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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systemPipeR: NGS workflow and report generation environment
Tyler W. H. Backman,Thomas Girke +1 more
TL;DR: The R/Bioconductor package systemPipeR accelerates the extraction of reproducible analysis results from NGS experiments by making efficient use of existing software resources without limiting the user to a set of predefined methods or environments.
Journal ArticleDOI
Characterization of the direct targets of FOXO transcription factors throughout evolution.
TL;DR: A meta‐analysis of direct FOXO targets across tissues and organisms provides insight into the evolution of the FOXO network and highlights downstream genes and cofactors that may be particularly important for FOXO's conserved function in adult homeostasis and longevity.
Journal ArticleDOI
Arid1a Has Context-Dependent Oncogenic and Tumor Suppressor Functions in Liver Cancer
Xuxu Sun,Sam C. Wang,Yonglong Wei,Xin Luo,Yuemeng Jia,Lin Li,Purva Gopal,Min Zhu,Ibrahim Nassour,Jen Chieh Chuang,Thomas Maples,Cemre Celen,Liem H. Nguyen,Linwei Wu,Shunjun Fu,Weiping Li,Lijian Hui,Feng Tian,Yuan Ji,Shuyuan Zhang,Mahsa Sorouri,Tae Hyun Hwang,Lynda Letzig,Laura P. James,Zixi Wang,Adam C. Yopp,Amit G. Singal,Hao Zhu +27 more
TL;DR: Mechanistically, loss of Arid1a within tumors decreased chromatin accessibility and reduced transcription of genes associated with migration, invasion, and metastasis, and ARID1A has context-dependent tumor-suppressive and oncogenic roles in cancer.
Journal ArticleDOI
Systematic evaluation of factors influencing ChIP-seq fidelity
Yiwen Chen,Nicolas Nègre,Nicolas Nègre,Qiang Li,Joanna O. Mieczkowska,Matthew Slattery,Tao Liu,Yong Zhang,Tae Kyung Kim,Tae Kyung Kim,Housheng Hansen He,Jennifer Zieba,Yijun Ruan,Peter J. Bickel,Richard M. Myers,Barbara J. Wold,Kevin P. White,Jason D. Lieb,X. Shirley Liu +18 more
TL;DR: Evaluation of widely used ChIP-seq analysis tools suggests that adjustments or algorithm improvements are required to handle data sets with deep coverage, and a chromatin-state bias was detected: open chromatin regions yielded higher coverage, which led to false positives if not corrected.
Journal ArticleDOI
Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.
Christopher M. Vockley,Anthony D'Ippolito,Ian C. McDowell,William H. Majoros,Alexias Safi,Lingyun Song,Gregory E. Crawford,Timothy E. Reddy +7 more
TL;DR: It is shown that those interactions can synergistically modulate the activity of direct GBSs and may therefore play a major role in driving gene activation in response to GCs.
References
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