Identification and characterization of the potential promoter regions of 1031 kinds of human genes.

PubWeight™: 4.03‹?› | Rank: Top 1%

🔗 View Article (PMC 311086)

Published in Genome Res on May 01, 2001

Authors

Y Suzuki1, T Tsunoda, J Sese, H Taira, J Mizushima-Sugano, H Hata, T Ota, T Isogai, T Tanaka, Y Nakamura, A Suyama, Y Sakaki, S Morishita, K Okubo, S Sugano

Author Affiliations

1: Department of Virology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan. ysuzuki@ims.u-tokyo.ac.jp

Articles citing this

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73

Identification and functional analysis of human transcriptional promoters. Genome Res (2003) 6.23

Computational analysis of core promoters in the Drosophila genome. Genome Biol (2002) 5.60

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res (2004) 3.73

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50

Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep (2001) 3.47

DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11

EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res (2006) 2.49

Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene (2006) 2.31

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res (2002) 2.30

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res (2002) 2.30

miR-200a regulates SIRT1 expression and epithelial to mesenchymal transition (EMT)-like transformation in mammary epithelial cells. J Biol Chem (2011) 1.98

Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res (2007) 1.80

Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res (2004) 1.69

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res (2006) 1.55

Regulation of the p53 transcriptional response by structurally diverse core promoters. Genes Dev (2009) 1.52

Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics (2006) 1.51

Predicting transcription factor binding sites using local over-representation and comparative genomics. BMC Bioinformatics (2006) 1.50

Determining promoter location based on DNA structure first-principles calculations. Genome Biol (2007) 1.44

Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes. Proc Natl Acad Sci U S A (2005) 1.40

The histone-like NF-Y is a bifunctional transcription factor. Mol Cell Biol (2008) 1.40

Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res (2005) 1.39

A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response. Nucleic Acids Res (2008) 1.32

Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells. Genome Res (2004) 1.20

Long-range function of an intergenic retrotransposon. Proc Natl Acad Sci U S A (2010) 1.20

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic Acids Res (2007) 1.19

Requirement for down-regulation of the CCAAT-binding activity of the NF-Y transcription factor during skeletal muscle differentiation. Mol Biol Cell (2003) 1.19

NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res (2013) 1.15

The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters. Mol Cell Biol (2007) 1.11

Diversity of core promoter elements comprising human bidirectional promoters. BMC Genomics (2008) 1.10

A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes. BMC Evol Biol (2009) 1.08

Characterization of transcription from TATA-less promoters: identification of a new core promoter element XCPE2 and analysis of factor requirements. PLoS One (2009) 1.07

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y? Cell Death Differ (2013) 1.01

Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis. Plant Physiol (2008) 0.98

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver. BMC Genomics (2013) 0.97

DNA compaction by the nuclear factor-Y. Biophys J (2007) 0.97

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants. Plant Cell (2016) 0.95

Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Res (2005) 0.94

Palate morphogenesis: current understanding and future directions. Birth Defects Res C Embryo Today (2010) 0.94

Analysis of intron sequence features associated with transcriptional regulation in human genes. PLoS One (2012) 0.93

NF-Y recruits both transcription activator and repressor to modulate tissue- and developmental stage-specific expression of human γ-globin gene. PLoS One (2012) 0.90

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. BMC Genomics (2013) 0.89

Genomic structure and functional characterization of the promoter region of human IkappaB kinase-related kinase IKKi/IKKvarepsilon gene. Gene (2005) 0.87

Diversification and molecular evolution of ATOH8, a gene encoding a bHLH transcription factor. PLoS One (2011) 0.87

Nuclear factor-kappaB is a critical mediator of Ste20-like proline-/alanine-rich kinase regulation in intestinal inflammation. Am J Pathol (2008) 0.86

cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis. Nucleic Acids Res (2005) 0.86

Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana. DNA Res (2011) 0.84

Frequency distribution of TATA Box and extension sequences on human promoters. BMC Bioinformatics (2006) 0.84

Intrinsic promoter activities of primary DNA sequences in the human genome. DNA Res (2007) 0.84

Regulation of transketolase like 1 gene expression in the murine one-cell stage embryos. PLoS One (2014) 0.83

Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics (2012) 0.83

SLC1 glutamate transporters. Pflugers Arch (2013) 0.83

hRDH-E2 gene polymorphisms, variable transcriptional start sites, and psoriasis. Mamm Genome (2004) 0.82

