBP is dispensable for regulation of the Dpp pathway in the early embryo, Developmental Biology, vol.305, issue.2, pp.650-658, 1985. ,
DOI : 10.1016/j.ydbio.2007.01.036
Drosophila CBP is a co-activator of cubitus interruptus in hedgehog signalling, Nature, vol.386, issue.6626, pp.386735-386743, 1997. ,
DOI : 10.1038/386735a0
Drosophila CBP is required for dorsal???dependent twist gene expression, Nature Genetics, vol.82, issue.2, pp.211-215, 1997. ,
DOI : 10.1016/0378-1119(88)90177-1
Drosophila CBP represses the transcription factor TCF to antagonize Wingless signalling, Nature, vol.395, issue.6701, pp.521-526, 1998. ,
MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation, The EMBO Journal, vol.272, issue.15, pp.3545-57, 2007. ,
DOI : 10.1038/sj.emboj.7601797
CREB-binding protein and p300 in transcriptional regulation CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing, The Journal of biological chemistry Development, vol.276122, issue.8618, pp.13505-13513, 2001. ,
Dynamic acetylation of all lysine-4 trimethylated histone H3 is evolutionarily conserved and mediated by p300/CBP, Proceedings of the National Academy of Sciences of the United States of America, pp.7814-7823, 2011. ,
DOI : 10.1073/pnas.1100099108
A cis-regulatory map of the Drosophila genome, Nature, vol.86, issue.7339, pp.471527-471558, 2011. ,
Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at Polycomb target genes, The EMBO Journal, vol.14, issue.18, pp.264078-88, 2007. ,
DOI : 10.1038/sj.emboj.7601837
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development, Genome Biology, vol.12, issue.5, pp.43-87, 2011. ,
DOI : 10.1093/nar/gkp335
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding, Genome Biology, vol.12, issue.4, pp.34-86, 2011. ,
DOI : 10.1186/gb-2007-8-2-r24
Model-based Analysis of ChIP-Seq (MACS), Genome Biology, vol.9, issue.9, p.137, 2008. ,
DOI : 10.1186/gb-2008-9-9-r137
BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-843, 2010. ,
DOI : 10.1093/bioinformatics/btq033
The UCSC Genome Browser database: update 2011, Nucleic Acids Research, vol.39, issue.Database, pp.39-876, 2011. ,
DOI : 10.1093/nar/gkq963
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila, Nucleic Acids Research, vol.39, issue.Database, pp.118-141, 2011. ,
DOI : 10.1093/nar/gkq999
Drosophila GAGA factor directs histone H3.3 replacement that prevents the heterochromatin spreading, Genes & Development, vol.21, issue.5, pp.552-61, 2007. ,
DOI : 10.1101/gad.1503407
The double face of the histone variant H3.3, Cell Research, vol.10, issue.3, pp.421-455, 2011. ,
DOI : 10.1128/MCB.02019-06
URL : https://hal.archives-ouvertes.fr/hal-00742959
Purification and properties of an ATP-dependent nucleosome remodeling factor, Cell, vol.83, issue.6, pp.1011-1031, 1995. ,
DOI : 10.1016/0092-8674(95)90216-3
Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3, Developmental biology, vol.317, issue.2, pp.660-70, 0114. ,
A developmentally regulated GAGA box-binding factor and Sp1 are required for transcription of the hsp70.1 gene at the onset of mouse zygotic genome activation, Development, vol.127, issue.7, pp.1541-51, 2000. ,
NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila, Molecular and Cellular Biology, vol.28, issue.10, pp.3290-300, 0115. ,
DOI : 10.1128/MCB.02224-07
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo, Proceedings of the National Academy of Sciences, vol.105, issue.22, pp.7762-7769, 2008. ,
DOI : 10.1073/pnas.0802406105
