Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
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TLDR
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.Abstract:
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.read more
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Journal ArticleDOI
Identifying ChIP-seq enrichment using MACS
TL;DR: This protocol provides a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and theH3K36me3 mark with broad enrichment.
Book ChapterDOI
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
TL;DR: DiffBind is used to identify ERα sites significantly differentially bound between those found in tumours from patients with good prognosis vs. those with poor prognosis and metastases, and to show the plasticity of ERα binding capacity.
Journal ArticleDOI
Transcriptional Amplification in Tumor Cells with Elevated c-Myc
Charles Y. Lin,Jakob Lovén,Peter B. Rahl,Ronald M. Paranal,Christopher B. Burge,James E. Bradner,Tong Ihn Lee,Richard A. Young +7 more
TL;DR: It is reported here that in tumor cells expressing high levels of c-Myc the transcription factor accumulates in the promoter regions of active genes and causes transcriptional amplification, producing increased levels of transcripts within the cell's gene expression program.
Journal ArticleDOI
A rapid and robust method for single cell chromatin accessibility profiling
Xi Chen,Ricardo J. Miragaia,Ricardo J. Miragaia,Kedar Nath Natarajan,Sarah A. Teichmann,Sarah A. Teichmann +5 more
TL;DR: A simple and robust plate-based single-cell ATAC-seq method that works in fresh and cryopreserved cells and identifies distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors is developed.
Journal ArticleDOI
Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing.
Wen Xiao,Samir Adhikari,Samir Adhikari,Ujwal Dahal,Ujwal Dahal,Yu-Sheng Chen,Yu-Sheng Chen,Ya-Juan Hao,Ya-Juan Hao,Bao-Fa Sun,Hui-Ying Sun,Hui-Ying Sun,Ang Li,Ang Li,Xiao-Li Ping,Weiyi Lai,Xing Wang,Xing Wang,Hai-Li Ma,Hai-Li Ma,Chun-Min Huang,Ying Yang,Niu Huang,Guibin Jiang,Hailin Wang,Qi Zhou,Xiu-Jie Wang,Yong-Liang Zhao,Yun-Gui Yang,Yun-Gui Yang +29 more
TL;DR: The findings provide the direct evidence that m(6)A reader YTHDC1 regulates mRNA splicing through recruiting and modulating pre-mRNA splicing factors for their access to the binding regions of targeted mRNAs.
References
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PatentDOI
Genome-wide location and function of dna binding proteins
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