A p53-dependent promoter associated with polymorphic tandem repeats controls the expression of a viral transcript encoding clustered microRNAs. RNA (2010) 0.82

Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res (2011) 0.81

The Gene Resource Locator: gene locus maps for transcriptome analysis. Nucleic Acids Res (2002) 0.81

Developmental epigenetics of the murine secondary palate. ILAR J (2012) 0.81

Gene structure and chromosomal localization of mouse Opa1 : its exclusion from the Bst locus. BMC Genet (2003) 0.80

Genome-wide detection of a TFIID localization element from an initial human disease mutation. Nucleic Acids Res (2010) 0.79

The tert-butylhydroquinone-mediated activation of the human thioredoxin gene reveals a novel promoter structure. Biochem J (2006) 0.78

Characterization of gene expression in mouse embryos at the 1-cell stage. J Reprod Dev (2015) 0.78

NF-YC complexity is generated by dual promoters and alternative splicing. J Biol Chem (2009) 0.78

PAX5 is the transcriptional activator of mucolipin-2 (MCOLN2) gene. Gene (2014) 0.78

Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter. Mol Cell Biol (2010) 0.76

Constitutive overexpression of the TaNF-YB4 gene in transgenic wheat significantly improves grain yield. J Exp Bot (2015) 0.76

RhoA regulation of cardiomyocyte differentiation. ScientificWorldJournal (2013) 0.75

RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PLoS One (2009) 0.75

Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. Genome Res (2015) 0.75

Insights into a key sulfite scavenger enzyme sulfite oxidase (SOX) gene in plants. Physiol Mol Biol Plants (2017) 0.75

Maximal Expression of the Evolutionarily Conserved Slit2 Gene Promoter Requires Sp1. Cell Mol Neurobiol (2015) 0.75

Establishment of DNA methylation patterns of the Fibrillin1 (FBN1) gene in porcine embryos and tissues. J Reprod Dev (2017) 0.75

Involvement of DNA methylation in regulating rat Prop1 gene expression during pituitary organogenesis. J Reprod Dev (2016) 0.75

Expression of the CCAAT-binding factor NF-Y in Caenorhabditis elegans. J Mol Histol (2005) 0.75

Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.). Planta (2016) 0.75

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell (1977) 61.24

Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science (1989) 25.68

Transcriptional control signals of a eukaryotic protein-coding gene. Science (1982) 25.38

CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol (1990) 8.75

Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet (2000) 8.58

CpG islands as gene markers in the human genome. Genomics (1992) 7.45

The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci (1996) 7.00

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res (1999) 6.70

The essence of SNPs. Gene (1999) 6.44

Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene (1994) 5.28

The eukaryotic promoter database (EPD). Nucleic Acids Res (2000) 4.21

CENSOR--a program for identification and elimination of repetitive elements from DNA sequences. Comput Chem (1996) 4.09

Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. Gene (1997) 4.02

CpG islands and genes. Curr Opin Genet Dev (1995) 3.83

Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim Biophys Acta (1997) 3.53

Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends. Anal Biochem (1995) 3.39

A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat Genet (1999) 2.83

Carcinoembryonic antigen gene family: molecular biology and clinical perspectives. J Clin Lab Anal (1991) 2.70

Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries. Genomics (2000) 2.09

Estimating transcription factor bindability on DNA. Bioinformatics (1999) 2.00

Core promoters and transcriptional control. Trends Genet (1996) 1.49

Adaptor-tagged competitive PCR: a novel method for measuring relative gene expression. Nucleic Acids Res (1997) 1.36

Expression profiling by iAFLP: A PCR-based method for genome-wide gene expression profiling. Genome Res (1999) 1.20

Transcriptional regulation of the carcinoembryonic antigen gene. Identification of regulatory elements and multiple nuclear factors. J Biol Chem (1995) 0.94

Transcriptional control of the human biliary glycoprotein gene, a CEA gene family member down-regulated in colorectal carcinomas. Eur J Biochem (1994) 0.94

Articles by these authors

The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (1997) 33.47

Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res (1996) 28.37

Genetic alterations during colorectal-tumor development. N Engl J Med (1988) 26.82

Variable number of tandem repeat (VNTR) markers for human gene mapping. Science (1987) 25.71

Dideoxy sequencing method using denatured plasmid templates. Anal Biochem (1986) 17.34

Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A (2003) 14.01

Construction of a colicin E1-R factor composite plasmid in vitro: means for amplification of deoxyribonucleic acid. J Bacteriol (1975) 13.95

