FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122

Eukaryotic Promoter Database, EPD
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

epd
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122

Other names: EPD, Eukaryotic Promoter Database, EPD, epd

The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name “EPDnew”) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq (https://ccg.epfl.ch/chipseq) and Signal Search Analysis (https://ccg.epfl.ch/ssa), for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.

Webpage:

https://epd.epfl.ch/

Publications: (12)

Publications
More detailed information about this field from each metasource.

Compilation and analysis of eukaryotic POL II promoter sequences
PMID: 3808945
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools
PMID: 25378343
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era
PMID: 23193273
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

EPD in its twentieth year: towards complete promoter coverage of selected model organisms
PMID: 16381980
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The eukaryotic promoter database (EPD)
PMID: 10592254
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Eukaryotic Promoter Database EPD
PMID: 9399872
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
PMID: 14681364
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data
PMID: 11752326
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Eukaryotic Promoter Database (EPD): recent developments
PMID: 9847211
metasource: Fairsharing.org
version: FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

EPD in 2020: enhanced data visualization and extension to ncRNA promoters
PMID: 31680159
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122

http://dx.doi.org/10.1093/nar/gkz1014
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gkw1069
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:26.733122

Compilation and analysis of eukaryotic POL II promoter sequences PubMed citations: 101.

101 articles citing: Compilation and analysis of eukaryotic POL II promoter sequences

