The Human Epigenome Browser at Washington University.
paper
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- Authors
- Zhou, Xin; Maricque, Brett; Xie, Mingchao; Li, Daofeng; Sundaram, Vasavi; Martin, Eric A; Koebbe, Brian C; Nielsen, Cydney; Hirst, Martin; Farnham, Peggy; Kuhn, Robert M; Zhu, Jingchun; Smirnov, Ivan; Kent, W James; Haussler, David; Madden, Pamela A F; Costello, Joseph F; Wang, Ting
- Year
- 2011
- Journal
- Nature methods
- PMID
- 22127213
- DOI
- 10.1038/nmeth.1772
- PMCID
- PMC3552640
Epigenomic landscape of bivalent domains. (i) Genomic heatmap of 36 datasets over three regions. Green: H3K4me3 ChIP-seq; Red: H3K27me3 ChIP-seq; Brownish-red: MRE-seq; Pink: MeDIP-seq. (ii) Metadata heatmap. Epigenetic marks and sample types are in different feature columns. For brain, yellow: substantia nigra; orange: hippocampus (middle portion); blue: anterior caudate. For institution, yellow: UCSF; blue: UCSD; orange: Broad Institute. (iii) Annotation tracks. Genomic coordinates of three regions are labeled with open boxes. Known genes are diagramed. (iv) Statistical correlation track. Pearson correlation coefficients were calculated between H3K4me3 track of H1 ES cell and all other tracks. (v) Color gradient scheme for genomic heatmap. In addition, green dashed-box highlights a bivalent promoter in H1 ES cells. Blue dashed-box highlights cell type specific loss of H3K27me3 compared to ES cells. Red dashed-box highlights a promoter whose bivalency is preserved in ES cells and in brain samples, but not in breast or blood.
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| Frequent Derepression of the Mesenchymal Transcription Factor Gene FOXC1 in Acute Myeloid Leukemia. | Somerville TD et al. | β | 2015 | β |
| Integrative analysis of 111 reference human epigenomes. | Roadmap Epigenomics Consortium et al. | β | 2015 | β |
| Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. | Ernst J et al. | β | 2015 | β |
| LayerCake: a tool for the visual comparison of viral deep sequencing data. | Correll M et al. | β | 2015 | β |
| Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis. | Carey CE et al. | β | 2015 | β |
| Neuroepigenomics: Resources, Obstacles, and Opportunities. | Satterlee JS et al. | β | 2015 | β |
| Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults. | Hochner H et al. | β | 2015 | β |
| Sequencing of the <i>TBX6</i> Gene in Families with Familial Idiopathic Scoliosis. | Baschal EE et al. | β | 2015 | β |
| Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. | Zhang B et al. | β | 2014 | β |
| Comprehensive analysis of DNA methylation data with RnBeads. | Assenov Y et al. | β | 2014 | β |
| Comprehensive genotyping and clinical characterisation reveal 27 novel NKX2-1 mutations and expand the phenotypic spectrum. | Thorwarth A et al. | β | 2014 | β |
| Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. | Ebert G et al. | β | 2014 | β |
| Epiviz: interactive visual analytics for functional genomics data. | Chelaru F et al. | β | 2014 | β |
| Functional interpretation of non-coding sequence variation: concepts and challenges. | Paul DS et al. | β | 2014 | β |
| Genomic architecture of histone 3 lysine 27 trimethylation during late ovine skeletal muscle development. | Byrne K et al. | β | 2014 | β |
| Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus. | Fogarty MP et al. | β | 2014 | β |
| methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. | Zhou X et al. | β | 2014 | β |
| VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery. | Coulombe C et al. | β | 2014 | β |
| visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data. | Scales M et al. | β | 2014 | β |
| A brief introduction to web-based genome browsers. | Wang J et al. | β | 2013 | β |
| Allele-specific transcriptional activity at type 2 diabetes-associated single nucleotide polymorphisms in regions of pancreatic islet open chromatin at the JAZF1 locus. | Fogarty MP et al. | β | 2013 | β |
| Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. | Karnik R et al. | β | 2013 | β |
| DNA unmethylome profiling by covalent capture of CpG sites. | KriukienΔ E et al. | β | 2013 | β |
| Enabling interspecies epigenomic comparison with CEpBrowser. | Cao X et al. | β | 2013 | β |
| Epigenomics: sequencing the methylome. | Hirst M | β | 2013 | β |
| Exploring long-range genome interactions using the WashU Epigenome Browser. | Zhou X et al. | β | 2013 | β |
| Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. | Zhang B et al. | β | 2013 | β |
| Methods for cancer epigenome analysis. | Nagarajan RP et al. | β | 2013 | β |
| Pathway analyses and understanding disease associations. | Liu Y et al. | β | 2013 | β |
| Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. | Miller CA et al. | β | 2013 | β |
| STAR: an integrated solution to management and visualization of sequencing data. | Wang T et al. | β | 2013 | β |
| Analysing and interpreting DNA methylation data. | Bock C | β | 2012 | β |
| EpiExplorer: live exploration and global analysis of large epigenomic datasets. | Halachev K et al. | β | 2012 | β |
| Genetics and epigenetics of the skin meet deep sequence. | Cheng JB et al. | β | 2012 | β |
| Online tools for bioinformatics analyses in nutrition sciences. | Malkaram SA et al. | β | 2012 | β |
| Spark: a navigational paradigm for genomic data exploration. | Nielsen CB et al. | β | 2012 | β |
| The NIH Roadmap Epigenomics Program data resource. | Chadwick LH | β | 2012 | β |
| The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. | Pham MH et al. | β | 2012 | β |
| Using the Wash U Epigenome Browser to examine genome-wide sequencing data. | Zhou X et al. | β | 2012 | β |
| What can epigenomics do for you? | Meissner A | β | 2012 | β |
| What does our genome encode? | Stamatoyannopoulos JA | β | 2012 | β |