Chromosome 17 deletions and p53 gene mutations in colorectal carcinomas. Science (1989) 11.53

Mutations of chromosome 5q21 genes in FAP and colorectal cancer patients. Science (1991) 9.89

The genome of the social amoeba Dictyostelium discoideum. Nature (2005) 9.18

Mutational pressure as the main cause of molecular evolution and polymorphism. Nature (1974) 8.03

Preliminary criteria for classification of adult Still's disease. J Rheumatol (1992) 7.53

Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res (1999) 7.39

Targeted disruption of the mouse Stat3 gene leads to early embryonic lethality. Proc Natl Acad Sci U S A (1997) 7.08

The nucleotide sequence of pUB110: some salient features in relation to replication and its regulation. Plasmid (1986) 7.07

Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell (1999) 6.83

Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res (1998) 6.79

Quantum computers. Nature (2010) 6.79

Essential role of Stat6 in IL-4 signalling. Nature (1996) 6.56

The immune responses in CD40-deficient mice: impaired immunoglobulin class switching and germinal center formation. Immunity (1994) 6.18

Prevention of second primary tumors by an acyclic retinoid, polyprenoic acid, in patients with hepatocellular carcinoma. Hepatoma Prevention Study Group. N Engl J Med (1996) 6.01

A ribonucleotide reductase gene involved in a p53-dependent cell-cycle checkpoint for DNA damage. Nature (2000) 6.01

When is cancer pain mild, moderate or severe? Grading pain severity by its interference with function. Pain (1995) 5.97

Typing hepatitis C virus by polymerase chain reaction with type-specific primers: application to clinical surveys and tracing infectious sources. J Gen Virol (1992) 5.93

p53AIP1, a potential mediator of p53-dependent apoptosis, and its regulation by Ser-46-phosphorylated p53. Cell (2000) 5.64

Allelotype of colorectal carcinomas. Science (1989) 5.54

Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins. Mol Cell (2000) 5.49

The 5'-terminal sequence of the hepatitis C virus genome. Jpn J Exp Med (1990) 5.46

The action of tetrodotoxin on electrogenic components of squid giant axons. J Gen Physiol (1965) 5.42

Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus. J Virol (1993) 5.41

Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene (1994) 5.28

AXIN1 mutations in hepatocellular carcinomas, and growth suppression in cancer cells by virus-mediated transfer of AXIN1. Nat Genet (2000) 5.26

Interleukin-2 receptor gamma chain: a functional component of the interleukin-7 receptor. Science (1993) 5.22

On the stochastic model for estimation of mutational distance between homologous proteins. J Mol Evol (1972) 5.16

Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology (1992) 5.16

Somatic mutations of the APC gene in colorectal tumors: mutation cluster region in the APC gene. Hum Mol Genet (1992) 5.14

Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res (2000) 4.94

Syringe method for stepwise chemical synthesis of oligonucleotides. Nucleic Acids Res (1982) 4.70

Interleukin-2 receptor gamma chain: a functional component of the interleukin-4 receptor. Science (1993) 4.63

Rapid colorectal adenoma formation initiated by conditional targeting of the Apc gene. Science (1997) 4.62

On the constancy of the evolutionary rate of cistrons. J Mol Evol (1971) 4.49

The gene for familial polyposis coli maps to the long arm of chromosome 5. Science (1987) 4.48

Transient regulation of protein synthesis in Escherichia coli upon shift-up of growth temperature. J Bacteriol (1978) 4.38

Norwalk virus infection of volunteers: new insights based on improved assays. J Infect Dis (1994) 4.37

Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res (2001) 4.27

A primary genetic map of markers of human chromosome 10. Genomics (1988) 4.23

Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res (1992) 4.21

Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res (2000) 4.11

Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. Gene (1997) 4.02

Multiple endocrine neoplasia type 1 gene maps to chromosome 11 and is lost in insulinoma. Nature (1988) 3.96

A novel signaling molecule, p130, forms stable complexes in vivo with v-Crk and v-Src in a tyrosine phosphorylation-dependent manner. EMBO J (1994) 3.88

A neomycin resistance gene cassette selectable in a single copy state in the Bacillus subtilis chromosome. Nucleic Acids Res (1989) 3.87

An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy. Nature (1998) 3.86

Real-time detection system for quantification of hepatitis C virus genome. Gastroenterology (1999) 3.83

