ConSite: web-based prediction of regulatory elements using cross-species comparison.
paper
Cited
Public
Unavailable
- Authors
- Sandelin, Albin; Wasserman, Wyeth W; Lenhard, Boris
- Year
- 2004
- Journal
- Nucleic acids research
- PMID
- 15215389
- DOI
- 10.1093/nar/gkh372
- PMCID
- PMC441510
ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite.
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| Hypoxia-mediated regulation of mitochondrial transcription factors in renal epithelial cells: implications for hypertensive renal physiology. | Natarajan B et al. | β | 2021 | β |
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| Regulation of PD-L1 expression is a novel facet of cyclic-AMP-mediated immunosuppression. | Sasi B et al. | β | 2021 | β |
| Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene. | Di Pietro L et al. | β | 2021 | β |
| Evolutionary-driven C-MYC gene expression in mammalian fibroblasts. | Moura MT et al. | β | 2020 | β |
| Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. | Ambrosini G et al. | β | 2020 | β |
| Novel genetic associations with interferon in systemic lupus erythematosus identified by replication and fine-mapping of trait-stratified genome-wide screen. | Ghodke-Puranik Y et al. | β | 2020 | β |
| SNAIL Promotes Metastatic Behavior of Rhabdomyosarcoma by Increasing EZRIN and AKT Expression and Regulating MicroRNA Networks. | Skrzypek K et al. | β | 2020 | β |
| Transcription factors-DNA interactions in rice: identification and verification. | Shen Z et al. | β | 2020 | β |
| 15-epi-lipoxin A<sub>4</sub> inhibits TNF-Ξ±-induced tissue factor expression via the PI3K/AKT/ NF-ΞΊB axis in human umbilical vein endothelial cells. | Chen Y et al. | β | 2019 | β |
| Consulting prostate cancer cohort data uncovers transcriptional control: Regulation of the MARCH6 gene. | Coates HW et al. | β | 2019 | β |
| DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer. | Weigel C et al. | β | 2019 | β |
| Identification of neuron-type specific promoters in monkey genome and their functional validation in mice. | Nagai Y et al. | β | 2019 | β |
| Loss of p53 Causes Stochastic Aberrant X-Chromosome Inactivation and Female-Specific Neural Tube Defects. | Delbridge ARD et al. | β | 2019 | β |
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| BRACHYURY directs histone acetylation to target loci during mesoderm development. | Beisaw A et al. | β | 2018 | β |
| Circular RNA circITGA7 inhibits colorectal cancer growth and metastasis by modulating the Ras pathway and upregulating transcription of its host gene ITGA7. | Li X et al. | β | 2018 | β |
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| Identification of novel GLI1 target genes and regulatory circuits in human cancer cells. | Diao Y et al. | β | 2018 | β |
| Molecular cloning of vitellogenin gene promoters and in vitro and in vivo transcription profiles following estradiol-17Ξ² administration in the cutthroat trout. | Mushirobira Y et al. | β | 2018 | β |
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| The role of lnc-DC long non-coding RNA and SOCS1 in the regulation of STAT3 in coronary artery disease and type 2 diabetes mellitus. | Alikhah A et al. | β | 2018 | β |
| The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma. | Giricz O et al. | β | 2018 | β |
| Thymidine phosphorylase: A potential new target for treating cardiovascular disease. | Li W et al. | β | 2018 | β |
| Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. | Teng M et al. | β | 2017 | β |
| Aldosterone-induced expression of ENaC-Ξ± is associated with activity of p65/p50 in renal epithelial cells. | Chen R et al. | β | 2017 | β |
| An Advanced Omic Approach to Identify Co-Regulated Clusters and Transcription Regulation Network with AGCT and SHOE Methods. | Polouliakh N et al. | β | 2017 | β |
| Association of oligodendrocytes differentiation regulator gene DUSP15 with autism. | Tian Y et al. | β | 2017 | β |
| DNA methylation of the Fthl17 5'-upstream region regulates differential Fthl17 expression in lung cancer cells and germline stem cells. | Aoki N et al. | β | 2017 | β |
| Functional promoter polymorphisms direct the expression of cystathionine gamma-lyase gene in mouse models of essential hypertension. | Gupta V et al. | β | 2017 | β |
| Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences. | Chen ZY et al. | β | 2017 | β |
| <i>Drosophila</i> Model for the Analysis of Genesis of LIM-kinase 1-Dependent Williams-Beuren Syndrome Cognitive Phenotypes: INDELs, Transposable Elements of the Tc1/<i>Mariner</i> Superfamily and MicroRNAs. | Savvateeva-Popova EV et al. | β | 2017 | β |
