Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

[1]  M. Rienstra,et al.  The LifeLines Cohort Study: Prevalence and treatment of cardiovascular disease and risk factors. , 2017, International journal of cardiology.

[2]  Howard Y. Chang,et al.  Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution , 2016, Nature Genetics.

[3]  Tim J. Carver,et al.  CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets , 2016, Bioinform..

[4]  P. Visscher,et al.  Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets , 2016, Nature Genetics.

[5]  Kenneth G. C. Smith,et al.  Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease , 2016, PLoS genetics.

[6]  Daniel R. Zerbino,et al.  Ensembl regulation resources , 2016, Database J. Biol. Databases Curation.

[7]  Guangchuang Yu,et al.  ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. , 2016, Molecular bioSystems.

[8]  Matthew D. Edwards,et al.  High-throughput mapping of regulatory DNA , 2016, Nature Biotechnology.

[9]  N. Morrell,et al.  Generation and Culture of Blood Outgrowth Endothelial Cells from Human Peripheral Blood , 2015, Journal of visualized experiments : JoVE.

[10]  Stefan Schoenfelder,et al.  Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci , 2015, Nature Communications.

[11]  Philip A. Ewels,et al.  HiCUP: pipeline for mapping and processing Hi-C data , 2015, F1000Research.

[12]  J. Rioux,et al.  Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus , 2015, Nature Genetics.

[13]  Jonathan M. Cairns,et al.  CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data , 2015, Genome Biology.

[14]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[15]  Casey S. Greene,et al.  International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways , 2015, Nature Communications.

[16]  O. Delaneau,et al.  Population Variation and Genetic Control of Modular Chromatin Architecture in Humans , 2015, Cell.

[17]  P. Fraser,et al.  Comparison of Hi-C results using in-solution versus in-nucleus ligation , 2015, Genome Biology.

[18]  R. Sandberg,et al.  Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution , 2015, Genome Biology.

[19]  B. Stranger,et al.  Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci , 2015, American journal of human genetics.

[20]  Philip A. Ewels,et al.  Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C , 2015, Nature Genetics.

[21]  Cameron S. Osborne,et al.  The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements , 2015, Genome research.

[22]  P. Flicek,et al.  The Ensembl Regulatory Build , 2015, Genome Biology.

[23]  Mary D. Fortune,et al.  Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases , 2015, Human molecular genetics.

[24]  Ross M. Fraser,et al.  Genetic studies of body mass index yield new insights for obesity biology , 2015, Nature.

[25]  E. Matteson,et al.  T-cell metabolism in autoimmune disease , 2015, Arthritis Research & Therapy.

[26]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[27]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[28]  Randy J. Read,et al.  Transcriptional diversity during lineage commitment of human blood progenitors , 2014, Science.

[29]  Ross M. Fraser,et al.  Defining the role of common variation in the genomic and biological architecture of adult human height , 2014, Nature Genetics.

[30]  Philip D. Gregory,et al.  Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping , 2014, Cell.

[31]  A. Ashworth,et al.  Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C , 2014, Genome research.

[32]  Wolfgang Huber,et al.  Enhancer loops appear stable during development and are associated with paused polymerase , 2014, Nature.

[33]  C. Lippert,et al.  LIMIX: genetic analysis of multiple traits , 2014, bioRxiv.

[34]  S. Malcolm Faculty Opinions recommendation of Obesity-associated variants within FTO form long-range functional connections with IRX3. , 2014 .

[35]  Supat Thongjuea,et al.  HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. , 2013, The Journal of clinical investigation.

[36]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[37]  D. Duboule,et al.  Topology of mammalian developmental enhancers and their regulatory landscapes , 2013, Nature.

[38]  Yan Li,et al.  A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.

[39]  C. Glass,et al.  Impact of natural genetic variation on enhancer selection and function , 2013, Nature.

[40]  M. Peters,et al.  Systematic identification of trans eQTLs as putative drivers of known disease associations , 2013, Nature Genetics.

[41]  Lorna M. Lopez,et al.  Seventy-five genetic loci influencing the human red blood cell , 2012, Nature.

[42]  G. Natoli,et al.  Noncoding transcription at enhancers: general principles and functional models. , 2012, Annual review of genetics.