Transcriptional sequencing: A method for DNA sequencing using RNA polymerase. Proc Natl Acad Sci U S A (1998) 3.78

High guanine plus cytosine content in the third letter of codons of an extreme thermophile. DNA sequence of the isopropylmalate dehydrogenase of Thermus thermophilus. J Biol Chem (1984) 3.76

An endothelial receptor for oxidized low-density lipoprotein. Nature (1997) 3.76

Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nat Struct Biol (1995) 3.75

The M1- and M2-type isozymes of rat pyruvate kinase are produced from the same gene by alternative RNA splicing. J Biol Chem (1986) 3.64

IL-12 up-regulates IL-18 receptor expression on T cells, Th1 cells, and B cells: synergism with IL-18 for IFN-gamma production. J Immunol (1998) 3.56

Transformation by Rous sarcoma virus induces a novel gene with homology to a mitogenic platelet protein. Cell (1987) 3.50

The average number of generations until extinction of an individual mutant gene in a finite population. Genetics (1969) 3.49

Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep (2001) 3.47

Results of surgical and nonsurgical treatment for small-sized hepatocellular carcinomas: a retrospective and nationwide survey in Japan. The Liver Cancer Study Group of Japan. Hepatology (2000) 3.42

Molecular mechanics of calcium-myristoyl switches. Nature (1997) 3.36

Sequence analysis of hepatitis C virus isolated from a fulminant hepatitis patient. J Med Virol (2001) 3.29

Altered urinary bladder function in mice lacking the vanilloid receptor TRPV1. Nat Neurosci (2002) 3.28

Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability. Virology (1992) 3.22

Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res (1994) 3.19

Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res (2001) 3.18

A high-throughput SNP typing system for genome-wide association studies. J Hum Genet (2001) 3.18

Isolation and mapping of a polymorphic DNA sequence (pTHH22) on chromosome 9 [D9S12]. Nucleic Acids Res (1988) 3.17

IL-6 is produced by osteoblasts and induces bone resorption. J Immunol (1990) 3.14

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol (1992) 3.11

Size and shape effects in the biodistribution of intravascularly injected particles. J Control Release (2009) 3.08

Identification of the spinocerebellar ataxia type 2 gene using a direct identification of repeat expansion and cloning technique, DIRECT. Nat Genet (1996) 3.07

Altered pain perception and inflammatory response in mice lacking prostacyclin receptor. Nature (1997) 3.07

N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide, a calmodulin antagonist, inhibits cell proliferation. Proc Natl Acad Sci U S A (1981) 3.04

Spin Seebeck insulator. Nat Mater (2010) 3.01

Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res (2001) 2.99

Molecular detection of microscopic and submicroscopic deletions associated with Miller-Dieker syndrome. Am J Hum Genet (1988) 2.97

Mapping of mutation causing Friedreich's ataxia to human chromosome 9. Nature (1988) 2.96

Cloning of the genes for penicillinase, penP and penI, of Bacillus licheniformis in some vector plasmids and their expression in Escherichia coli, Bacillus subtilis, and Bacillus licheniformis. J Bacteriol (1981) 2.93

A tripeptide 'anticodon' deciphers stop codons in messenger RNA. Nature (2000) 2.90

Single-molecule analysis of chemotactic signaling in Dictyostelium cells. Science (2001) 2.89

Initiation of simian virus 40 DNA replication in vitro. J Virol (1983) 2.88

Localisation of atopy and beta subunit of high-affinity IgE receptor (Fc epsilon RI) on chromosome 11q. Lancet (1993) 2.88

Impaired febrile response in mice lacking the prostaglandin E receptor subtype EP3. Nature (1998) 2.88

Specific deficit of the ON response in visual transmission by targeted disruption of the mGluR6 gene. Cell (1995) 2.81

A mapped set of genetic markers for human chromosome 9. Genomics (1988) 2.80

Familial gastrointestinal stromal tumours with germline mutation of the KIT gene. Nat Genet (1998) 2.80

Detrimental genes with partial selfing and effects on a neutral locus. Genet Res (1974) 2.79

Early-onset ataxia with ocular motor apraxia and hypoalbuminemia is caused by mutations in a new HIT superfamily gene. Nat Genet (2001) 2.79

Nature of phosphorus limitation in the ultraoligotrophic eastern Mediterranean. Science (2005) 2.79

Efficient gene activation in mammalian cells by using recombinant adenovirus expressing site-specific Cre recombinase. Nucleic Acids Res (1995) 2.79