Pathogenic Tau Causes a Toxic Depletion of Nuclear Calcium. PMID:32668249
EPD in 2020: enhanced data visualization and extension to ncRNA promoters. PMID:31680159
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. PMID:27899657
The Transcription Factor ATF5 Mediates a Mammalian Mitochondrial UPR. PMID:27426517
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. PMID:25378343
Promoting developmental transcription. PMID:20023156
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. PMID:19589141
A transcription factor affinity-based code for mammalian transcription initiation. PMID:19141595
Novel expression of the ribosomal RNA genes in the extreme thermophile and archaebacterium Desulfurococcus mobilis. PMID:16453807
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. PMID:16381980
Characterization of a strong, constitutive mung bean (Vigna radiata L.) promoter with a complex mode of regulation in planta. PMID:16315097
Osteo-Promoter Database (OPD) -- promoter analysis in skeletal cells. PMID:15790428
Databases, models, and algorithms for functional genomics: a bioinformatics perspective. PMID:15699571
Specific TATAA and bZIP requirements suggest that HTLV-I Tax has transcriptional activity subsequent to the assembly of an initiation complex. PMID:15285791
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. PMID:14681364
Signal search analysis server. PMID:12824379
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. PMID:11752326
Development of an effective polyvalent vaccine against both Marek's and Newcastle diseases based on recombinant Marek's disease virus type 1 in commercial chickens with maternal antibodies. PMID:10708438
The eukaryotic promoter database (EPD). PMID:10592254
Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. PMID:10077607
Identification of human gene core promoters in silico. PMID:9521935
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. PMID:9399875
The Eukaryotic Promoter Database EPD. PMID:9399872
The EMBL nucleotide sequence database. PMID:9399791
Polymorphism and structure of the gene coding for the alpha 1 subunit of the Artemia franciscana Na/K-ATPase. PMID:9020888
Isolation and characterization of the androgen-dependent mouse cysteine-rich secretory protein-1 (CRISP-1) gene. PMID:9020862
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. PMID:9016550
The EMBL Nucleotide Sequence Database. PMID:9016493
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. PMID:8942976
Over- and underrepresentation of short DNA words in herpesvirus genomes. PMID:8891954
Two alternative promoters direct neuron-specific expression of the rat microtubule-associated protein 1B gene. PMID:8756433
Mutation spectra of TA*, the major photoproduct of thymidylyl-(3'5')-deoxyadenosine, in Escherichia coli under SOS conditions. PMID:8628692
TATA elements direct bi-directional transcription by RNA polymerases II and III. PMID:8604352
The European Bioinformatics Institute (EBI) databases. PMID:8594602
Cloning and analysis of the nuclear gene MRP-S9 encoding mitochondrial ribosomal protein S9 of Saccharomyces cerevisiae. PMID:8536310
Mutations of the microsomal triglyceride-transfer-protein gene in abetalipoproteinemia. PMID:8533758
Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids. PMID:8479918
Profilaggrin is a major epidermal calcium-binding protein. PMID:8417356
The frequency of two-base tracts in eukaryotic genomes. PMID:8411201
Upstream basal promoter element important for exclusive RNA polymerase III transcription of the EBER 2 gene. PMID:8386314
The EMBL data library. PMID:8332519
Vectors for the expression of PCR-amplified immunoglobulin variable domains with human constant regions. PMID:8332501
DNA sequence requirement of a TATA element-binding protein from Arabidopsis for transcription in vitro. PMID:8260636
Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis. PMID:8254750
TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs. PMID:8208615
Second-site long terminal repeat (LTR) revertants of replication-defective human immunodeficiency virus: effects of revertant TATA box motifs on virus infectivity, LTR-directed expression, in vitro RNA synthesis, and binding of basal transcription factors TFIID and TFIIA. PMID:8151790
Identification of two initiator elements in the bidirectional promoter of the human dihydrofolate reductase and mismatch repair protein 1 genes. PMID:8029024
Glucocorticoid activation of chromogranin A gene expression. Identification and characterization of a novel glucocorticoid response element. PMID:7989592
The European Bioinformatics Institute (EBI) databases. PMID:7937043
In vivo definition of an archaeal promoter. PMID:7896710
Promoter elements in Drosophila melanogaster revealed by sequence analysis. PMID:7768444
Isolation of a differentially regulated splicing isoform of human NF-E2. PMID:7724591
BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). PMID:7689350
Inverse PCR-mediated cloning of the promoter for the rat vasopressin V2 receptor gene. PMID:7667072
Isolation and characterization of the androgen-dependent mouse cysteine-rich secretory protein-3 (CRISP-3) gene. PMID:7639699
Specific binding of proteins to the noncoding strand of a crucial element of the variant surface glycoprotein, procyclin, and ribosomal promoters of trypanosoma brucei. PMID:7565711