[43]  Jake K. Byrnes,et al.  Bayesian refinement of association signals for 14 loci in 3 common diseases , 2012, Nature Genetics.

[44]  Shane J. Neph,et al.  Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.

[45]  J. Dekker,et al.  The long-range interaction landscape of gene promoters , 2012, Nature.

[46]  L. Mirny,et al.  Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization , 2012, Nature Methods.

[47]  Tanya M. Teslovich,et al.  Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes , 2012, Nature Genetics.

[48]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[49]  May E. Montasser,et al.  A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance , 2012, Nature Genetics.

[50]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[51]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[52]  Hideo Tanaka,et al.  Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population , 2012, Nature Genetics.

[53]  F. Vannberg,et al.  GENETICS OF GENE EXPRESSION IN PRIMARY IMMUNE CELLS IDENTIFIES CELL-SPECIFIC MASTER REGULATORS AND ROLES OF HLA ALLELES , 2012, Nature Genetics.

[54]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[55]  Christian Gieger,et al.  New gene functions in megakaryopoiesis and platelet formation , 2011, Nature.

[56]  Nicola K. Wilson,et al.  Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene , 2011, Human molecular genetics.

[57]  Tom R. Gaunt,et al.  Genetic Variants in Novel Pathways Influence Blood Pressure and Cardiovascular Disease Risk , 2011, Nature.

[58]  Simon C. Potter,et al.  Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis , 2011, Nature.

[59]  A. Mancini,et al.  CD101 Expression and Function in Normal and Rheumatoid Arthritis-affected Human T Cells and Monocytes/Macrophages , 2011, The Journal of Rheumatology.

[60]  K. Zhao,et al.  Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription , 2011, Nature Structural &Molecular Biology.

[61]  L. Coin,et al.  Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads , 2011, Genome Biology.

[62]  Tariq Ahmad,et al.  Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47 , 2011, Nature Genetics.

[63]  Tariq Ahmad,et al.  Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci , 2010, Nature Genetics.

[64]  Gary D. Bader,et al.  GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop , 2010, Bioinform..

[65]  Tanya M. Teslovich,et al.  Biological, Clinical, and Population Relevance of 95 Loci for Blood Lipids , 2010, Nature.

[66]  G. K. Davis,et al.  Phenotypic robustness conferred by apparently redundant transcriptional enhancers , 2010, Nature.

[67]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[68]  Sylvia Richardson,et al.  sdef: an R package to synthesize lists of significant features in related experiments , 2010, BMC Bioinformatics.

[69]  Jing Cui,et al.  Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci , 2010, Nature Genetics.

[70]  P. Deloukas,et al.  Multiple common variants for celiac disease influencing immune gene expression , 2010, Nature Genetics.

[71]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[72]  Helen Schuilenburg,et al.  Genome-wide association study and meta-analysis finds over 40 loci affect risk of type 1 diabetes , 2009, Nature Genetics.

[73]  Jon Wakefield,et al.  Bayes factors for genome‐wide association studies: comparison with P‐values , 2009, Genetic epidemiology.

[74]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[75]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

[76]  Sylvia Richardson,et al.  Statistical tools for synthesizing lists of differentially expressed features in related experiments , 2007, Genome Biology.

[77]  Erik Splinter,et al.  Looping and interaction between hypersensitive sites in the active beta-globin locus. , 2002, Molecular cell.

[78]  Cameron S. Osborne,et al.  Long-range chromatin regulatory interactions in vivo , 2002, Nature Genetics.

[79]  Edward M. Rubin,et al.  Deletion of a coordinate regulator of type 2 cytokine expression in mice , 2001, Nature Immunology.

[80]  F. Grosveld,et al.  Importance of globin gene order for correct developmental expression. , 1991, Genes & development.

[81]  Browser’s Notes , 2012, Skeletal Radiology.

[82]  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Discovering collectively informative descriptors from high-throughput experiments , 2009 .

[83]  J. Stutz,et al.  Bayesian Classification , 2003 .

[84]  W. McLaren,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[85]  I. Amit,et al.  Supporting Online Material Materials and Methods Som Text Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome , 2022 .