| NRF2 Regulates HER1 Signaling Pathway to Modulate the Sensitivity of Ovarian Cancer Cells to Lapatinib and Erlotinib. | Kankia IH et al. | β | 2017 | β |
| Nurr1 promotes intestinal regeneration after ischemia/reperfusion injury by inhibiting the expression of p21 (Waf1/Cip1). | Zu G et al. | β | 2017 | β |
| Peroxisome proliferator-activated receptor-Ξ²/Ξ΄ inhibits human neuroblastoma cell tumorigenesis by inducing p53- and SOX2-mediated cell differentiation. | Yao PL et al. | β | 2017 | β |
| PTTG1, A novel androgen responsive gene is required for androgen-induced prostate cancer cell growth and invasion. | Zhang Z et al. | β | 2017 | β |
| An Ancient Fecundability-Associated Polymorphism Switches a Repressor into an Enhancer of Endometrial TAP2 Expression. | Mika KM et al. | β | 2016 | β |
| An Intronic Enhancer Element Regulates Angiotensin II Type 2 Receptor Expression during Satellite Cell Differentiation, and Its Activity Is Suppressed in Congestive Heart Failure. | Yoshida T et al. | β | 2016 | β |
| Association of variants in BAFF (rs9514828 and rs1041569) and BAFF-R (rs61756766) genes with the risk of chronic lymphocytic leukemia. | Jasek M et al. | β | 2016 | β |
| Blockade of the Hedgehog pathway downregulates estrogen receptor alpha signaling in breast cancer cells. | Diao Y et al. | β | 2016 | β |
| Characterization of Genomic Variants Associated with Scout and Recruit Behavioral Castes in Honey Bees Using Whole-Genome Sequencing. | Southey BR et al. | β | 2016 | β |
| ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites. | Lelieveld SH et al. | β | 2016 | β |
| Electromobility Shift Assay Reveals Evidence in Favor of Allele-Specific Binding of RUNX1 to the 5' Hypersensitive Site 4-Locus Control Region. | Dehghani H et al. | β | 2016 | β |
| Genome-wide identification of human- and primate-specific core promoter short tandem repeats. | Bushehri A et al. | β | 2016 | β |
| MiR-690, a Runx2-targeted miRNA, regulates osteogenic differentiation of C2C12 myogenic progenitor cells by targeting NF-kappaB p65. | Yu S et al. | β | 2016 | β |
| PPARgene: A Database of Experimentally Verified and Computationally Predicted PPAR Target Genes. | Fang L et al. | β | 2016 | β |
| Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches. | Martinez-Morales JR | β | 2016 | β |
| Transcriptional regulation of miR-15b by c-Rel and CREB in Japanese encephalitis virus infection. | Zhu B et al. | β | 2016 | β |
| Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. | Liu Q et al. | β | 2016 | β |
| Upregulation of E2F8 promotes cell proliferation and tumorigenicity in breast cancer by modulating G1/S phase transition. | Ye L et al. | β | 2016 | β |
| Vitamin D Regulates Fatty Acid Composition in Subcutaneous Adipose Tissue Through Elovl3. | Ji L et al. | β | 2016 | β |
| Basic helix loop helix (bHLH) transcription factor 3 (TCF3, E2A) is regulated by androgens in prostate cancer cells. | Patel D et al. | β | 2015 | β |
| Bioinformatics tools for discovery and functional analysis of single nucleotide polymorphisms. | Li L et al. | β | 2015 | β |
| Calcitriol increases Dicer expression and modifies the microRNAs signature in SiHa cervical cancer cells. | GonzΓ‘lez-Duarte RJ et al. | β | 2015 | β |
| Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene. | Ishibashi M et al. | β | 2015 | β |
| CRMP1 Inhibits Proliferation of Medulloblastoma and Is Regulated by HMGA1. | Li KK et al. | β | 2015 | β |
| Fine Mapping of a GWAS-Derived Obesity Candidate Region on Chromosome 16p11.2. | Volckmar AL et al. | β | 2015 | β |
| Functional Study of Haplotypes in UGT1A1 Promoter to Find a Novel Genetic Variant Leading to Reduced Gene Expression. | Shin HJ et al. | β | 2015 | β |
| Identification and analysis of a novel bmp4 enhancer in Fugu genome. | Wang Y et al. | β | 2015 | β |
| Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension. | Jeong S et al. | β | 2015 | β |
| Molecular mechanism of monoamine oxidase A gene regulation under inflammation and ischemia-like conditions: key roles of the transcription factors GATA2, Sp1 and TBP. | Gupta V et al. | β | 2015 | β |
| NF-ΞΊB and IRF pathways: cross-regulation on target genes promoter level. | Iwanaszko M et al. | β | 2015 | β |
| Polymorphisms of IKBKE gene are associated with major depressive disorder and panic disorder. | Traks T et al. | β | 2015 | β |
| Signatures of natural selection at the FTO (fat mass and obesity associated) locus in human populations. | Liu X et al. | β | 2015 | β |
| The FNTB promoter polymorphism rs11623866 as a potential predictive biomarker for lonafarnib treatment of ovarian cancer patients. | Bachmann HS et al. | β | 2015 | β |
| The gut microbiota engages different signaling pathways to induce Duox2 expression in the ileum and colon epithelium. | Sommer F et al. | β | 2015 | β |
