ArticleGenome research2015
Saturation analysis of ChIP-seq data for reproducible identification of binding peaks.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- peaksat: an R package for ChIP-seq peak saturation analysis.BMC genomics · 2023Article
- Article
- Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.Nucleic acids research · 2020Article
- 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.BMC genomics · 2019Article
- Rapid Response and Slow Recovery of the H3K4me3 Epigenomic Marker in the Liver after Light-mediated Phase Advances of the Circadian Clock.Journal of biological rhythms · 2018Article
- Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.Nature genetics · 2018Article
- Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.Nucleic acids research · 2017Article
- The haploinsufficient tumor suppressor, CUX1, acts as an analog transcriptional regulator that controls target genes through distal enhancers that loop to target promoters.Nucleic acids research · 2017Article
- Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.Briefings in bioinformatics · 2017Review
- Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.Genome research · 2017Article
- Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine.Cellular and molecular gastroenterology and hepatology · 2017Article
- Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of transcription factors and other DNA binding proteins. Computational ChIP-seq peak calling infers the location of protein-DNA interactions based on various measures of enrichment of sequence reads. In this work, we introduce an algorithm, Q, that uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by 5' ends of reads. We show that our method not only is substantially faster than several competing methods but also demonstrates statistically significant advantages with respect to reproducibility of results and in its ability to identify peaks with reproducible binding site motifs. We show that Q has superior performance in the delineation of double RNAPII and H3K4me3 peaks surrounding transcription start sites related to a better ability to resolve individual peaks. The method is implemented in C++ and is freely available under an open source license.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.