Published in Nucleic Acids Res on December 15, 2008
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res (2009) 1.45
Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet (2013) 1.35
Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Nucleic Acids Res (2009) 1.06
Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis. Genome Biol (2009) 0.89
Statistical significance of combinatorial regulations. Proc Natl Acad Sci U S A (2013) 0.88
DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions. BMC Genomics (2010) 0.80
Epigenetic modification of histone 3 lysine 27: mediator subunit MED25 is required for the dissociation of polycomb repressive complex 2 from the promoter of cytochrome P450 2C9. J Biol Chem (2014) 0.78
Transcription efficiency of different chicken mannose-binding lectin promoter alleles. Immunogenetics (2014) 0.75
Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (2000) 128.08
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05
MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res (2003) 11.82
Scanning human gene deserts for long-range enhancers. Science (2003) 9.75
Transcription regulation and animal diversity. Nature (2003) 9.22
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet (2003) 6.82
Gene regulatory networks and the evolution of animal body plans. Science (2006) 6.42
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res (2004) 4.93
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res (2004) 4.53
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol (2006) 3.15
Predicting tissue-specific enhancers in the human genome. Genome Res (2007) 2.72
GALA, a database for genomic sequence alignments and annotations. Genome Res (2003) 2.56
C/EBPalpha mutations in acute myeloid leukaemias. Nat Rev Cancer (2004) 2.40
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Mutations in the human genes encoding the transcription factors of the hepatocyte nuclear factor (HNF)1 and HNF4 families: functional and pathological consequences. J Mol Endocrinol (2001) 1.93
Foxa1 and Foxa2 interact with the androgen receptor to regulate prostate and epididymal genes differentially. Ann N Y Acad Sci (2005) 1.75
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res (2000) 1.72
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics (2006) 1.58
SREBP-1 interacts with hepatocyte nuclear factor-4 alpha and interferes with PGC-1 recruitment to suppress hepatic gluconeogenic genes. J Biol Chem (2004) 1.55
Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Res (2006) 1.50
Up-regulation of p300 binding and p50 acetylation in tumor necrosis factor-alpha-induced cyclooxygenase-2 promoter activation. J Biol Chem (2002) 1.44
Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. Bioessays (2004) 1.36
C/EBPalpha: a tumour suppressor in multiple tissues? Biochim Biophys Acta (2006) 1.33
Orphan nuclear receptor small heterodimer partner represses hepatocyte nuclear factor 3/Foxa transactivation via inhibition of its DNA binding. Mol Endocrinol (2004) 1.30
Foxa3 (hepatocyte nuclear factor 3gamma ) is required for the regulation of hepatic GLUT2 expression and the maintenance of glucose homeostasis during a prolonged fast. J Biol Chem (2001) 1.28
Transcriptional activation by hepatocyte nuclear factor-1 requires synergism between multiple coactivator proteins. J Biol Chem (2000) 1.27
Sterol regulatory element-binding protein-2 interacts with hepatocyte nuclear factor-4 to enhance sterol isomerase gene expression in hepatocytes. J Biol Chem (2003) 1.26
Functional association between CBP and HNF4 in trans-activation. Biochem Biophys Res Commun (1997) 1.24
Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both. Curr Opin Genet Dev (2005) 1.20
Transcription factors that regulate growth and differentiation of myeloid cells. Int Rev Immunol (2001) 1.20
Hepatocyte nuclear factor 1 alpha: a key mediator of the effect of bile acids on gene expression. Hepatology (2003) 1.15
Foxa2 (HNF3beta ) controls multiple genes implicated in metabolism-secretion coupling of glucose-induced insulin release. J Biol Chem (2002) 1.09
Transcriptional regulation in endoderm development: characterization of an enhancer controlling Hnf3g expression by transgenesis and targeted mutagenesis. EMBO J (1997) 1.04
Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network. Proc Natl Acad Sci U S A (2004) 1.03
Combinatorial regulation of transcription. I: General aspects of transcriptional control. Immunity (1995) 0.99
Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. Nucleic Acids Res (2004) 0.98
Transcriptional regulation of human CYP3A4 basal expression by CCAAT enhancer-binding protein alpha and hepatocyte nuclear factor-3 gamma. Mol Pharmacol (2003) 0.97
A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis. Biochem Biophys Res Commun (2003) 0.94
Direct physical interactions between HNF-4 and Sp1 mediate synergistic transactivation of the apolipoprotein CIII promoter. Biochemistry (2002) 0.93
Functional characterization of transcription factor binding sites for HNF1-alpha, HNF3-beta (FOXA2), HNF4-alpha, Sp1 and Sp3 in the human prothrombin gene enhancer. J Thromb Haemost (2003) 0.92
Role of hepatocyte nuclear factor 3 gamma in the expression of human CYP2C genes. Arch Biochem Biophys (2004) 0.90