| The Zinc Concentration in the Diet and the Length of the Feeding Period Affect the Methylation Status of the ZIP4 Zinc Transporter Gene in Piglets. | Karweina D et al. | β | 2015 | β |
| A 3'UTR polymorphism modulates mRNA stability of the oncogene and drug target Polo-like Kinase 1. | Akdeli N et al. | β | 2014 | β |
| A common functional regulatory variant at a type 2 diabetes locus upregulates ARAP1 expression in the pancreatic beta cell. | Kulzer JR et al. | β | 2014 | β |
| Changes in metabolite profiles caused by genetically determined obesity in mice. | SchΓ€fer N et al. | β | 2014 | β |
| Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. | Wortham M et al. | β | 2014 | β |
| CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining. | Navarro C et al. | β | 2014 | β |
| Coregulation and modulation of NFΞΊB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation. | Fernandez-Jimenez N et al. | β | 2014 | β |
| Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms. | Lindesay J et al. | β | 2014 | β |
| Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise. | Bertolusso R et al. | β | 2014 | β |
| Functional annotation of putative regulatory elements at cancer susceptibility Loci. | Rosse SA et al. | β | 2014 | β |
| In silico discovery of novel transcription factors regulated by mTOR-pathway activities. | Jablonska A et al. | β | 2014 | β |
| Nucleosomes are stably evicted from enhancers but not promoters upon induction of certain pro-inflammatory genes in mouse macrophages. | Gjidoda A et al. | β | 2014 | β |
| Pax6 regulates the expression of Dkk3 in murine and human cell lines, and altered responses to Wnt signaling are shown in FlpIn-3T3 cells stably expressing either the Pax6 or the Pax6(5a) isoform. | Forsdahl S et al. | β | 2014 | β |
| Plant promoters: an approach of structure and function. | Porto MS et al. | β | 2014 | β |
| Single nucleotide polymorphism scanning and expression of the pig PPARGC1A gene in different breeds. | Li Q et al. | β | 2014 | β |
| Suppression of FOXO1 is responsible for a growth regulatory repressive transcriptional sub-signature of EWS-FLI1 in Ewing sarcoma. | Niedan S et al. | β | 2014 | β |
| The catecholamine biosynthetic enzyme dopamine Ξ²-hydroxylase (DBH): first genome-wide search positions trait-determining variants acting additively in the proximal promoter. | Mustapic M et al. | β | 2014 | β |
| The RhoGEF GEF-H1 is required for oncogenic RAS signaling via KSR-1. | Cullis J et al. | β | 2014 | β |
| The transposable element Bari-Jheh mediates oxidative stress response in Drosophila. | Guio L et al. | β | 2014 | β |
| Understanding the transcriptional regulation of cervix cancer using microarray gene expression data and promoter sequence analysis of a curated gene set. | Srivastava P et al. | β | 2014 | β |
| VEGFA rSNPs, transcriptional factor binding sites and human disease. | Buroker NE | β | 2014 | β |
| 2mit, an intronic gene of Drosophila melanogaster timeless2, is involved in behavioral plasticity. | Baggio F et al. | β | 2013 | β |
| Allele-specific programming of Npy and epigenetic effects of physical activity in a genetic model of depression. | Melas PA et al. | β | 2013 | β |
| A polymorphism in the histone deacetylase 1 gene is associated with the response to corticosteroids in asthmatics. | Kim MH et al. | β | 2013 | β |
| A VIN1 GUS::GFP fusion reveals activated sucrose metabolism programming occurring in interspersed cells during tomato fruit ripening. | Estornell LH et al. | β | 2013 | β |
| Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. | Parveen N et al. | β | 2013 | β |
| Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens). | BΓ©langer-DeschΓͺnes S et al. | β | 2013 | β |
| Fine-mapping an association of FSHR with preterm birth in a Finnish population. | Chun S et al. | β | 2013 | β |
| Genetic variation at the delta-sarcoglycan (SGCD) locus elevates heritable sympathetic nerve activity in human twin pairs. | Hightower CM et al. | β | 2013 | β |
| Heparin-binding EGF-like growth factor and miR-1192 exert opposite effect on Runx2-induced osteogenic differentiation. | Yu S et al. | β | 2013 | β |
| Heredity and cardiometabolic risk: naturally occurring polymorphisms in the human neuropeptide Y(2) receptor promoter disrupt multiple transcriptional response motifs. | Wei Z et al. | β | 2013 | β |
| LASAGNA: a novel algorithm for transcription factor binding site alignment. | Lee C et al. | β | 2013 | β |
| MicroRNA-22 and promoter motif polymorphisms at the Chga locus in genetic hypertension: functional and therapeutic implications for gene expression and the pathogenesis of hypertension. | Friese RS et al. | β | 2013 | β |
