Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
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E. Ukkonen | J. Partanen | Kimmo Palin | J. Taipale | Outi Hallikas | N. Sinjushina | Reetta Rautiainen
[1] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[2] D. Crothers,et al. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. , 1981, Nucleic acids research.
[3] B. Hogan,et al. Manipulating the mouse embryo: A laboratory manual , 1986 .
[4] W. Schulz,et al. Dynamic expression pattern of the myc protooncogene in midgestation mouse embryos. , 1989, Science.
[5] K. Kinzler,et al. The GLI gene encodes a nuclear protein which binds specific sequences in the human genome , 1990, Molecular and cellular biology.
[6] J. Ghysdael,et al. Identification of nucleotide preferences in DNA sequences recognised specifically by c-Ets-1 protein. , 1992, Nucleic acids research.
[7] AC Tose. Cell , 1993, Cell.
[8] C. Pabo,et al. Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. , 1993, Science.
[9] T. Honjo,et al. Recognition sequence of a highly conserved DNA binding protein RBP-J kappa. , 1994, Nucleic acids research.
[10] C. Babinet,et al. The cis-acting elements known to regulate c-myc expression ex vivo are not sufficient for correct transcription in vivo. , 1994, Oncogene.
[11] B. Brunk,et al. Embryonic activation of the myoD gene is regulated by a highly conserved distal control element. , 1995, Development.
[12] J. Darnell,et al. A STAT protein domain that determines DNA sequence recognition suggests a novel DNA-binding domain. , 1995, Genes & development.
[13] David Ish-Horowicz,et al. Expression of a Delta homologue in prospective neurons in the chick , 1995, Nature.
[14] M. Levine,et al. Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo. , 1996, Developmental biology.
[15] P. Beachy,et al. Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function , 1996, Nature.
[16] K. Kinzler,et al. Constitutive Transcriptional Activation by a β-Catenin-Tcf Complex in APC−/− Colon Carcinoma , 1997, Science.
[17] A. Ruiz i Altaba,et al. Gli1 is a target of Sonic hedgehog that induces ventral neural tube development. , 1997, Development.
[18] N. Dahmane,et al. Activation of the transcription factor Gli1 and the Sonic hedgehog signalling pathway in skin tumours , 1997, Nature.
[19] M. Scott,et al. Altered neural cell fates and medulloblastoma in mouse patched mutants. , 1997, Science.
[20] M. Nakafuku,et al. A binding site for Gli proteins is essential for HNF-3beta floor plate enhancer activity in transgenics and can respond to Shh in vitro. , 1997, Development.
[21] D. S. Fields,et al. Specificity, free energy and information content in protein-DNA interactions. , 1998, Trends in biochemical sciences.
[22] D. Schlessinger,et al. Gpc3 expression correlates with the phenotype of the Simpson‐Golabi‐Behmel syndrome , 1998, Developmental dynamics : an official publication of the American Association of Anatomists.
[23] A. Sparks,et al. Identification of c-MYC as a target of the APC pathway. , 1998, Science.
[24] Yasunori Tanaka,et al. Sonic Hedgehog-induced Activation of the Gli1Promoter Is Mediated by GLI3* , 1999, The Journal of Biological Chemistry.
[25] I. Conlon,et al. Size Control in Animal Development , 1999, Cell.
[26] A. McMahon,et al. T (Brachyury) is a direct target of Wnt3a during paraxial mesoderm specification. , 1999, Genes & development.
[27] H. Clevers,et al. Linking Colorectal Cancer to Wnt Signaling , 2000, Cell.
[28] Carmen Birchmeier,et al. Requirement for beta-catenin in anterior-posterior axis formation in mice. , 2000 .
[29] D. Hanahan,et al. The Hallmarks of Cancer , 2000, Cell.
[30] M. Scott,et al. Effects of oncogenic mutations in Smoothened and Patched can be reversed by cyclopamine , 2000, Nature.
[31] Gary D. Stormo,et al. DNA binding sites: representation and discovery , 2000, Bioinform..
[32] J. Taipale,et al. The Hedgehog and Wnt signalling pathways in cancer , 2001, Nature.
