Supplementary information for Integrative model of genomic factors for determining binding site selection by estrogen receptor α

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Unknown venue

• Publication date

  Unknown publication date

• Fields of study

  Not labeled

• Identifiers

  No identifiers available.

• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Integrating multiple evidence sources to predict transcription factor binding in the human genome.

  2010cited by this paper
• ChIP‐Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

  2009influential reference
• MEME Suite: tools for motif discovery and searching

  2009cited by this paper
• An Oestrogen Receptor α-bound Human Chromatin Interactome

  2009cited by this paper
• Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

  2009cited by this paper
• Regulation of ERBB2 by oestrogen receptor–PAX2 determines response to tamoxifen

  2008influential reference
• Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

  2008cited by this paper
• Non-classical genomic estrogen receptor (ER)/specificity protein and ER/activating protein-1 signaling pathways.

  2008cited by this paper
• FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

  2007cited by this paper
• Whole-Genome Cartography of Estrogen Receptor α Binding Sites

  2007influential reference
• Genome-wide analysis of estrogen receptor binding sites

  2006influential reference
• Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

  2006cited by this paper
• Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE

  2006cited by this paper
• Comprehensive copy number profiles of breast cancer cell model genomes

  2006cited by this paper
• TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes

  2005influential reference
• DNA binding sites: representation and discovery

  2000influential reference
• Bioinformatics Original Paper Predicting Transcription Factor Affinities to Dna from a Biophysical Model

  year unknowncited by this paper

• MYC enhancer invasion promotes prognostic cancer type-specific gene programs through an epigenetic switch

  2023influential citation
• Estrogen receptors as potential therapeutic target in endometrial cancer

  2023cites this paper
• EstroGene database reveals diverse temporal, context-dependent and directional estrogen receptor regulomes in breast cancer

  2023cites this paper
• Chromatin modifiers - Coordinators of estrogen action.

  2022cites this paper
• Clear cell squamous cell carcinoma of the tongue exhibits characteristics as an undifferentiated squamous cell carcinoma.

  2022cites this paper
• Positive Regulation of Estrogen Receptor Alpha in Breast Tumorigenesis

  2021cites this paper
• Impact of estrogen population pharmacokinetics on a QSP model of mammary stem cell differentiation into myoepithelial cells

  2021cites this paper
• Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals

  2020cites this paper
• Estrogen-ERα signaling and DNA hypomethylation co-regulate expression of stem cell protein PIWIL1 in ERα-positive endometrial cancer cells

  2020cites this paper
• Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

  2020cites this paper
• 4sUDRB-sequencing for genome-wide transcription bursting quantification in breast cancer cells

  2020cites this paper
• Epigenetic downregulation of HER2 during EMT leads to tumor resistance to HER2-targeted therapies in breast cancer

  2020cites this paper
• Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines

  2020cites this paper
• Characterising the role of TET2 in oestrogen receptor positive breast cancer

  2020cites this paper
• Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching

  2019cites this paper
• Estrogen Signaling in Endometrial Cancer: a Key Oncogenic Pathway with Several Open Questions

  2019influential citation
• Molecular basis of distinct oestrogen responses in endometrial and breast cancer.

  2019cites this paper
• Complex sex-biased antibody responses: estrogen receptors bind estrogen response elements centered within immunoglobulin heavy chain gene enhancers

  2019cites this paper
• The transcriptional co-activator NCOA6 promotes estrogen-induced GREB1 transcription by recruiting ERα and enhancing enhancer–promoter interactions

  2019cites this paper
• Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the Genome

  2019cites this paper
• Classification of different types of estrogen receptor alpha binding sites in MCF-7 cells.

  2019cites this paper
• Cdx2 maintains stem-cell identity in the mouse trophoblast lineage by preventing default differentiation as trophoblast giant cells

  2019cites this paper
• ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells

  2019cites this paper
• Enhancement of Transgene Expression by NF-Y and CTCF

  2018cites this paper
• Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers

  2018cites this paper
• Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells

  2018cites this paper
• Estrogen Receptor-Mediated Gene Transcription and Cistrome

  2018cites this paper
• KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function

  2018cites this paper
• Bioinformatic analysis of changes in RNA polymerase II transcription stimulated by estradiol in MCF7 cells.

  2018influential citation
• Signaling by Steroid Hormones in the 3D Nuclear Space

  2018cites this paper
• Comprehensive Profiling of DNA Repair Defects in Breast Cancer Identifies a Novel Class of Endocrine Therapy Resistance Drivers

  2018cites this paper
• Shared nucleotide flanks confer transcriptional competency to bZip core motifs

  2018cites this paper
• Enhancement of transgene expression by nuclear transcription factor Y and CCCTC‐binding factor

  2018cites this paper
• Predicting Functional Interactions Among DNA-Binding Proteins

  2018cites this paper
• A long-range flexible billboard model of gene activation

  2017cites this paper
• An integrative method to decode regulatory logics in gene transcription

  2017cites this paper
• DNA Sequence Constraints Define Functionally Active Steroid Nuclear Receptor Binding Sites in Chromatin

  2017cites this paper
• Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution

  2017cites this paper
• Cancer cell line specific co-factors modulate the FOXM1 cistrome

  2017cites this paper
• Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1

  2017influential citation
• Transcriptional coregulator RIP140: an essential regulator of physiology.