| Systematic functional study of cytochrome P450 2D6 promoter polymorphisms in the Chinese Han population. | Gong X et al. | β | 2013 | β |
| The E2F transcription factor 1 transactives stathmin 1 in hepatocellular carcinoma. | Chen YL et al. | β | 2013 | β |
| The Grainyhead transcription factor Grhl3/Get1 suppresses miR-21 expression and tumorigenesis in skin: modulation of the miR-21 target MSH2 by RNA-binding protein DND1. | Bhandari A et al. | β | 2013 | β |
| The transcription factor Sp3 regulates the expression of a metastasis-related marker of sarcoma, actin filament-associated protein 1-like 1 (AFAP1L1). | Kajita Y et al. | β | 2013 | β |
| Three promoters regulate the transcriptional activity of the human holocarboxylase synthetase gene. | Xia M et al. | β | 2013 | β |
| VEGFA SNPs and transcriptional factor binding sites associated with high altitude sickness in Han and Tibetan Chinese at the Qinghai-Tibetan Plateau. | Buroker NE et al. | β | 2013 | β |
| 3T3 cell lines stably expressing Pax6 or Pax6(5a)--a new tool used for identification of common and isoform specific target genes. | Kiselev Y et al. | β | 2012 | β |
| A common polymorphism in the 5' region of the human protein c gene binds USF1. | Thain KR et al. | β | 2012 | β |
| AKT3, ANGPTL4, eNOS3, and VEGFA associations with high altitude sickness in Han and Tibetan Chinese at the Qinghai-Tibetan Plateau. | Buroker NE et al. | β | 2012 | β |
| Antidepressant treatment is associated with epigenetic alterations in the promoter of P11 in a genetic model of depression. | Melas PA et al. | β | 2012 | β |
| Calcium/calmodulin-dependent protein kinase II regulates IL-10 production by human T lymphocytes: a distinct target in the calcium dependent pathway. | Boubali S et al. | β | 2012 | β |
| Comparative genomics-based identification and analysis of cis-regulatory elements. | Ogino H et al. | β | 2012 | β |
| CTCF and Sp1 interact with the Murine gammaherpesvirus 68 internal repeat elements. | Stevens HC et al. | β | 2012 | β |
| Evidence for directed evolution of larger size motif in Arabidopsis thaliana genome. | Mehrotra R et al. | β | 2012 | β |
| Functional analysis of HapMap SNPs. | Liu CT et al. | β | 2012 | β |
| Identification of ectodysplasin target genes reveals the involvement of chemokines in hair development. | Lefebvre S et al. | β | 2012 | β |
| Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. | Sheffield NC et al. | β | 2012 | β |
| Integrated computational and experimental analysis of the neuroendocrine transcriptome in genetic hypertension identifies novel control points for the cardiometabolic syndrome. | Friese RS et al. | β | 2012 | β |
| Involvement of NF-ΞΊB transcription factors in antimicrobial peptide gene induction in the red flour beetle, Tribolium castaneum. | Yokoi K et al. | β | 2012 | β |
| Molecular subtyping of primary prostate cancer reveals specific and shared target genes of different ETS rearrangements. | Paulo P et al. | β | 2012 | β |
| Novel Tfap2-mediated control of soxE expression facilitated the evolutionary emergence of the neural crest. | Van Otterloo E et al. | β | 2012 | β |
| Overexpression of HMGA1 deregulates tumor growth via cdc25A and alters migration/invasion through a cdc25A-independent pathway in medulloblastoma. | Lau KM et al. | β | 2012 | β |
| Phorbol esters enhance 1Ξ±,25-dihydroxyvitamin D3-regulated 25-hydroxyvitamin D-24-hydroxylase (CYP24A1) gene expression through ERK-mediated phosphorylation of specific protein 3 (Sp3) in Caco-2 cells. | Jiang Y et al. | β | 2012 | β |
| Potential downstream target genes of aberrant ETS transcription factors are differentially affected in Ewing's sarcoma and prostate carcinoma. | CamΓ΅es MJ et al. | β | 2012 | β |
| Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia. | Jablensky A et al. | β | 2012 | β |
| Regulatory versus coding signatures of natural selection in a candidate gene involved in the adaptive divergence of whitefish species pairs (Coregonus spp.). | Jeukens J et al. | β | 2012 | β |
| RelB/NF-ΞΊB2 regulates corticotropin-releasing hormone in the human placenta. | Wang B et al. | β | 2012 | β |
| Searching for transcription factor binding sites in vector spaces. | Lee C et al. | β | 2012 | β |
| The dependence of expression of NF-ΞΊB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR. | Iwanaszko M et al. | β | 2012 | β |
| The distribution of GC nucleotides and regulatory sequence motifs in genes and their adjacent sequences. | Jaksik R et al. | β | 2012 | β |
| USF-1 is critical for maintaining genome integrity in response to UV-induced DNA photolesions. | Baron Y et al. | β | 2012 | β |