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing, Nature Methods, vol.128, issue.8, p.651, 2007. ,
DOI : 10.1038/nmeth1068
Genome-Wide Mapping of in Vivo Protein-DNA Interactions, Science, vol.316, issue.5830, p.1497, 2007. ,
DOI : 10.1126/science.1141319
Next-generation gap, Nature Methods, vol.6, issue.11s, p.2, 2009. ,
DOI : 10.1101/gr.089532.108
Computation for ChIP-seq and RNA-seq studies, Nature Methods, vol.18, issue.11s, p.22, 2009. ,
DOI : 10.1038/nmeth.1360
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci, BMC Bioinformatics, vol.11, issue.1, p.415, 2010. ,
DOI : 10.1186/1471-2105-11-415
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, Nucleic Acids Research, vol.38, issue.Database, p.105, 2010. ,
DOI : 10.1093/nar/gkp950
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation, Briefings in Bioinformatics, vol.9, issue.4, p.326, 2008. ,
DOI : 10.1093/bib/bbn016
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units), Nucleic Acids Research, vol.39, issue.Database, p.98, 2011. ,
DOI : 10.1093/nar/gkq1110
Theoretical and empirical quality assessment of transcription factor-binding motifs, Nucleic Acids Research, vol.39, issue.3, p.808, 2011. ,
DOI : 10.1093/nar/gkq710
Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells, Cell, vol.133, issue.6, p.1106, 2008. ,
DOI : 10.1016/j.cell.2008.04.043
The UCSC Genome Browser database: update 2011, Nucleic Acids Research, vol.39, issue.Database, p.876, 2011. ,
DOI : 10.1093/nar/gkq963
Deep and wide digging for binding motifs in ChIP-Seq data, Bioinformatics, vol.26, issue.20, p.2622, 2010. ,
DOI : 10.1093/bioinformatics/btq488
Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species, PLoS Biology, vol.15, issue.8, p.1000343, 2010. ,
DOI : 10.1371/journal.pbio.1000343.s034
NCBI GEO: archive for functional genomics data sets--10 years on, Nucleic Acids Research, vol.39, issue.Database, p.1005, 2011. ,
DOI : 10.1093/nar/gkq1184
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biology, vol.11, issue.8, p.86, 2010. ,
DOI : 10.1186/gb-2010-11-8-r86
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, p.25, 2009. ,
DOI : 10.1186/gb-2009-10-3-r25
Model-based Analysis of ChIP-Seq (MACS), Genome Biology, vol.9, issue.9, p.137, 2008. ,
DOI : 10.1186/gb-2008-9-9-r137
Ensembl 2011, Nucleic Acids Research, vol.39, issue.Database, p.800, 2011. ,
DOI : 10.1093/nar/gkq1064
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster, Bioinformatics, vol.21, issue.8, p.1747, 2005. ,
DOI : 10.1093/bioinformatics/bti173
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies 1 1Edited by G. von Heijne, Journal of Molecular Biology, vol.281, issue.5, p.827, 1998. ,
DOI : 10.1006/jmbi.1998.1947
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads, Nucleic Acids Research, vol.28, issue.8, p.1808, 2000. ,
DOI : 10.1093/nar/28.8.1808
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals, Nucleic Acids Research, vol.28, issue.4, p.1000, 2000. ,
DOI : 10.1093/nar/28.4.1000
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences, Nature Protocols, vol.3, issue.10, p.1589, 2008. ,
DOI : 10.1038/nprot.2008.98
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
The gain and loss of genes during 600 million years of vertebrate evolution, Genome Biology, vol.7, issue.5, p.43, 2006. ,
DOI : 10.1186/gb-2006-7-5-r43
Widespread genome duplications throughout the history of flowering plants, Genome Research, vol.16, issue.6, pp.738-749, 2006. ,
DOI : 10.1101/gr.4825606
