A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

By Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, Weiqun Peng. Bioinform., 2009

1,065 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2899dc04584681c7e987ff17feec25ee4267a42e

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Citations in the corpus

Target analysis by integration of transcriptome and ChIP-seq data with BETA (2013, methodology): “Model-based analysis of ChIP-seq (MACS) 8 , CisGenome 9 and SICER 10 are some of the peak caller tools globally used to identify precise TF-binding sites.”
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data (2011, background): “Most of the tools published for the analysis of ChIP-Seq data focus on punctuated signals (Fejes et al., 2008; Nix et al., 2008; Park, 2009; Pepke et al., 2009; Zhang et al., 2008), with only few methods devoted to analyse broad signals (Shin et al., 2009; Zang et al., 2009).”
LncRNA-Dependent Mechanisms of Androgen Receptor-regulated Gene Activation Programs (2013, positive): “For ChIP-Seq data (AR and H3K4me 1 ), peak finding was performed by using HOMER or SICER 26 .”
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection (2010, methodology): “Several algorithms have been written to specifically address this issue and should be chosen in lieu of those evaluated herein if non-transcription factors are being studied [35,36,37,38,39,40,41].”
Identifying ChIP-seq enrichment using MACS (2012, methodology): “To identify binding sites more accurately, MACS extends reads in the 3 ′ direction until the estimated DNA fragment size is reached, a strategy also used by SICER 24 .”
Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes (2009, methodology): “The signals highlighted in the red box are not statistically significant as determined using SICER (Zang et al., 2009).”
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool (2013, methodology): “ChIP-seq datasets from the Roadmap Epigenomics project deposited to the GEO database were analyzed and converted to gene sets with the use of the software, SICER [21].”
The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. (2013, methodology): “for H3K4me3 and using SICER (Zang et al. 2009) for H3K27me3 and EZH2.”
ChIP-Seq: advantages and challenges of a maturing technology (2009, background): “will soon be modified for ChIP–seq, and new approaches are being develope”
H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions in the human genome (2009, methodology): “In preference to measuring local enrichment, we used a slightly different version of SICE”