Published in Nucleic Acids Res on January 01, 2004
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics (2006) 5.50
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol (2005) 5.19
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res (2005) 3.85
Direct isolation and identification of promoters in the human genome. Genome Res (2005) 3.68
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet (2007) 3.24
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res (2005) 2.73
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res (2006) 2.54
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res (2006) 2.52
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
Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput Biol (2006) 2.11
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res (2006) 1.89
Genome-wide promoter analysis uncovers portions of the cancer methylome. Cancer Res (2008) 1.70
Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics (2004) 1.68
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics (2006) 1.51
Mice and men: their promoter properties. PLoS Genet (2006) 1.50
Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol Cell Biol (2005) 1.46
Erythroid Krüppel-like factor directly activates the basic Krüppel-like factor gene in erythroid cells. Mol Cell Biol (2007) 1.45
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Res (2006) 1.40
Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res (2005) 1.39
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet (2012) 1.29
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. Nucleic Acids Res (2006) 1.28
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res (2007) 1.28
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
An endosomally localized isoform of Eps15 interacts with Hrs to mediate degradation of epidermal growth factor receptor. J Cell Biol (2008) 1.08
Boosting with stumps for predicting transcription start sites. Genome Biol (2007) 1.08
Search for basonuclin target genes. Biochem Biophys Res Commun (2006) 1.07
IRF9 is a key factor for eliciting the antiproliferative activity of IFN-alpha. J Immunother (2009) 1.07
Prediction and analysis of nucleosome exclusion regions in the human genome. BMC Genomics (2008) 1.04
A composite intronic element directs dynamic binding of the progesterone receptor and GATA-2. Mol Endocrinol (2008) 1.04
Induction of PPM1D following DNA-damaging treatments through a conserved p53 response element coincides with a shift in the use of transcription initiation sites. Nucleic Acids Res (2008) 1.01
'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res (2006) 1.01
Periodicity of SNP distribution around transcription start sites. BMC Genomics (2006) 1.00
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res (2008) 0.99
Computational analyses of eukaryotic promoters. BMC Bioinformatics (2007) 0.99
A promoter polymorphism in the Per3 gene is associated with alcohol and stress response. Transl Psychiatry (2012) 0.96
A distance difference matrix approach to identifying transcription factors that regulate differential gene expression. Genome Biol (2007) 0.96
Landscape of transcriptional deregulations in the preeclamptic placenta. PLoS One (2013) 0.94
5'SAGE: 5'-end Serial Analysis of Gene Expression database. Nucleic Acids Res (2005) 0.94
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics (2007) 0.94
ATG deserts define a novel core promoter subclass. Genome Res (2005) 0.92
Cis-acting genetic variation at an E2F1/YY1 response site and putative p53 site is associated with altered allele-specific expression of ERCC5 (XPG) transcript in normal human bronchial epithelium. Carcinogenesis (2010) 0.91
Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J (2004) 0.90
Identification of the TFII-I family target genes in the vertebrate genome. Proc Natl Acad Sci U S A (2008) 0.90
Functional analysis of human and chimpanzee promoters. Genome Biol (2005) 0.89
Transcriptional protein Sp1 regulates LEDGF transcription by directly interacting with its cis-elements in GC-rich region of TATA-less gene promoter. PLoS One (2012) 0.88
Computational method for discovery of estrogen responsive genes. Nucleic Acids Res (2004) 0.87
Comparative promoter region analysis powered by CORG. BMC Genomics (2005) 0.86
Mapping of transcription start sites of human retina expressed genes. BMC Genomics (2007) 0.84
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. Mamm Genome (2006) 0.84
NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors. Nucleic Acids Res (2006) 0.83
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. BMC Genomics (2008) 0.82
Computational identification of transcription frameworks of early committed spermatogenic cells. Mol Genet Genomics (2008) 0.80
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions. BMC Genomics (2008) 0.79
GDNF-inducible zinc finger protein 1 is a sequence-specific transcriptional repressor that binds to the HOXA10 gene regulatory region. Nucleic Acids Res (2005) 0.79
K-SPMM: a database of murine spermatogenic promoters modules & motifs. BMC Bioinformatics (2006) 0.78
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Res (2007) 0.78
Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes. Genetica (2008) 0.77
Identification and characterization of the human inhibitor of caspase-activated DNase gene promoter. Apoptosis (2008) 0.76
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication. Bioinformatics (2009) 0.76
Functional single nucleotide polymorphism-based association studies. Hum Genomics (2006) 0.75
Promoter analysis: gene regulatory motif identification with A-GLAM. Methods Mol Biol (2009) 0.75
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
Database resources of the National Center for Biotechnology. Nucleic Acids Res (2003) 18.26