  2017cites this paper
• Membrane and Nuclear Estrogen Receptor Alpha Actions: From Tissue Specificity to Medical Implications.

  2017cites this paper
• Stochastic Modeling of RNA Polymerase Predicts Transcription Factor Activity

  2017influential citation
• Nuclear Receptor Function through Genomics: Lessons from the Glucocorticoid Receptor.

  2017cites this paper
• Title An integrative method to decode regulatory logics in genetranscription

  2017cites this paper
• Changes in gene expression and Estrogen Receptor 1 cistrome in mouse liver upon acute E 2 treatment 2 3

  2016cites this paper
• Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements

  2016cites this paper
• Chromatin remodeling effects on enhancer activity

  2016cites this paper
• Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer

  2016cites this paper
• Non-coding single nucleotide variants affecting estrogen receptor binding and activity

  2016cites this paper
• Histone Posttranslational Modifications in Breast Cancer and Their Use in Clinical Diagnosis and Prognosis

  2016cites this paper
• Dynamics of Protein Expression Reveals Primary Targets and Secondary Messengers of Estrogen Receptor Alpha Signaling in MCF-7 Breast Cancer Cells*

  2016cites this paper
• An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression.

  2016cites this paper
• Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium.

  2016cites this paper
• Monoubiquitination of Histone H2B Blocks Eviction of Histone Variant H2A.Z from Inducible Enhancers.

  2016cites this paper
• Determining ERβ Binding Affinity to Singly Mutant ERE Using Dual Polarization Interferometry

  2016cites this paper
• ASXL2 promotes proliferation of breast cancer cells by linking ERα to histone methylation

  2016cites this paper
• OP-HMGJ160147 3269..3283

  2016cites this paper
• Estrogen Receptor α Promotes Breast Cancer by Reprogramming Choline Metabolism.

  2016cites this paper
• Nucleosome dynamics: HMGB1 facilitates nucleosome restructuring and collaborates in estrogen-responsive gene expression

  2016cites this paper
• The long range regulation of breast cancer associated genes

  2016cites this paper
• The Chromatin-looping Factor ZNF143 is Genetically Altered and Promotes the Oestrogen Response in Breast Cancer

  2016cites this paper
• How far have we come in terms of estrogens in breast cancer? [Review].

  2016cites this paper
• Estrogen receptor alpha (ERα/ESR1) mediates the p53-independent overexpression of MDM4/MDMX and MDM2 in human breast cancer

  2016cites this paper
• Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells

  2015influential citation
• DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer

  2015cites this paper
• Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells

  2015cites this paper
• LncRNA HOTAIR enhances ER signaling and confers tamoxifen resistance in breast cancer

  2015cites this paper
• H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription

  2015influential citation
• The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers.

  2015cites this paper
• Towards a Systematic Approach for Characterizing Regulatory Variation

  2015cites this paper
• Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo

  2015cites this paper
• Study of the transcriptional regulation of α-synuclein

  2015cites this paper
• Determinants of Receptor- and Tissue-Specific Actions in Androgen Signaling.

  2015cites this paper
• miR-137 Targets p160 Steroid Receptor Coactivators SRC1, SRC2, and SRC3 and Inhibits Cell Proliferation.

  2015cites this paper
• Development of novel software tools and methods for investigating the significance of overlapping transcription factor genomic interactions

  2015influential citation
• The histone variant H2A.Z is an important regulator of enhancer activity

  2015cites this paper
• Single-Molecule Sequencing Reveals Estrogen-Regulated Clinically Relevant lncRNAs in Breast Cancer.

  2015cites this paper
• Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas

  2015cites this paper
• GC skew defines distinct RNA polymerase pause sites in CpG island promoters

  2015influential citation
• Addendum: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

  2014cites this paper
• Nuclear receptors and chromatin: an inducible couple.

  2014cites this paper
• Spacer effect of cooperative binding of estrogen receptor α and specificity protein 1 to composite DNA: A surface plasmon resonance study

  2014cites this paper
• Emergence and Characterization of the p23 Molecular Chaperone

  2014cites this paper
• Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes.

  2014cites this paper
• Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes.

  2014cites this paper
• Steroid receptor crosstalk in breast cancer cells.

  2014cites this paper
• Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions

  2014cites this paper
• Integrative genomics analysis identifies pericentromeric regions of human chromosomes affecting patterns of inter-chromosomal interactions

  2014cites this paper
• Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

  2014cites this paper
• Molecular basis of gametocytogenesis in malaria parasites

  2014cites this paper
• Long‐range transcriptional regulation of breast cancer genes

  2013cites this paper
• Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells

  2013cites this paper
• Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer.

  2013cites this paper
• A high-resolution map of three-dimensional chromatin interactome in human cells

  2013cites this paper
• The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins

  2013cites this paper
• Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression

  2013cites this paper
• Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

  2013cites this paper
• Estrogen represses gene expression through reconfiguring chromatin structures

  2013influential citation
• Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer.

  2013cites this paper