| Vitamin D dependent effects of APOA5 polymorphisms on HDL cholesterol. | Shirts BH et al. | β | 2012 | β |
| Cis-regulation of microRNA expression by scaffold/matrix-attachment regions. | Chavali PL et al. | β | 2011 | β |
| Cysteine-rich secretory protein-3 (CRISP3) is strongly up-regulated in prostate carcinomas with the TMPRSS2-ERG fusion gene. | Ribeiro FR et al. | β | 2011 | β |
| Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module. | Irvine SQ et al. | β | 2011 | β |
| Functional characterization of human Kindlin-2 core promoter identifies a key role of SP1 in Kindlin-2 transcriptional regulation. | Khan AA et al. | β | 2011 | β |
| Functional consequences of two HTR2C polymorphisms associated with antipsychotic-induced weight gain. | Hill MJ et al. | β | 2011 | β |
| Functional dissection of the Oct6 Schwann cell enhancer reveals an essential role for dimeric Sox10 binding. | Jagalur NB et al. | β | 2011 | β |
| Functional promoter polymorphisms govern differential expression of HMG-CoA reductase gene in mouse models of essential hypertension. | Sonawane PJ et al. | β | 2011 | β |
| Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation. | Emons J et al. | β | 2011 | β |
| Human dopamine Ξ²-hydroxylase promoter variant alters transcription in chromaffin cells, enzyme secretion, and blood pressure. | Chen Y et al. | β | 2011 | β |
| Molecular characterization of caveolin-1 in pigs infected with Haemophilus parasuis. | Liu XD et al. | β | 2011 | β |
| ORS1, an HβOβ-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana. | Balazadeh S et al. | β | 2011 | β |
| Regulatory function of conserved sequences upstream of the long-wave sensitive opsin genes in teleost fishes. | Tam KJ et al. | β | 2011 | β |
| Rhythmic diel pattern of gene expression in juvenile maize leaf. | JoΕczyk M et al. | β | 2011 | β |
| Shared genetic background for regulation of mood and sleep: association of GRIA3 with sleep duration in healthy Finnish women. | Utge S et al. | β | 2011 | β |
| Systematic clustering of transcription start site landscapes. | Zhao X et al. | β | 2011 | β |
| Transcriptional regulation of epidermal barrier formation. | Bhandari A et al. | β | 2011 | β |
| Transcriptional repression and DNA looping associated with a novel regulatory element in the final exon of the lymphotoxin-Ξ² gene. | Wicks K et al. | β | 2011 | β |
| Transcription factor CCAAT enhancer-binding protein beta (C/EBPbeta) regulates the formation of a unique extracellular matrix that controls uterine stromal differentiation and embryo implantation. | Ramathal C et al. | β | 2011 | β |
| An improved in silico selection of phenotype affecting polymorphisms in SLC6A4, HTR1A and HTR2A genes. | Piva F et al. | β | 2010 | β |
| An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. | Garcia-Alcalde F et al. | β | 2010 | β |
| Caenopores are antimicrobial peptides in the nematode Caenorhabditis elegans instrumental in nutrition and immunity. | Roeder T et al. | β | 2010 | β |
| C/EBPΞ΄ gene targets in human keratinocytes. | Borrelli S et al. | β | 2010 | β |
| Circadian transcription in liver. | Bozek K et al. | β | 2010 | β |
| Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels. | O'Seaghdha CM et al. | β | 2010 | β |
| DGAT1 participates in the effect of HNF4A on hepatic secretion of triglyceride-rich lipoproteins. | Krapivner S et al. | β | 2010 | β |
| Differential proteomics analysis reveals a role for E2F2 in the regulation of the Ahr pathway in T lymphocytes. | Azkargorta M et al. | β | 2010 | β |
| ER regulates an evolutionarily conserved apoptosis pathway. | Liu Z et al. | β | 2010 | β |
| Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions. | Paakinaho V et al. | β | 2010 | β |
| Homozygosity for the EPHX2 K55R polymorphism increases the long-term risk of ischemic stroke in men: a study in Swedes. | Fava C et al. | β | 2010 | β |
| Human dopamine beta-hydroxylase (DBH) regulatory polymorphism that influences enzymatic activity, autonomic function, and blood pressure. | Chen Y et al. | β | 2010 | β |
| Human tyrosine hydroxylase natural genetic variation: delineation of functional transcriptional control motifs disrupted in the proximal promoter. | Zhang K et al. | β | 2010 | β |
| Identification and characterization of odorant-binding protein 1 gene from the Asian malaria mosquito, Anopheles stephensi. | Sengul MS et al. | β | 2010 | β |
| Impact of Neuritin 1 (NRN1) polymorphisms on fluid intelligence in schizophrenia. | Chandler D et al. | β | 2010 | β |
| Induction of neuronal apoptosis inhibitory protein expression in response to androgen deprivation in prostate cancer. | Chiu HH et al. | β | 2010 | β |
