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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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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featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features
TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal Article
An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
High-resolution profiling of histone methylations in the human genome.
Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
Journal ArticleDOI
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Feng Yue,Audrey Kim,Yan-Yan Li,Yin-Zhong Shen,Ming Hu,Jun Liu,Bing Ren,Bing Ren +10 more
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
References
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Journal ArticleDOI
Model-based analysis of tiling-arrays for ChIP-chip
W. Evan Johnson,Wei Li,Clifford A. Meyer,Raphael Gottardo,Jason S. Carroll,Myles Brown,X. Shirley Liu +6 more
TL;DR: A fast and powerful analysis algorithm to reliably detect regions enriched by transcription factor chromatin immunoprecipitation on Affymetrix tiling arrays (ChIP-chip), developed in open-source Python and available at http://chip.dfci.harvard.edu/∼wli/MAT.
Journal ArticleDOI
Genome-Wide Analysis of Protein-DNA Interactions
Tae Hoon Kim,Bing Ren +1 more
TL;DR: Recent advances in ChIP-based methods for genome-wide detection of protein-DNA interactions are reviewed, and their significance in enhancing knowledge of the gene regulatory networks and epigenetic mechanisms in cells are discussed.
Journal ArticleDOI
Model-based analysis of two-color arrays (MA2C)
Jun S. Song,W. Evan Johnson,Xiaopeng Zhu,Xinmin Zhang,Wei Li,Arjun K. Manrai,Jun Liu,Runsheng Chen,X. Shirley Liu +8 more
TL;DR: A novel normalization method based on the GC content of probes is developed for two-color tiling arrays and a robust algorithm for detecting peak regions is formulated and shown to perform well compared to other approaches.