Molecular cloning of LSIRF, a lymphoid-specific member of the interferon regulatory factor family that binds the interferon-stimulated response element (ISRE). PMID:7541907
Human eosinophil major basic protein, a mediator of allergic inflammation, is expressed by alternative splicing from two promoters. PMID:7531438
Discrimination of phytochrome dependent light inducible from non-light inducible plant genes. Prediction of a common light-responsive element (LRE) in phytochrome dependent light inducible plant genes. PMID:3697087
Thymine methyls and DNA-protein interactions. PMID:3320959
The conserved decanucleotide from the immunoglobulin heavy chain promoter induces a very high transcriptional activity in B-cells when introduced into an heterologous promoter. PMID:3111845
Organization of the murine Mx gene and characterization of its interferon- and virus-inducible promoter. PMID:2974922
Both alpha-tubulin genes are transcriptionally active in Stylonychia lemnae. PMID:2841032
Type 1 plasminogen activator inhibitor gene: functional analysis and glucocorticoid regulation of its promoter. PMID:2840665
Histone genes of Volvox carteri: DNA sequence and organization of two H3-H4 gene loci. PMID:2836811
Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters. PMID:2829113
Human thrombomodulin gene is intron depleted: nucleic acid sequences of the cDNA and gene predict protein structure and suggest sites of regulatory control. PMID:2819876
Induction and repression of the Drosophila Sgs-3 glue gene are mediated by distinct sequences in the proximal promoter. PMID:2721493
Sp1 activates transcription without enhancing DNA-binding activity of the TATA box factor. PMID:2677669
Functional identification of regulatory elements within the promoter region of platelet-derived growth factor 2. PMID:2651898
Drosophila Sgs3 TATA: effects of point mutations on expression in vivo and protein binding in vitro with staged nuclear extracts. PMID:2583107
Mammalian multidrug-resistance gene: correlation of exon organization with structural domains and duplication of an ancestral gene. PMID:2570420
5' flanking sequence and structure of a gene encoding rat 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. PMID:2549541
Structure and expression of a muscle specific gene which is adjacent to the Drosophila myosin heavy-chain gene and can encode a cytochrome b related protein. PMID:2549511
Transcription of the chicken myb proto-oncogene starts within a CpG island. PMID:2548166
Secretory pancreatic stone protein messenger RNA. Nucleotide sequence and expression in chronic calcifying pancreatitis. PMID:2525567
Organization and nucleotide sequence of the genes encoding the large subunits A, B and C of the DNA-dependent RNA polymerase of the archaebacterium Sulfolobus acidocaldarius. PMID:2501756
Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. PMID:2499884
Levels of RNA from a family of putative serine protease genes are reduced in Drosophila melanogaster dunce mutants and are regulated by cyclic AMP. PMID:2469005
New services of the EMBL Data Library. PMID:2388823
Identification of positive and negative regulatory elements governing cell-type-specific expression of the neural cell adhesion molecule gene. PMID:2325642
Cell-specific activity of cis-acting regulatory elements in the promoter of the mouse multidrug resistance gene mdr1. PMID:2248681
Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. PMID:2196437
A sequence pattern that occurs at the transcription initiation region of yeast RNA polymerase II promoters. PMID:2192362
Mutational analysis of an archaebacterial promoter: essential role of a TATA box for transcription efficiency and start-site selection in vitro. PMID:2124695
The EMBL data library. PMID:2041807
Dystrophin is transcribed in brain from a distant upstream promoter. PMID:1996328
Sequence and functional characterization of the human purine nucleoside phosphorylase promoter. PMID:1923769
Complex pattern of alternative splicing generates unusual diversity in the leader sequence of the chicken link protein mRNA. PMID:1923766
Dhr6, a Drosophila homolog of the yeast DNA-repair gene RAD6. PMID:1902572
Differential ability of proximal and remote element pairs to cooperate in activating RNA polymerase II transcription. PMID:1875939
Anatomy of the parp gene promoter of Trypanosoma brucei. PMID:1840521
Host-derived 5' ends and overlapping complementary 3' ends of the two mRNAs transcribed from the ambisense S segment of Uukuniemi virus. PMID:1831239
Sequence analysis of wheat mitochondrial transcripts capped in vitro: definitive identification of transcription initiation sites. PMID:1718611
Molecular and functional analysis of the virus- and interferon-inducible human MxA promoter. PMID:1706589
Regulation of herpes simplex virus true late gene expression: sequences downstream from the US11 TATA box inhibit expression from an unreplicated template. PMID:1658372
The EMBL Data Library. PMID:1598236
Expression in vivo and in vitro of the major structural protein (VP73) of African swine fever virus. PMID:1550491
Structure of the chicken myelomonocytic growth factor gene and specific activation of its promoter in avian myelomonocytic cells by protein kinases. PMID:1549124
Mammalian promoter element function in the fission yeast Schizosaccharomyces pombe. PMID:1321414
The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements. PMID:1312710
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools PubMed citations: 100.

