EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations.
Reads0
Chats0
TLDR
A new R package named EnrichedHeatmap is presented that efficiently visualizes genomic signal enrichment and provides advanced solutions for normalizing genomic signals within target regions as well as offering highly customizable visualizations.Abstract:
High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a specific form of heatmap that visualizes how genomic signals are enriched over specific target regions. It is commonly used and efficient at revealing enrichment patterns especially for high dimensional genomic and epigenomic datasets. We present a new R package named EnrichedHeatmap that efficiently visualizes genomic signal enrichment. It provides advanced solutions for normalizing genomic signals within target regions as well as offering highly customizable visualizations. The major advantage of EnrichedHeatmap is the ability to conveniently generate parallel heatmaps as well as complex annotations, which makes it easy to integrate and visualize comprehensive overviews of the patterns and associations within and between complex datasets. EnrichedHeatmap facilitates comprehensive understanding of high dimensional genomic and epigenomic data. The power of EnrichedHeatmap is demonstrated by visualization of the complex associations between DNA methylation, gene expression and various histone modifications.read more
Citations
More filters
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Chromatin-state discovery and genome annotation with ChromHMM
Jason Ernst,Manolis Kellis +1 more
TL;DR: ChromHMM combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type, and provides an automated enrichment analysis of the resulting annotations to facilitate the functional interpretations of each chromatin state.
Journal ArticleDOI
Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin.
Michael Borg,Yannick Jacob,Daichi Susaki,Chantal LeBlanc,Daniel Buendía,Elin Axelsson,Tomokazu Kawashima,Tomokazu Kawashima,Philipp Voigt,Leonor C. Boavida,Jörg Becker,Tetsuya Higashiyama,Robert A. Martienssen,Frédéric Berger +13 more
TL;DR: Plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome, which facilitates the transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation.
Journal ArticleDOI
KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer.
Hunain Alam,Ming Tang,Mayinuer Maitituoheti,Shilpa S. Dhar,Manish Kumar,Chae Young Han,Chandrashekar R. Ambati,Samir B. Amin,Bingnan Gu,Tsai Yu Chen,Yu Hsi Lin,Jichao Chen,Florian L. Muller,Nagireddy Putluri,Elsa R. Flores,Francesco J. DeMayo,Laura Baseler,Kunal Rai,Min Gyu Lee +18 more
TL;DR: It is shown that lung-specific loss of Kmt2d promotes lung tumorigenesis in mice and upregulates pro-tumorigenic programs, including glycolysis, which indicates that KMT2D is a lung tumor suppressor and that K MT2D deficiency confers a therapeutic vulnerability to Glycolytic inhibitors.
Journal ArticleDOI
MeCP2 Represses the Rate of Transcriptional Initiation of Highly Methylated Long Genes
Lisa D. Boxer,William Renthal,Alexander W. Greben,Tess Whitwam,Andrew Silberfeld,Hume Stroud,Emmy Li,Marty G. Yang,Benyam Kinde,Eric C. Griffith,Boyan B. Bonev,Michael E. Greenberg +11 more
TL;DR: It is demonstrated here that MeCP2 represses nascent RNA transcription of highly methylated long genes in the brain through its interaction with the NCoR co-repressor complex, and suggests a new model of Me CP2 function in which MeCP 2 binds broadly across highlymethylated regions of DNA, but acts at transcription start sites to attenuate transcriptional initiation.
References
More filters
Journal ArticleDOI
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Wouter Meuleman,Jason Ernst,Misha Bilenky,Angela Yen,Angela Yen,Alireza Heravi-Moussavi,Pouya Kheradpour,Pouya Kheradpour,Zhizhuo Zhang,Zhizhuo Zhang,Jianrong Wang,Jianrong Wang,Michael J. Ziller,Viren Amin,John W. Whitaker,Matthew D. Schultz,Lucas D. Ward,Lucas D. Ward,Abhishek Sarkar,Abhishek Sarkar,Gerald Quon,Gerald Quon,Richard Sandstrom,Matthew L. Eaton,Matthew L. Eaton,Yi-Chieh Wu,Yi-Chieh Wu,Andreas R. Pfenning,Andreas R. Pfenning,Xinchen Wang,Xinchen Wang,Melina Claussnitzer,Melina Claussnitzer,Yaping Liu,Yaping Liu,Cristian Coarfa,R. Alan Harris,Noam Shoresh,Charles B. Epstein,Elizabeta Gjoneska,Elizabeta Gjoneska,Danny Leung,Wei Xie,R. David Hawkins,Ryan Lister,Chibo Hong,Philippe Gascard,Andrew J. Mungall,Richard A. Moore,Eric Chuah,Angela Tam,Theresa K. Canfield,R. Scott Hansen,Rajinder Kaul,Peter J. Sabo,Mukul S. Bansal,Mukul S. Bansal,Mukul S. Bansal,Annaick Carles,Jesse R. Dixon,Kai How Farh,Soheil Feizi,Soheil Feizi,Rosa Karlic,Ah Ram Kim,Ah Ram Kim,Ashwinikumar Kulkarni,Daofeng Li,Rebecca F. Lowdon,Ginell Elliott,Tim R. Mercer,Shane Neph,Vitor Onuchic,Paz Polak,Paz Polak,Nisha Rajagopal,Pradipta R. Ray,Richard C Sallari,Richard C Sallari,Kyle Siebenthall,Nicholas A Sinnott-Armstrong,Nicholas A Sinnott-Armstrong,Michael Stevens,Robert E. Thurman,Jie Wu,Bo Zhang,Xin Zhou,Arthur E. Beaudet,Laurie A. Boyer,Philip L. De Jager,Philip L. De Jager,Peggy J. Farnham,Susan J. Fisher,David Haussler,Steven J.M. Jones,Steven J.M. Jones,Wei Li,Marco A. Marra,Michael T. McManus,Shamil R. Sunyaev,Shamil R. Sunyaev,James A. Thomson,Thea D. Tlsty,Li-Huei Tsai,Li-Huei Tsai,Wei Wang,Robert A. Waterland,Michael Q. Zhang,Lisa Helbling Chadwick,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Joseph F. Costello,Joseph R. Ecker,Martin Hirst,Alexander Meissner,Aleksandar Milosavljevic,Bing Ren,John A. Stamatoyannopoulos,Ting Wang,Manolis Kellis,Manolis Kellis +123 more
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Journal ArticleDOI
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
TL;DR: The power of ComplexHeatmap is demonstrated to easily reveal patterns and correlations among multiple sources of information with four real-world datasets.
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal ArticleDOI
Software for computing and annotating genomic ranges.
Michael F. Lawrence,Wolfgang Huber,Hervé Pagès,Patrick Aboyoun,Marc R. J. Carlson,Robert Gentleman,Martin Morgan,Vincent J. Carey +7 more
TL;DR: This work describes Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions, including those for sequence analysis, differential expression analysis and visualization.
Journal ArticleDOI
deepTools: a flexible platform for exploring deep-sequencing data
TL;DR: A Galaxy based web server for processing and visualizing deeply sequenced data, called deepTools, that enables users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting and can be used without registration.