Hepatocyte nuclear factor 4alpha enhances the hepatocyte nuclear factor 1alpha-mediated activation of transcription. Nucleic Acids Res (2004) 0.87
Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells. Nucleic Acids Res (2008) 0.85
Control of IL-2Ralpha gene expression: structural changes within the proximal enhancer/core promoter during T-cell development. Nucleic Acids Res (2002) 0.82
LFB1/HNF1 acts as a repressor of its own transcription. Nucleic Acids Res (1994) 0.80
A role for HNF-3 in the regulation of the HNF-1 gene of the Atlantic salmon. Mol Genet Genomics (2001) 0.76
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
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
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate. N Engl J Med (2004) 7.91
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res (2002) 6.61
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet (2007) 5.75
High-throughput mapping of a dynamic signaling network in mammalian cells. Science (2005) 5.21
CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Tiny RNAs associated with transcription start sites in animals. Nat Genet (2009) 4.19
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res (2003) 4.01
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
TagDust--a program to eliminate artifacts from next generation sequencing data. Bioinformatics (2009) 3.64
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res (2003) 3.21
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6). Nat Genet (2006) 3.14
Small RNAs derived from snoRNAs. RNA (2009) 3.04
An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. Nature (2009) 3.04
Rapid detection of epidermal growth factor receptor mutations in lung cancer by the SMart-Amplification Process. Clin Cancer Res (2007) 3.02
A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res (2010) 2.87
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol (2009) 2.86
RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res (2005) 2.84
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One (2009) 2.67
Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A (2008) 2.66
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res (2003) 2.63
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics (2002) 2.59
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res (2006) 2.54
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A (2003) 2.33
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods (2010) 2.30
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol (2011) 2.18
Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol (2011) 2.18
Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res (2003) 2.15
Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc Natl Acad Sci U S A (2005) 2.09
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A (2006) 2.02
Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res (2003) 1.98
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. Structure (2007) 1.97
The abundance of short proteins in the mammalian proteome. PLoS Genet (2006) 1.96
SAMStat: monitoring biases in next generation sequencing data. Bioinformatics (2010) 1.95
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Biochem Biophys Res Commun (2002) 1.92
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. Nucleic Acids Res (2002) 1.91
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 1.91
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol (2006) 1.87
Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res (2005) 1.85
Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res (2003) 1.82
Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol (2006) 1.82
Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res (2011) 1.79
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res (2006) 1.75
A genome-wide and nonredundant mouse transcription factor database. Biochem Biophys Res Commun (2004) 1.75
Metagenomic diagnosis of bacterial infections. Emerg Infect Dis (2008) 1.74
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res (2010) 1.73
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci U S A (2012) 1.72
Heterotachy in mammalian promoter evolution. PLoS Genet (2006) 1.71
Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics (2009) 1.71
CDS annotation in full-length cDNA sequence. Genome Res (2003) 1.70
Antisense transcripts with rice full-length cDNAs. Genome Biol (2003) 1.69
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res (2006) 1.67
MiR-148a attenuates paclitaxel resistance of hormone-refractory, drug-resistant prostate cancer PC3 cells by regulating MSK1 expression. J Biol Chem (2010) 1.66
The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Genome Res (2003) 1.61
Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Biotechniques (2008) 1.61
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biol (2009) 1.60
A simple physical model predicts small exon length variations. PLoS Genet (2006) 1.59
Exciton Primer-mediated SNP detection in SmartAmp2 reactions. Hum Mutat (2010) 1.59
Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (2015) 1.58
A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Dev Cell (2009) 1.53
Multifaceted mammalian transcriptome. Curr Opin Cell Biol (2008) 1.52