ArticleNature protocols2011
A computational pipeline for comparative ChIP-seq analyses.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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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
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules.BMC genomics · 2013Pooled it
- Appropriate normalization is critical to improve reproducibility of tissue ChIP-seq.Serican journal of medicine · 2025Article
- p53 regulates DREAM complex-mediated repression in a p21-independent manner.The EMBO journal · 2025Article
- MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets.Nucleic acids research · 2024Article
- An AI Agent for Fully Automated Multi-Omic Analyses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator.eLife · 2024Article
- A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.Nature communications · 2023Article
- Rare diseases of epigenetic origin: Challenges and opportunities.Frontiers in genetics · 2023Review
- ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect,Frontiers in genetics · 2023Article
- Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse.Epigenetics & chromatin · 2021Article
- Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- WACS: improving ChIP-seq peak calling by optimally weighting controls.BMC bioinformatics · 2021Article
- Article
- Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Measuring the reproducibility and quality of Hi-C data.Genome biology · 2019Article
- The NCirculation · 2019Article
- SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevity.eLife · 2018Article
- Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.Cell systems · 2018Article
- Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci.Frontiers in immunology · 2018Article
- Mapping DNA Breaks by Next-Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2018Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Chromatin immunoprecipitation (ChIP) followed by deep sequencing can now easily be performed across different conditions, time points and even species. However, analyzing such data is not trivial and standard methods are as yet unavailable. Here we present a protocol to systematically compare ChIP-sequencing (ChIP-seq) data across conditions. We first describe technical guidelines for data preprocessing, read mapping, read-density visualization and peak calling. We then describe methods and provide code with specific examples to compare different data sets across species and across conditions, including a threshold-free approach to measure global similarity, a strategy to assess the binary conservation of binding events and measurements for quantitative changes of binding. We discuss how differences in binding can be related to gene functions, gene expression and sequence changes. Once established, this protocol should take about 2 d to complete and be generally applicable to many data sets.
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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.