| Lack of CCAAT enhancer binding protein beta (C/EBPbeta) in uterine epithelial cells impairs estrogen-induced DNA replication, induces DNA damage response pathways, and promotes apoptosis. | Ramathal C et al. | β | 2010 | β |
| Proximal human FOXP3 promoter transactivated by NF-kappaB and negatively controlled by feedback loop and SP3. | Eckerstorfer P et al. | β | 2010 | β |
| Some single-nucleotide polymorphisms of the TSSK2 gene may be associated with human spermatogenesis impairment. | Zhang H et al. | β | 2010 | β |
| SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. | Saccone SF et al. | β | 2010 | β |
| Statistical analysis strategies for association studies involving rare variants. | Bansal V et al. | β | 2010 | β |
| Systematic analysis of circadian genes in a population-based sample reveals association of TIMELESS with depression and sleep disturbance. | Utge SJ et al. | β | 2010 | β |
| The promoter for intestinal cell kinase is head-to-head with F-Box 9 and contains functional sites for TCF7L2 and FOXA factors. | Sturgill TW et al. | β | 2010 | β |
| A dedicated promoter drives constitutive expression of the cell-autonomous immune resistance GTPase, Irga6 (IIGP1) in mouse liver. | Zeng J et al. | β | 2009 | β |
| An integrative scoring system for ranking SNPs by their potential deleterious effects. | Lee PH et al. | β | 2009 | β |
| A novel role for the forkhead transcription factor FOXL2 in activin A-regulated follicle-stimulating hormone beta subunit transcription. | Lamba P et al. | β | 2009 | β |
| cAMP regulates IL-10 production by normal human T lymphocytes at multiple levels: a potential role for MEF2. | Liopeta K et al. | β | 2009 | β |
| COTRASIF: conservation-aided transcription-factor-binding site finder. | Tokovenko B et al. | β | 2009 | β |
| Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. | Corcoran DL et al. | β | 2009 | β |
| Lentiviral transfection of ependymal primary cultures facilitates the characterisation of kinocilia-specific promoters. | Kowtharapu BS et al. | β | 2009 | β |
| Microarray analysis of altered gene expression in ERbeta-overexpressing HEK293 cells. | Zhao C et al. | β | 2009 | β |
| New scoring schema for finding motifs in DNA Sequences. | Zare-Mirakabad F et al. | β | 2009 | β |
| New Variations in the Promoter Regions of Human DOCK4 and RAP1A Genes, and Coding Regions of RAP1A in Sporadic Breast Tumors. | Jalali A et al. | β | 2009 | β |
| Regulatory feedback loop between NF-kappaB and MCP-1-induced protein 1 RNase. | Skalniak L et al. | β | 2009 | β |
| Resources and transgenesis techniques for functional genomics in Xenopus. | Ogino H et al. | β | 2009 | β |
| Structural properties of gene regulatory networks: definitions and connections. | Narasimhan S et al. | β | 2009 | β |
| The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. | Portales-Casamar E et al. | β | 2009 | β |
| The transcription factor PITX3 is associated with sporadic Parkinson's disease. | Fuchs J et al. | β | 2009 | β |
| Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks. | Colecchia F et al. | β | 2009 | β |
| Two modes of transcriptional activation at native promoters by NF-kappaB p65. | van Essen D et al. | β | 2009 | β |
| An enhancer 20 kilobases upstream of the human receptor activator of nuclear factor-kappaB ligand gene mediates dominant activation by 1,25-dihydroxyvitamin D3. | Nerenz RD et al. | β | 2008 | β |
| An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. | Lampe X et al. | β | 2008 | β |
| Asap: a framework for over-representation statistics for transcription factor binding sites. | Marstrand TT et al. | β | 2008 | β |
| Characterization and expression of the odorant-binding protein 7 gene in Anopheles stephensi and comparative analysis among five mosquito species. | Sengul MS et al. | β | 2008 | β |
| Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure. | Chen Y et al. | β | 2008 | β |
| Connections between ETV6-modulated genes: identification of shared features. | Boily G et al. | β | 2008 | β |
| CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. | Ray P et al. | β | 2008 | β |
| From SNPs to functional studies in cardiovascular pharmacogenomics. | Cresci S | β | 2008 | β |
| F-SNP: computationally predicted functional SNPs for disease association studies. | Lee PH et al. | β | 2008 | β |
| Further evidence for the role of ENPP1 in obesity: association with morbid obesity in Finns. | Valli-Jaakola K et al. | β | 2008 | β |
| Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. | Jia L et al. | β | 2008 | β |
| Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. | Loots GG | β | 2008 | β |
| Hepatocyte nuclear factor 1 and hypertensive nephropathy. | Dmitrieva RI et al. | β | 2008 | β |
| Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. | Liu GE et al. | β | 2008 | β |
| Interactions of functional apolipoprotein E gene promoter polymorphisms with smoking on aortic atherosclerosis. | Viiri LE et al. | β | 2008 | β |
| Nucleotide sequence variation within the PI3K p85 alpha gene associates with alcohol risk drinking behaviour in adolescents. | DesriviΓ¨res S et al. | β | 2008 | β |
| Oct2 enhances antibody-secreting cell differentiation through regulation of IL-5 receptor alpha chain expression on activated B cells. | Emslie D et al. | β | 2008 | β |
| Prediction of regulatory elements. | Sandelin A | β | 2008 | β |
| Probabilistic inference of transcription factor binding from multiple data sources. | LΓ€hdesmΓ€ki H et al. | β | 2008 | β |
| Progesterone induction of the 11beta-hydroxysteroid dehydrogenase type 2 promoter in breast cancer cells involves coordinated recruitment of STAT5A and progesterone receptor to a distal enhancer and polymerase tracking. | Subtil-RodrΓguez A et al. | β | 2008 | β |
| ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. | Iwama H et al. | β | 2008 | β |
| Sequence segmentation. | Keith JM | β | 2008 | β |
| Strategies for reliable exploitation of evolutionary concepts in high throughput biology. | Levasseur A et al. | β | 2008 | β |
| Yin yang 1 directly regulates the transcription of RE-1 silencing transcription factor. | Jiang L et al. | β | 2008 | β |
| Abscisic acid and stress signals induce Viviparous1 expression in seed and vegetative tissues of maize. | Cao X et al. | β | 2007 | β |
| Alternative promoters and repetitive DNA elements define the species-dependent tissue-specific expression of the FMO1 genes of human and mouse. | Shephard EA et al. | β | 2007 | β |
| Androgen receptor regulation of the versican gene through an androgen response element in the proximal promoter. | Read JT et al. | β | 2007 | β |
| BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences. | Meng H et al. | β | 2007 | β |
| CardioSignal: a database of transcriptional regulation in cardiac development and hypertrophy. | Zhen Y et al. | β | 2007 | β |
| Comparative analysis of regulatory motif discovery tools for transcription factor binding sites. | Wei W et al. | β | 2007 | β |
| Comparative genomic analysis of allatostatin-encoding (Ast) genes in Drosophila species and prediction of regulatory elements by phylogenetic footprinting. | Bowser PR et al. | β | 2007 | β |
| Computation and analysis of genomic multi-sequence alignments. | Blanchette M | β | 2007 | β |
| Context specific transcription factor prediction. | Yang E et al. | β | 2007 | β |
| Differential regulation of clusterin and its isoforms by androgens in prostate cells. | Cochrane DR et al. | β | 2007 | β |
| Histamine receptor H1 and dermatopontin: new downstream targets of the vitamin D receptor. | Pochampally RR et al. | β | 2007 | β |
| Human evidence for the involvement of insulin-induced gene 1 in the regulation of plasma glucose concentration. | Krapivner S et al. | β | 2007 | β |
| Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. | Abbasi AA et al. | β | 2007 | β |
| Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. | Jin VX et al. | β | 2007 | β |
| Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes. | Moroni E et al. | β | 2007 | β |
| In vivo transcript profiling and phylogenetic analysis identifies suppressor of cytokine signaling 2 as a direct signal transducer and activator of transcription 5b target in liver. | Vidal OM et al. | β | 2007 | β |
| Neuroadaptations in human chronic alcoholics: dysregulation of the NF-kappaB system. | Okvist A et al. | β | 2007 | β |
| PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. | Chang LW et al. | β | 2007 | β |
| Position dependencies in transcription factor binding sites. | Tomovic A et al. | β | 2007 | β |
| Reciprocal regulation of p63 by C/EBP delta in human keratinocytes. | Borrelli S et al. | β | 2007 | β |
| Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. | Mahony S et al. | β | 2007 | β |
| Signal transducer and activator of transcription (Stat) 5b-mediated inhibition of insulin-like growth factor binding protein-1 gene transcription: a mechanism for repression of gene expression by growth hormone. | Ono M et al. | β | 2007 | β |
| Simultaneous alignment and annotation of cis-regulatory regions. | Bais AS et al. | β | 2007 | β |
| TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. | Lee AP et al. | β | 2007 | β |
| The 5' untranslated regions (UTRs) of CCN1, CCN2, and CCN4 exhibit cryptic promoter activity. | Huang BL et al. | β | 2007 | β |
