Model-based analysis of tiling-arrays for ChIP-chip

By W. Johnson, Clifford A. Meyer, Raphael Gottardo, Jason S. Carroll, Myles A. Brown, X. S. Liu. Proceedings of the National Academy of Sciences of the United States of America, 2006

481 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9e166741dd0208c186463f06b579fccf3bf27603

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Citations in the corpus

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. (2008, background): “A similar pattern occurred at the linker/nucleosome borders in C. elegans (Johnson et al. 2006a).”
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. (2008, methodology): “Whole-genome arrays were analyzed with MAT ( Johnson et al. 2006 ), with probes remapped to the February 2006 Mouse Genome Assembly (mm8) using xMAN (Li et al. 2008).”
Global Quantitative Modeling of Chromatin Factor Interactions (2014, methodology): “ChIP-tilling array probe signals were first standardized using Model-based Analysis of Tilling-array (MAT) algorithm [44,45].”
Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer (2009, methodology): “ChIP-on-chip data were analyzed using MAT algorithm (Johnson et al., 2006).”
An extended transcriptional network for pluripotency of embryonic stem cells. (2008, methodology): “0R arrays and Model-based Analysis of Tiling-array (MAT) was applied to predict the target loci (Johnson et al., 2006).”
Design and analysis of ChIP-seq experiments for DNA-binding proteins (2008, methodology): “Processing of ChIP-chip data has focused on compensating for array limitations, such as probe-speciﬁc behavior, dye bias and tiling resolution 8–10 .”
Target analysis by integration of transcriptome and ChIP-seq data with BETA (2013, methodology): “We use the peak-calling program model-based analysis of tiling array (MAT) 23 to identify the binding events from ChIP-chip data.”
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. (2008, unknown): “In comparison, the ERa cistrome in MCF7 cells (Carroll et al., 2006) reanalyzed using the MAT algorithm (Johnson et al., 2006) and updated to the most recent human genome sequence (Hg18) revealed 5782 high-confidence sites (FDR 1”
EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. (2008, methodology): “Model-based analysis of tiling array (MAT) was used to predict target loci (p 1e À7 ) (Johnson et al., 2006).”
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm (2008, background): “the 25-bp oligonucleotides [28,29], we divided the mean”
Model-based Analysis of ChIP-Seq (MACS) (2008, methodology): “%) were also detected by ChIP-chip (MAT [13] cutoff at FDR <1% and fold-enrichment >2).”
Cistrome: an integrative platform for transcriptional regulation studies (2011, methodology): “We deployed the MAT tool [8] for Affymetrix promoter or tiling arrays and have supported nine different array designs from Caenorhabditis elegans to human.”
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection (2010, background): “Identifying putative protein binding sites from large, sequencebased datasets presents a bioinformatic challenge that has required considerable computational innovation despite the availability of numerous programs for ChIP-Chip analysis [3,4,5,6,7,8,9].”