100 articles citing: The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense-Antisense Gene Pair in Human Cancers. PMID:35893234
Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes. PMID:35806206
A successful hybrid deep learning model aiming at promoter identification. PMID:35641900
Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code. PMID:35613619
Exploring Diverse Coagulation Factor XIII Subunit Expression Datasets: A Bioinformatic Analysis. PMID:35563115
HPV infection alters vaginal microbiome through down-regulating host mucosal innate peptides used by Lactobacilli as amino acid sources. PMID:35228537
Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes. PMID:35224327
ZHX2 inhibits thyroid cancer metastasis through transcriptional inhibition of S100A14. PMID:35151335
Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in Drosophila. PMID:35052398
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. PMID:35021193
UBE2S promotes cell chemoresistance through PTEN-AKT signaling in hepatocellular carcinoma. PMID:34785642
Proteasome inhibition alters mitotic progression through the upregulation of centromeric α-Satellite RNAs. PMID:34739170
Hypoxia induces DOT1L in articular cartilage to protect against osteoarthritis. PMID:34727094
RabA2b Overexpression Alters the Plasma-Membrane Proteome and Improves Drought Tolerance in Arabidopsis. PMID:34691115
RING finger protein TOPORS modulates the expression of tumor suppressor SMAR1 in colorectal cancer via the TLR4-TRIF pathway. PMID:34689394
Genomic organization of the autonomous regulatory domain of eyeless locus in Drosophila melanogaster. PMID:34570231
HIV-Proteins-Associated CNS Neurotoxicity, Their Mediators, and Alternative Treatments. PMID:34562223
MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma. PMID:34551968
The mRNA decapping protein 2 (DCP2) is a major regulator of developmental events in Drosophila-insights from expression paradigms. PMID:34536141
A prelude to the proximity interaction mapping of CXXC5. PMID:34475492
Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus. PMID:34325731
The H3.3K27M oncohistone antagonizes reprogramming in Drosophila. PMID:34280185
NR5A2 Is One of 12 Transcription Factors Predicting Prognosis in HNSCC and Regulates Cancer Cell Proliferation in a p53-Dependent Manner. PMID:34277436
Circadian clock protein BMAL1 regulates melanogenesis through MITF in melanoma cells. PMID:34160901
A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver. PMID:34038707
In vivo Engineering of Chromosome 19 q-arm by Employing the CRISPR/AsCpf1 and ddAsCpf1 Systems in Human Malignant Gliomas (Hypothesis). PMID:33990905
Programming to S1PR1+ Endothelial Cells Promotes Restoration of Vascular Integrity. PMID:33926208
Investigation of the Wilson gene ATP7B transcriptional start site and the effect of core promoter alterations. PMID:33828154
Targeting the IL-6/STAT3 Signalling Cascade to Reverse Tamoxifen Resistance in Estrogen Receptor Positive Breast Cancer. PMID:33806019
TFEB Promotes Prostate Cancer Progression via Regulating ABCA2-Dependent Lysosomal Biogenesis. PMID:33732651
Disruption of CTNND2, encoding delta-catenin, causes a penetrant attention deficit disorder and myopia. PMID:33718894
Aurora Kinase B Expression, Its Regulation and Therapeutic Targeting in Human Retinoblastoma. PMID:33704359
Transcriptional Profiling of STAT1 Gain-of-Function Reveals Common and Mutation-Specific Fingerprints. PMID:33679782
Differentiation of two human neuroblastoma cell lines alters SV2 expression patterns. PMID:33588752
AAV-Mediated CRISPRi and RNAi Based Gene Silencing in Mouse Hippocampal Neurons. PMID:33557342
iPTT(2 L)-CNN: A Two-Layer Predictor for Identifying Promoters and Their Types in Plant Genomes by Convolutional Neural Network. PMID:33488763
Interferon Regulatory Factor 9 Promotes Lung Cancer Progression via Regulation of Versican. PMID:33430083
On the role of transcription in positioning nucleosomes. PMID:33417594
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. PMID:33227813
The UCSC Genome Browser database: 2021 update. PMID:33221922
Targeting SKA3 suppresses the proliferation and chemoresistance of laryngeal squamous cell carcinoma via impairing PLK1-AKT axis-mediated glycolysis. PMID:33106477
Analyzing a putative enhancer of optic disc morphology. PMID:33092545
Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo. PMID:32950053
STAT3 isoforms differentially affect ACE2 expression: A potential target for COVID-19 therapy. PMID:32949179
Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts. PMID:32873781
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. PMID:32746900
Peptidyl Arginine Deiminase Type 4 Gene Promoter Hypo-Methylation in Rheumatoid Arthritis. PMID:32629762
ZEB1/miR-200c/AGR2: A New Regulatory Loop Modulating the Epithelial-Mesenchymal Transition in Lung Adenocarcinomas. PMID:32570918
Negative elongation factor complex enables macrophage inflammatory responses by controlling anti-inflammatory gene expression. PMID:32385332
