annotatr: genomic regions in context.
TLDR
The annotatr Bioconductor package is developed to flexibly and quickly summarize and plot annotations of genomic regions, giving a better understanding of the genomic context of the regions.Abstract:
Motivation Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof. Results We developed the annotatr Bioconductor package to flexibly and quickly summarize and plot annotations of genomic regions. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of graphics functions are implemented to easily plot numerical or categorical data associated with the regions across the annotations, and across annotation intersections, providing insight into how characteristics of the regions differ across the annotations. We demonstrate that annotatr is up to 27× faster than comparable R packages. Overall, annotatr enables a richer biological interpretation of experiments. Availability and implementation http://bioconductor.org/packages/annotatr/ and https://github.com/rcavalcante/annotatr. Contact rcavalca@umich.edu. Supplementary information Supplementary data are available at Bioinformatics online.read more
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Journal ArticleDOI
Decade-long leukaemia remissions with persistence of CD4+ CAR T cells
J. Joseph Melenhorst,Gregory M. Chen,Meng Wang,David L. Porter,Changya Chen,McKensie Collins,Peng Gao,Shovik Bandyopadhyay,Hongxing Sun,Ziran Zhao,Stefan Lundh,Iulian Pruteanu-Malinici,Christopher L. Nobles,Sayantan Maji,Noelle V. Frey,Saar Gill,Lifeng Tian,Irina Kulikovskaya,Minnal Gupta,David E Ambrose,Megan M. Davis,Joseph A. Fraietta,Jennifer Brogdon,Regina M. Young,Anne Chew,Bruce L. Levine,Don L. Siegel,Cécile Alanio,E. John Wherry,Frederic D. Bushman,Simon F. Lacey,Kai Tan,Carl H. June +32 more
TL;DR: In this article , the authors studied long-lasting CD19-redirected chimeric antigen receptor (CAR) T cells in two patients with chronic lymphocytic leukaemia who achieved a complete remission in 2010.
Journal ArticleDOI
IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response.
Felipe J Nunez,Flor M. Mendez,Padma Kadiyala,Mahmoud S. Alghamri,Masha G. Savelieff,Maria B. Garcia-Fabiani,Santiago Haase,Carl Koschmann,Anda Alexandra Calinescu,Neha Kamran,Meghna Saxena,Rohin Patel,Stephen Carney,Marissa Z Guo,Marta Edwards,Mats Ljungman,Tingting Qin,Maureen A. Sartor,Rebecca Tagett,Sriram Venneti,Jacqueline A. Brosnan-Cashman,Alan K. Meeker,Vera Gorbunova,Lili Zhao,Daniel M. Kremer,Li Zhang,Costas A. Lyssiotis,Lindsey E Jones,Cameron Herting,James Ross,Dolores Hambardzumyan,Shawn L. Hervey-Jumper,Maria E. Figueroa,Maria E. Figueroa,Pedro R. Lowenstein,Maria G. Castro +35 more
TL;DR: It is discovered that IDH1R132H expression in the genetic context of ATRX and TP53 gene inactivation increases median survival in the absence of treatment, enhances DNA damage response (DDR) via epigenetic up-regulation of the ataxia-telangiectasia–mutated (ATM) signaling pathway, and elicits tumor radioresistance.
Journal ArticleDOI
A whole lifespan mouse multi-tissue DNA methylation clock.
Margarita Meer,Dmitriy I. Podolskiy,Alexander Tyshkovskiy,Alexander Tyshkovskiy,Vadim N. Gladyshev +4 more
TL;DR: A robust multi-tissue age predictor based on 435 CpG sites, which covers the entire mouse lifespan and remains unbiased with respect to any particular age group is constructed.
Journal ArticleDOI
Reprogramming roadmap reveals route to human induced trophoblast stem cells.
Xiaodong Liu,Xiaodong Liu,Xiaodong Liu,John F. Ouyang,Fernando J. Rossello,Jia Ping Tan,Jia Ping Tan,Jia Ping Tan,Kathryn C. Davidson,Kathryn C. Davidson,Kathryn C. Davidson,Daniela S. Valdes,Jan Schröder,Jan Schröder,Jan Schröder,Yu Bo Yang Sun,Yu Bo Yang Sun,Yu Bo Yang Sun,Joseph Chen,Joseph Chen,Joseph Chen,Anja S Knaupp,Anja S Knaupp,Anja S Knaupp,Guizhi Sun,Guizhi Sun,Guizhi Sun,Hun S. Chy,Hun S. Chy,Ziyi Huang,Ziyi Huang,Jahnvi Pflueger,Jahnvi Pflueger,Jaber Firas,Jaber Firas,Jaber Firas,Vincent Tano,Vincent Tano,Vincent Tano,Sam Buckberry,Sam Buckberry,Jacob M. Paynter,Jacob M. Paynter,Jacob M. Paynter,Michael R. Larcombe,Michael R. Larcombe,Michael R. Larcombe,Daniel Poppe,Daniel Poppe,Xin Yi Choo,Xin Yi Choo,Xin Yi Choo,Carmel M. O’Brien,Carmel M. O’Brien,William A. Pastor,William A. Pastor,Di Chen,Anna L. Leichter,Haroon Naeem,Pratibha Tripathi,Pratibha Tripathi,Partha Pratim Das,Partha Pratim Das,Alexandra Grubman,Alexandra Grubman,Alexandra Grubman,David R. Powell,Andrew L. Laslett,Andrew L. Laslett,Laurent David,Susan K. Nilsson,Susan K. Nilsson,Amander T. Clark,Ryan Lister,Ryan Lister,Christian M. Nefzger,Luciano G. Martelotto,Owen J. L. Rackham,Jose M. Polo,Jose M. Polo,Jose M. Polo +80 more
TL;DR: This work reconstructs molecular reprogramming trajectories of human dermal fibroblasts using single-cell transcriptomics and indicates a role for the trophectoderm-lineage-specific regulatory program during this process, and facilitates the direct reprograming of somatic cells into induced trophoblast stem cells.
Journal ArticleDOI
H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
Yichao Cai,Ying Zhang,Yan Ping Loh,Jia Qi Tng,Mei Chee Lim,Zhendong Cao,Zhendong Cao,Anandhkumar Raju,Erez Lieberman Aiden,Shang Li,Lakshmanan Manikandan,Vinay Tergaonkar,Greg Tucker-Kellogg,Melissa J. Fullwood,Melissa J. Fullwood,Melissa J. Fullwood +15 more
TL;DR: In this paper, the authors investigate the hypothesis that H3K27me3-rich regions of the genome, defined from clusters of H 3K 27me3 peaks, may be used to identify silencers that can regulate gene expression via proximity or looping.
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