Two rounds of whole genome duplication in the ancestral vertebrate Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease, PLoS Biol Immunol Rev, vol.3, issue.167, pp.275-304, 1999. ,
Preservation of duplicate genes by complementary, degenerative mutations, Genetics, vol.151, pp.1531-1545, 1999. ,
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity, Genome Research, vol.16, issue.7, pp.805-814, 2006. ,
DOI : 10.1101/gr.3681406
FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform, BMC Bioinformatics, vol.6, issue.1, p.198, 2005. ,
DOI : 10.1186/1471-2105-6-198
B30.2-like domain proteins: update and new insights into a rapidly expanding family of proteins, Molecular Biology and Evolution, vol.15, issue.12, pp.1696-1705, 1998. ,
DOI : 10.1093/oxfordjournals.molbev.a025896
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, vol.194, issue.7018, pp.695-716, 2004. ,
DOI : 10.1101/gr.794803
Gene map of the extended human MHC, Nature Reviews Genetics, vol.4, issue.12, pp.889-899, 2004. ,
DOI : 10.1006/jmbi.1995.0301
Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection., Proceedings of the National Academy of Sciences, vol.86, issue.3, pp.958-962, 1989. ,
DOI : 10.1073/pnas.86.3.958
A new taxonomy of mammalian MHC class I molecules, Immunology Today, vol.20, issue.1, pp.22-26, 1999. ,
DOI : 10.1016/S0167-5699(98)01377-2
Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution, Nature Genetics, vol.16, issue.11, pp.1361-1368, 2007. ,
DOI : 10.1038/ng.2007.9
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature, vol.428, issue.6983, pp.617-624, 2004. ,
DOI : 10.1038/nature02424
Detecting a local signature of genetic hitchhiking along a recombining chromosome, Genetics, vol.160, pp.765-777, 2002. ,
Identification of Ligands for Olfactory Receptors by Functional Expression of a Receptor Library, Cell, vol.95, issue.7, pp.917-926, 1998. ,
DOI : 10.1016/S0092-8674(00)81716-X
A molecular timescale for vertebrate evolution, Nature, vol.392, pp.917-920, 1998. ,
Evolution of the Vertebrate Genome as Reflected in Paralogous Chromosomal Regions in Man and the House Mouse, Genomics, vol.16, issue.1, pp.1-19, 1993. ,
DOI : 10.1006/geno.1993.1133
The evolutionary demography of duplicate genes, J Struct Funct Genomics, vol.3, pp.35-44, 2003. ,
DOI : 10.1007/978-94-010-0263-9_4
The probability of preservation of a newly arisen gene duplicate, Genetics, vol.159, pp.1789-1804, 2001. ,
Phylogenomics of the nucleosome, Nature Structural Biology, vol.10, issue.11, pp.882-891, 2003. ,
DOI : 10.1038/nsb996
Extensive genomic duplication during early chordate evolution, Nature Genetics, vol.31, issue.2, pp.204-205, 2002. ,
DOI : 10.1038/ng884
16 The evolution of gene duplicates, Adv Genet, vol.46, pp.451-483, 2002. ,
DOI : 10.1016/S0065-2660(02)46017-8
Dosage sensitivity and the evolution of gene families in yeast, Nature, vol.424, issue.6945, pp.194-197, 2003. ,
DOI : 10.1038/nature01771
Regulating olfactory receptor expression: controlling globally, acting locally, Nat Neurosci, vol.7, pp.638-639, 2000. ,
Comparative Genomics of the Eukaryotes, Science, vol.287, issue.5461, pp.2204-2215, 2000. ,
DOI : 10.1126/science.287.5461.2204
Cloning, localization, and structure of new members of the butyrophilin gene family in the juxta-telomeric region of the major histocompatibility complex, Immunogenetics, vol.47, issue.1, pp.55-63, 1997. ,
DOI : 10.1007/s002510050326
Trim5?? protein restricts both HIV-1 and murine leukemia virus, Proceedings of the National Academy of Sciences, vol.101, issue.29, pp.10786-10791, 2004. ,
DOI : 10.1073/pnas.0402876101