Methylation Pattern of the SOCS3 and IL6R Promoters in Rheumatoid Arthritis. PMID:32292581
Acid Sphingomyelinase Downregulation Enhances Mitochondrial Fusion and Promotes Oxidative Metabolism in a Mouse Model of Melanoma. PMID:32244541
SPHK2-Generated S1P in CD11b+ Macrophages Blocks STING to Suppress the Inflammatory Function of Alveolar Macrophages. PMID:32209471
Epitranscriptomic 5-Methylcytosine Profile in PM2.5-induced Mouse Pulmonary Fibrosis. PMID:32135311
Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways. PMID:31926431
NOTCH1 signaling in oral squamous cell carcinoma via a TEL2/SERPINE1 axis. PMID:31827722
EPD in 2020: enhanced data visualization and extension to ncRNA promoters. PMID:31680159
TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression. PMID:31527052
Loss of PSP94 expression is associated with early PSA recurrence and deteriorates outcome of PTEN deleted prostate cancers. PMID:31516752
Role of irisin in androgen-deficient muscle wasting and osteopenia in mice. PMID:31494773
17-β estradiol exerts anti-inflammatory effects through activation of Nrf2 in mouse embryonic fibroblasts. PMID:31442293
IL-22Ra1 is induced during influenza infection by direct and indirect TLR3 induction of STAT1. PMID:31416461
TERC promotes cellular inflammatory response independent of telomerase. PMID:31294790
Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PMID:30998799
Glucocorticoid-dependent expression of IAP participates in the protection against TNF-mediated cytotoxicity in MCF7 cells. PMID:30987626
Comprehensive sequencing of the myocilin gene in a selected cohort of severe primary open-angle glaucoma patients. PMID:30816137
FOXM1 plays a role in autophagy by transcriptionally regulating Beclin-1 and LC3 genes in human triple-negative breast cancer cells. PMID:30729279
Human skeletal muscle macrophages increase following cycle training and are associated with adaptations that may facilitate growth. PMID:30700754
Upregulation of centromere protein F is linked to aggressive prostate cancers. PMID:30519097
A novel molecular mechanism for a long non-coding RNA PCAT92 implicated in prostate cancer. PMID:30197753
Regulatory variants: from detection to predicting impact. PMID:29893792
Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo. PMID:29727464
Allopregnanolone Alters the Gene Expression Profile of Human Glioblastoma Cells. PMID:29543748
NRF2-regulated metabolic gene signature as a prognostic biomarker in non-small cell lung cancer. PMID:29050246
ARNT is a potential direct HIF-1 target gene in human Hep3B hepatocellular carcinoma cells. PMID:28855849
New tricks for an old dog: Brf2-dependent RNA Polymerase III transcription in oxidative stress and cancer. PMID:28854119
MiRNAs regulate oxidative stress related genes via binding to the 3' UTR and TATA-box regions: a new hypothesis for cataract pathogenesis. PMID:28806956
Kaiso differentially regulates components of the Notch signaling pathway in intestinal cells. PMID:28637464
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. PMID:28605766
A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner. PMID:28539359
Connective Tissue Growth Factor Promotes Efficient Generation of Human Induced Pluripotent Stem Cell-Derived Choroidal Endothelium. PMID:28474838
NF-κB regulates neuronal ankyrin-G via a negative feedback loop. PMID:28181483
TSSPlant: a new tool for prediction of plant Pol II promoters. PMID:28082394
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
The application of powerful promoters to enhance gene expression in industrial microorganisms. PMID:28044271
Expression of Cav1.3 calcium channel in the human and mouse colon: posttranscriptional inhibition by IFNγ. PMID:27932504
Molecular mechanism(s) involved in differential expression of vitamin C transporters along the intestinal tract. PMID:27932501
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. PMID:27899657
European Nucleotide Archive in 2016. PMID:27899630
Structural features of DNA that determine RNA polymerase II core promoter. PMID:27884105
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. PMID:27863463
A researcher's guide to the galaxy of IRESs. PMID:27853833
What Is the Impact of mRNA 5' TL Heterogeneity on Translational Start Site Selection and the Mammalian Cellular Phenotype? PMID:27630668
BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data. PMID:27559732
Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data. PMID:26951854
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. PMID:26818008
The ATF6 pathway of the ER stress response contributes to enhanced viability in glioblastoma. PMID:26716508
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
IMP2/p62 induces genomic instability and an aggressive hepatocellular carcinoma phenotype. PMID:26426686
Chronic alcohol exposure affects pancreatic acinar mitochondrial thiamin pyrophosphate uptake: studies with mouse 266-6 cell line and primary cells. PMID:26316591
A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences. PMID:26034056
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era PubMed citations: 65.

