ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Lihua Julie Zhu,Claude Gazin,Nathan D. Lawson,Hervé Pagès,Simon Lin,David S. Lapointe,Michael R. Green +6 more
TLDR
ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, Chip-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R.Abstract:
Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as GenomicFeatures and BSgenom e, provides flexibility. Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database.read more
Citations
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ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
TL;DR: UNLABELLED ChIPseeker is an R package for annotating ChIP-seq data analysis and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions.
Journal ArticleDOI
Nrf2 suppresses macrophage inflammatory response by blocking proinflammatory cytokine transcription
Eri H. Kobayashi,Takafumi Suzuki,Ryo Funayama,Takeshi Nagashima,Makiko Hayashi,Hiroki Sekine,Nobuyuki Tanaka,Takashi Moriguchi,Hozumi Motohashi,Keiko Nakayama,Masayuki Yamamoto +10 more
TL;DR: It is demonstrated that Nrf2 interferes with lipopolysaccharide-induced transcriptional upregulation of proinflammatory cytokines, including IL-6 and IL-1β, and establishes a molecular basis for an NRF2-mediated anti-inflammation approach.
Journal ArticleDOI
Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo
Hao Yin,Chun-Qing Song,Joseph R. Dorkin,Lihua Julie Zhu,Yingxiang Li,Qiongqiong Wu,Angela I. Park,Junghoon Yang,Sneha Suresh,Aizhan Bizhanova,Ankit Gupta,Mehmet Fatih Bolukbasi,Stephen Walsh,Roman L. Bogorad,Guangping Gao,Zhiping Weng,Yizhou Dong,Victor Koteliansky,Victor Koteliansky,Scot A. Wolfe,Robert Langer,Wen Xue,Daniel G. Anderson +22 more
TL;DR: The delivery strategy is applied to a mouse model of human hereditary tyrosinemia and it is shown that the treatment generated fumarylacetoacetate hydrolase (Fah)-positive hepatocytes by correcting the causative Fah-splicing mutation and rescued disease symptoms such as weight loss and liver damage.
Journal ArticleDOI
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Manu J. Dubin,Pei Zhang,Dazhe Meng,Marie Stanislas Remigereau,Edward J. Osborne,Francesco Paolo Casale,Philipp Drewe,André Kahles,Géraldine Jean,Bjarni J. Vilhjálmsson,Joanna Jagoda,Selen Irez,Viktor Voronin,Qiang Song,Quan Long,Gunnar Rätsch,Oliver Stegle,Richard M. Clark,Magnus Nordborg +18 more
TL;DR: Investigation of DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures finds that accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected.
Journal ArticleDOI
Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light
Ullas V. Pedmale,Shao-shan Carol Huang,Mark Zander,Benjamin J. Cole,Benjamin J. Cole,Jonathan Hetzel,Jonathan Hetzel,Karin Ljung,Pedro A. B. Reis,Pedro A. B. Reis,Priya Sridevi,Kazumasa Nito,Joseph R. Nery,Joseph R. Ecker,Joanne Chory +14 more
TL;DR: The results indicate that CRYs signal by modulating PIF activity genome wide and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions.
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