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res (2001) 4.03
High-efficiency full-length cDNA cloning. Methods Enzymol (1999) 3.56
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep (2001) 3.47
A space-efficient algorithm for local similarities. Comput Appl Biosci (1990) 2.98
Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method. Methods Mol Biol (2003) 2.45
Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44
WoLF PSORT: protein localization predictor. Nucleic Acids Res (2007) 10.14
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98
Mapping human genetic diversity in Asia. Science (2009) 7.40
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
A transcription factor response element for gene expression during circadian night. Nature (2002) 6.55
The medaka draft genome and insights into vertebrate genome evolution. Nature (2007) 5.77
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (2002) 5.16
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature (2004) 5.08
Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell (2007) 4.73
The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol (2010) 4.66
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res (2003) 4.25
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Phosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species. Proc Natl Acad Sci U S A (2010) 4.18
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res (2007) 3.80
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res (2006) 3.74
Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways. Oncogene (2003) 3.53
A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J (2003) 3.44
The landscape of C. elegans 3'UTRs. Science (2010) 3.32
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science (2008) 3.10
T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development. Immunity (2012) 2.78
DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway. Oncogene (2004) 2.73
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res (2004) 2.61
Thyrotrophin in the pars tuberalis triggers photoperiodic response. Nature (2008) 2.60
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res (2006) 2.52
The functional consequences of alternative promoter use in mammalian genomes. Trends Genet (2008) 2.47
Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method. Methods Mol Biol (2003) 2.45
5'-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol (2004) 2.34
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol (2011) 2.18
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics (2009) 2.07
Rate of evolution in brain-expressed genes in humans and other primates. PLoS Biol (2007) 1.87
Inhibition of angiogenesis and vascular leakiness by angiopoietin-related protein 4. Cancer Res (2003) 1.78
Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr Biol (2013) 1.69
Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation. J Biol Chem (2007) 1.66
Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res (2004) 1.63
Deletion of angiotensin-converting enzyme 2 accelerates pressure overload-induced cardiac dysfunction by increasing local angiotensin II. Hypertension (2006) 1.61
Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res (2009) 1.60
Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol (2004) 1.58
Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene (2005) 1.57
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57
Ezh2 augments leukemogenicity by reinforcing differentiation blockage in acute myeloid leukemia. Blood (2012) 1.56
The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes. RNA (2009) 1.54
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res (2010) 1.50
High-density association study and nomination of susceptibility genes for hypertension in the Japanese National Project. Hum Mol Genet (2007) 1.44
MAML1 enhances the transcriptional activity of Runx2 and plays a role in bone development. PLoS Genet (2013) 1.42
SYT associates with human SNF/SWI complexes and the C-terminal region of its fusion partner SSX1 targets histones. J Biol Chem (2001) 1.40
Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics (2007) 1.39
Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res (2007) 1.37
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res (2009) 1.36
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res (2005) 1.35
Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism. Mol Cell Biol (2010) 1.35
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res (2006) 1.34
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res (2011) 1.33
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. Nucleic Acids Res (2008) 1.32
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. Nucleic Acids Res (2006) 1.31
Identification of expressed genes linked to malignancy of human colorectal carcinoma by parametric clustering of quantitative expression data. Genome Biol (2003) 1.31
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. BMC Genomics (2009) 1.29
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii. Genome Res (2006) 1.28
Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene (2005) 1.27
Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Genome Res (2004) 1.25
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3. Nucleic Acids Res (2009) 1.23
Cell surface labeling and mass spectrometry reveal diversity of cell surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells. Mol Cell Proteomics (2005) 1.23
Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodysplastic disorders. J Exp Med (2013) 1.23
Prediction of subcellular locations of proteins: where to proceed? Proteomics (2010) 1.22
Role of a BCL9-related beta-catenin-binding protein, B9L, in tumorigenesis induced by aberrant activation of Wnt signaling. Cancer Res (2004) 1.21