65 articles citing: EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

Chronic Exposure to the Food Additive tBHQ Modulates Expression of Genes Related to SARS-CoV-2 and Influenza Viruses. PMID:35629310
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes. PMID:35452518
CD90 is regulated by notch1 and hallmarks a more aggressive intrahepatic cholangiocarcinoma phenotype. PMID:35172861
Genomic studies controvert the existence of the CUX1 p75 isoform. PMID:34997000
DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events. PMID:34871444
Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. PMID:34410491
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer. PMID:34135941
Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype. PMID:33960642
Genome-Wide Methylation Mapping Using Nanopore Sequencing Technology Identifies Novel Tumor Suppressor Genes in Hepatocellular Carcinoma. PMID:33920410
Epigenetic Regulation of the N-Terminal Truncated Isoform of Matrix Metalloproteinase-2 (NTT-MMP-2) and Its Presence in Renal and Cardiac Diseases. PMID:33732288
Modulation of IGF2 Expression in the Murine Thymus and Thymic Epithelial Cells Following Coxsackievirus-B4 Infection. PMID:33672010
Long Non-Coding RNA FENDRR: Gene Structure, Expression, and Biological Relevance. PMID:33513839
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. PMID:33227813
Pivotal Role of Fatty Acid Synthase in c-MYC Driven Hepatocarcinogenesis. PMID:33187130
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. PMID:32887686
Familial analysis reveals rare risk variants for migraine in regulatory regions. PMID:32076896
Crenigacestat, a selective NOTCH1 inhibitor, reduces intrahepatic cholangiocarcinoma progression by blocking VEGFA/DLL4/MMP13 axis. PMID:32042099
Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma. PMID:31861475
UCSC Genome Browser enters 20th year. PMID:31691824
EPD in 2020: enhanced data visualization and extension to ncRNA promoters. PMID:31680159
iProEP: A Computational Predictor for Predicting Promoter. PMID:31299595
mTORC1 amplifies the ATF4-dependent de novo serine-glycine pathway to supply glycine during TGF-β1-induced collagen biosynthesis. PMID:31113850
DeePromoter: Robust Promoter Predictor Using Deep Learning. PMID:31024615
Ethanol sensitizes skeletal muscle to ammonia-induced molecular perturbations. PMID:30872403
Designing a whole cell bioreporter to show antioxidant activities of agents that work by promotion of the KEAP1-NRF2 signaling pathway. PMID:30824775
NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration. PMID:30684219
Comprehensive Analysis of Hepatitis B Virus Promoter Region Mutations. PMID:30388827
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. PMID:29945659
Motifome comparison between modern human, Neanderthal and Denisovan. PMID:29914355
The evolution of CpG density and lifespan in conserved primate and mammalian promoters. PMID:29661983
Intragenic transcriptional interference regulates the human immune ligand MICA. PMID:29643123
The expression profile and prognostic significance of eukaryotic translation elongation factors in different cancers. PMID:29342219
Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome. PMID:28977633
MiRNAs regulate oxidative stress related genes via binding to the 3' UTR and TATA-box regions: a new hypothesis for cataract pathogenesis. PMID:28806956
Lhx1/5 control dendritogenesis and spine morphogenesis of Purkinje cells via regulation of Espin. PMID:28516904
Connective Tissue Growth Factor Promotes Efficient Generation of Human Induced Pluripotent Stem Cell-Derived Choroidal Endothelium. PMID:28474838
OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans. PMID:28241052
HRGFish: A database of hypoxia responsive genes in fishes. PMID:28205556
Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PMID:28158264
Interferons Induce Expression of SAMHD1 in Monocytes through Down-regulation of miR-181a and miR-30a. PMID:27909056
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. PMID:27899657
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. PMID:27899593
Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis. PMID:27811935
Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. PMID:27716823
Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. PMID:27558259
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. PMID:27522922
Precision Modulation of Neurodegenerative Disease-Related Gene Expression in Human iPSC-Derived Neurons. PMID:27341390
Construction of an integrative regulatory element and variation map of the murine Tst locus. PMID:27287690
Serpin peptidase inhibitor (SERPINB5) haplotypes are associated with susceptibility to hepatocellular carcinoma. PMID:27221742
TLR Stimulation Dynamically Regulates Heme and Iron Export Gene Expression in Macrophages. PMID:27006955
Obesity-Dependent Increases in Oocyte mRNAs Are Associated With Increases in Proinflammatory Signaling and Gut Microbial Abundance of Lachnospiraceae in Female Mice. PMID:26881311
The ATF6 pathway of the ER stress response contributes to enhanced viability in glioblastoma. PMID:26716508
Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity. PMID:26703594
TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis. PMID:26394619
Methylation of the DCLK1 promoter region in circulating free DNA and its prognostic value in lung cancer patients. PMID:26311076
Structure of silent transcription intervals and noise characteristics of mammalian genes. PMID:26215071
Integrative network-based approach identifies key genetic elements in breast invasive carcinoma. PMID:26040466
The integral membrane protein ITM2A, a transcriptional target of PKA-CREB, regulates autophagic flux via interaction with the vacuolar ATPase. PMID:25951193
Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression. PMID:25627242
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. PMID:25378343
Optimizations of siRNA design for the activation of gene transcription by targeting the TATA-box motif. PMID:25250958
Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. PMID:24973216
Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species. PMID:24955394
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157
EPD in its twentieth year: towards complete promoter coverage of selected model organisms PubMed citations: 56.