| The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. | Scheele C et al. | β | 2007 | β |
| Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome. | Wang HY et al. | β | 2007 | β |
| YB-1 is a Transcription/Translation Factor that Orchestrates the Oncogenome by Hardwiring Signal Transduction to Gene Expression. | Wu J et al. | β | 2007 | β |
| A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. | Jin VX et al. | β | 2006 | β |
| A CXCL2 tandem repeat promoter polymorphism is associated with susceptibility to severe sepsis in the Spanish population. | Flores C et al. | β | 2006 | β |
| Alternative promoter usage of the membrane glycoprotein CD36. | Andersen M et al. | β | 2006 | β |
| A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. | Vlieghe D et al. | β | 2006 | β |
| A web server for transcription factor binding site prediction. | Su G et al. | β | 2006 | β |
| BAL1 and BBAP are regulated by a gamma interferon-responsive bidirectional promoter and are overexpressed in diffuse large B-cell lymphomas with a prominent inflammatory infiltrate. | Juszczynski P et al. | β | 2006 | β |
| BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences. | Meng H et al. | β | 2006 | β |
| Foot differentiation and genomic plasticity in Hydra: lessons from the PPOD gene family. | Thomsen S et al. | β | 2006 | β |
| FootPrinter3: phylogenetic footprinting in partially alignable sequences. | Fang F et al. | β | 2006 | β |
| Heterotachy in mammalian promoter evolution. | Taylor MS et al. | β | 2006 | β |
| Incorporating genetic analyses into birth defects cluster investigations: strategies for identifying candidate genes. | Green RF et al. | β | 2006 | β |
| New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. | GΓ³mez-Skarmeta JL et al. | β | 2006 | β |
| Prediction of cis-regulatory elements for drug-activated transcription factors in the regulation of drug-metabolising enzymes and drug transporters. | Podvinec M et al. | β | 2006 | β |
| PromAn: an integrated knowledge-based web server dedicated to promoter analysis. | Lardenois A et al. | β | 2006 | β |
| The Grainyhead-like epithelial transactivator Get-1/Grhl3 regulates epidermal terminal differentiation and interacts functionally with LMO4. | Yu Z et al. | β | 2006 | β |
| TNF-alpha and IFN-gamma inversely modulate expression of the IL-17E receptor in airway smooth muscle cells. | Lajoie-Kadoch S et al. | β | 2006 | β |
| Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. | Ponjavic J et al. | β | 2006 | β |
| Transforming omics data into context: bioinformatics on genomics and proteomics raw data. | Perco P et al. | β | 2006 | β |
| Ab initio identification of putative human transcription factor binding sites by comparative genomics. | CorΓ D et al. | β | 2005 | β |
| Androgen receptor-dependent PSA expression in androgen-independent prostate cancer cells does not involve androgen receptor occupancy of the PSA locus. | Jia L et al. | β | 2005 | β |
| A simple promoter containing two Sp1 sites controls the expression of sterol-regulatory-element-binding protein 1a (SREBP-1a). | Zhang C et al. | β | 2005 | β |
| Complete functional rescue of the ABCA1-/- mouse by human BAC transgenesis. | Coutinho JM et al. | β | 2005 | β |
| CONREAL web server: identification and visualization of conserved transcription factor binding sites. | Berezikov E et al. | β | 2005 | β |
| Control of foot differentiation in Hydra: phylogenetic footprinting indicates interaction of head, bud and foot patterning systems. | Siebert S et al. | β | 2005 | β |
| Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. | Lee S et al. | β | 2005 | β |
| Identification and characterization of functional hepatocyte nuclear factor 1-binding sites in UDP-glucuronosyltransferase genes. | Gardner-Stephen DA et al. | β | 2005 | β |
| Identification of a DNA methylation-dependent activator sequence in the pseudoxanthoma elasticum gene, ABCC6. | ArΓ‘nyi T et al. | β | 2005 | β |
| MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. | Marinescu VD et al. | β | 2005 | β |
| MatInspector and beyond: promoter analysis based on transcription factor binding sites. | Cartharius K et al. | β | 2005 | β |
| Regulation of gene expression: probing DNA-protein interactions in vivo and in vitro. | Vigneault F et al. | β | 2005 | β |
| Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. | Xie X et al. | β | 2005 | β |
| The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. | Marinescu VD et al. | β | 2005 | β |
| MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. | Moses AM et al. | β | 2004 | β |
| Small proline-rich protein 1A is a gp130 pathway- and stress-inducible cardioprotective protein. | Pradervand S et al. | β | 2004 | β |