[33] Peter W. Markstein,et al. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[34] P. T. Sharpe,et al. Sonic hedgehog Regulates Epithelial Proliferation and Cell Survival in the Developing Tooth Germ , 2001, Journal of dental research.
[35] P. Ingham,et al. Hedgehog signaling in animal development: paradigms and principles. , 2001, Genes & development.
[36] Michael R. Green,et al. Expressing the human genome , 2001, Nature.
[37] J. Tyson. Does Indomethacin Prophylaxis Benefit Extremely Low Birth Weight Infants? Results of a Placebo-Controlled Multicenter Trial , 2002, Pediatric Research.
[38] N. D. Clarke,et al. Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. , 2002, Journal of molecular biology.
[39] R. Behringer,et al. Manipulating the Mouse Embryo: A Laboratory Manual , 2002 .
[40] G. Evan,et al. Suppression of Myc-Induced Apoptosis in β Cells Exposes Multiple Oncogenic Properties of Myc and Triggers Carcinogenic Progression , 2002, Cell.
[41] Stella Pelengaris,et al. c-MYC: more than just a matter of life and death , 2002, Nature Reviews Cancer.
[42] P. Bucher,et al. High-throughput SELEX–SAGE method for quantitative modeling of transcription-factor binding sites , 2002, Nature Biotechnology.
[43] R. Kemler,et al. Functional analysis of cis‐regulatory elements controlling initiation and maintenance of early Cdx1 gene expression in the mouse , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.
[44] G. Rubin,et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[45] C. Emerson,et al. Myf5 is a direct target of long-range Shh signaling and Gli regulation for muscle specification. , 2002, Genes & development.
[46] A. McMahon,et al. A direct requirement for Hedgehog signaling for normal specification of all ventral progenitor domains in the presumptive mammalian spinal cord. , 2002, Genes & development.
[47] Massimo Vergassola,et al. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo , 2002, BMC Bioinformatics.
[48] A. Michelson. Deciphering genetic regulatory codes: A challenge for functional genomics , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[49] Choun-Ki Joo,et al. Wnt/β-Catenin/Tcf Signaling Induces the Transcription of Axin2, a Negative Regulator of the Signaling Pathway , 2002, Molecular and Cellular Biology.
[50] Andrew P McMahon,et al. Ectodermal Wnt3/beta-catenin signaling is required for the establishment and maintenance of the apical ectodermal ridge. , 2003, Genes & development.
[51] P. Rigby,et al. The initial somitic phase of Myf5 expression requires neither Shh signaling nor Gli regulation. , 2003, Genes & development.
[52] Roderic Guigó,et al. gff2aplot: Plotting sequence comparisons , 2003, Bioinform..
[53] Michael D. Cole,et al. Nmyc upregulation by sonic hedgehog signaling promotes proliferation in developing cerebellar granule neuron precursors , 2003, Development.
[54] Denis Duboule,et al. A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster , 2003, Cell.
[55] Robert J. Wechsler-Reya,et al. Transcriptional profiling of the Sonic hedgehog response: A critical role for N-myc in proliferation of neuronal precursors , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[56] Anders Gorm Pedersen,et al. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences , 2003, Nucleic Acids Res..
[57] Michael D. Stone,et al. Structural transitions and elasticity from torque measurements on DNA , 2003, Nature.
[58] R. Young,et al. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays , 2004, Nature Genetics.
[59] P. Kogerman,et al. Expression of the PTCH1 tumor suppressor gene is regulated by alternative promoters and a single functional Gli-binding site. , 2004, Gene.
[60] Ian P Newton,et al. Loss of Apc in vivo immediately perturbs Wnt signaling, differentiation, and migration. , 2004, Genes & development.
[61] K. Nakai,et al. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. , 2004, Genome research.
[62] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[63] Saurabh Sinha,et al. Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila , 2004, BMC Bioinformatics.
[64] K. Lindblad-Toh,et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.
[65] Klaudia Walter,et al. Open access, freely available online PLoS BIOLOGY Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2022 .
[66] N. D. Clarke,et al. DIP-chip: rapid and accurate determination of DNA-binding specificity. , 2005, Genome research.