56 articles citing: EPD in its twentieth year: towards complete promoter coverage of selected model organisms

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PMID:28945760
Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. PMID:27092172
Sequence information gain based motif analysis. PMID:26553056
Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PMID:24205361
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. PMID:24129253
MEF2 is an in vivo immune-metabolic switch. PMID:24075010
Role of helicase-like transcription factor (hltf) in the G2/m transition and apoptosis in brain. PMID:23826137
Gene promoters show chromosome-specificity and reveal chromosome territories in humans. PMID:23617842
Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. PMID:23020586
P-value-based regulatory motif discovery using positional weight matrices. PMID:22990209
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites. PMID:22913572
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. PMID:22897824
Rapid identification of novel functional promoters for gene therapy. PMID:22767241
Aberrant DNA methylation and prostate cancer. PMID:22547956
LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. PMID:22267903
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. PMID:22253291
Functional activity of the novel Alzheimer's amyloid β-peptide interacting domain (AβID) in the APP and BACE1 promoter sequences and implications in activating apoptotic genes and in amyloidogenesis. PMID:21708232
The Alzheimer's amyloid β-peptide (Aβ) binds a specific DNA Aβ-interacting domain (AβID) in the APP, BACE1, and APOE promoters in a sequence-specific manner: characterizing a new regulatory motif. PMID:21699964
Evolution of hsp70 gene expression: a role for changes in AT-richness within promoters. PMID:21655251
Genome-wide analysis of mobile genetic element insertion sites. PMID:21609951
mirConnX: condition-specific mRNA-microRNA network integrator. PMID:21558324
Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PMID:21464922
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. PMID:21372179
Adaptive seeds tame genomic sequence comparison. PMID:21209072
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. PMID:21097880
Eukaryotic and prokaryotic promoter prediction using hybrid approach. PMID:21046474
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. PMID:20861161
Identification of cis-regulatory elements in the mammalian genome: the cREMaG database. PMID:20824209
phiSITE: database of gene regulation in bacteriophages. PMID:19900969
Transcriptional regulation of mitochondrial glycerophosphate acyltransferase is mediated by distal promoter via ChREBP and SREBP-1. PMID:19682972
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. PMID:19589141
Modulation of the E2F1-driven cancer cell fate by the DNA damage response machinery and potential novel E2F1 targets in osteosarcomas. PMID:19541929
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PMID:19390574
Promoter analysis: gene regulatory motif identification with A-GLAM. PMID:19378149
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. PMID:19128496
Conservation and implications of eukaryote transcriptional regulatory regions across multiple species. PMID:19099599
An optimized procedure for the design and evaluation of Ecotilling assays. PMID:18973671
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach. PMID:18834544
PCA-HPR: a principle component analysis model for human promoter recognition. PMID:18795109
In silico regulatory analysis for exploring human disease progression. PMID:18564415
Profiling the thermodynamic softness of adenoviral promoters. PMID:18390611
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. PMID:18257925
Generic eukaryotic core promoter prediction using structural features of DNA. PMID:18096745
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. PMID:18093302
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. PMID:18006571
Computational analyses of eukaryotic promoters. PMID:17903284
MethyCancer: the database of human DNA methylation and cancer. PMID:17890243
Indexing strategies for rapid searches of short words in genome sequences. PMID:17593978
Integrative content-driven concepts for bioinformatics "beyond the cell". PMID:17426389
Recognition of interferon-inducible sites, promoters, and enhancers. PMID:17309789
Mapping of transcription start sites of human retina expressed genes. PMID:17286855
TRED: a transcriptional regulatory element database, new entries and other development. PMID:17202159
Beyond microarrays: find key transcription factors controlling signal transduction pathways. PMID:17118134
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. PMID:17068082
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. PMID:16845074
The eukaryotic promoter database (EPD) PubMed citations: 50.

50 articles citing: The eukaryotic promoter database (EPD)

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. PMID:35021193
lncRNAfunc: a knowledgebase of lncRNA function in human cancer. PMID:34791419
BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. PMID:33552037
Differential Methylation in Promoter Regions of the Genes NR3C1 and HSP90AA1, Involved in the Regulation, and Bioavailability of Cortisol in Leukocytes of Women With Preeclampsia. PMID:32656215
Characterization of the CCAAT-binding transcription factor complex in the plant pathogenic fungus Fusarium graminearum. PMID:32184445
DeePromoter: Robust Promoter Predictor Using Deep Learning. PMID:31024615
Prediction of Human Immunodeficiency Virus Type 1 Subtype-Specific Off-Target Effects Arising from CRISPR-Cas9 Gene Editing Therapy. PMID:31021222
Aberrant expression of the microtubule-associated protein tau is an independent prognostic feature in prostate cancer. PMID:30823906
Genetic polymorphisms and haplotypes of the DJ-1 gene promoter associated with the susceptibility to male infertility. PMID:28932933
XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T Gene Polymorphisms Associated with Male Infertility Risk: Evidences from Case-Control and In Silico Studies. PMID:28421111
Recognition Code of ZNF191(243-368) and Its Interaction with DNA. PMID:26457075
Genome-wide analysis of tandem repeats in plants and green algae. PMID:24192840
Transcriptional regulation of immediate-early gene response by THOC5, a member of mRNA export complex, contributes to the M-CSF-induced macrophage differentiation. PMID:24157873
Gene promoters show chromosome-specificity and reveal chromosome territories in humans. PMID:23617842
Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. PMID:23355428
Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. PMID:23020586
Cryptic transcripts from a ubiquitous plasmid origin of replication confound tests for cis-regulatory function. PMID:22618870
Epithelial cells in fetal intestine produce chemerin to recruit macrophages. PMID:19443732
Structure, expression, and biological function of INSM1 transcription factor in neuroendocrine differentiation. PMID:19246490
Interferon regulatory factors are transcriptional regulators of adipogenesis. PMID:18177728
Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism. PMID:17576671
Unravelling the world of cis-regulatory elements. PMID:17541666
Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. PMID:17204484
Automatic annotation of eukaryotic genes, pseudogenes and promoters. PMID:16925832
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. PMID:16845086
AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. PMID:16524982
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. PMID:16381980
A core promoter element downstream of the TATA box that is recognized by TFIIB. PMID:16230532
Recent additions and improvements to the Onto-Tools. PMID:15980579
PromoterPlot: a graphical display of promoter similarities by pattern recognition. PMID:15980503
Promoter features related to tissue specificity as measured by Shannon entropy. PMID:15833120
Mapping and functional characterization of the TAF11 interaction with TFIIA. PMID:15657423
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. PMID:15608156
Down-regulation of Rad51 and decreased homologous recombination in hypoxic cancer cells. PMID:15367671
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. PMID:14681364
FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. PMID:12824363
PromH: Promoters identification using orthologous genomic sequences. PMID:12824362
Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. PMID:12654722
Computational analysis of core promoters in the Drosophila genome. PMID:12537576
Identification and utilization of arbitrary correlations in models of recombination signal sequences. PMID:12537561
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. PMID:12136103
Cellular transcription factor Sp1 recruits simian virus 40 capsid proteins to the viral packaging signal, ses. PMID:12021324
Computational detection and location of transcription start sites in mammalian genomic DNA. PMID:11875034
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. PMID:11752326
The EMBL Nucleotide Sequence Database. PMID:11752244
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. PMID:11375929
Identification and characterization of the potential promoter regions of 1031 kinds of human genes. PMID:11337467
First pass annotation of promoters on human chromosome 22. PMID:11230158
The EMBL nucleotide sequence database. PMID:11125039
Genome annotation assessment in Drosophila melanogaster. PMID:10779488