ArticleF1000Research2015
From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data.
Article in F1000Research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- PolyP inhibits CobB deacetylase triggering a regulatory coupling to prevent DNA replication initiation.Nucleic acids research · 2026Article
- Selecting ChIP-seq normalization methods from the perspective of their technical conditions.Briefings in bioinformatics · 2025Article
- EZH2 inhibition stimulates repetitive element expression and viral mimicry in resting splenic B cells.The EMBO journal · 2023Article
- Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach.Nature communications · 2023Article
- Enhanced binding of an HU homologue under increased DNA supercoiling preserves chromosome organisation and sustains Streptomyces hyphal growth.Nucleic acids research · 2022Article
- HNF4A modulates glucocorticoid action in the liver.Cell reports · 2022Article
- Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development.Nature communications · 2021Article
- Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells.The EMBO journal · 2021Article
- MAnorm2 for quantitatively comparing groups of ChIP-seq samples.Genome research · 2021Article
- A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division.Nature communications · 2020Article
- A practical guide to methods controlling false discoveries in computational biology.Genome biology · 2019Article
- A step-by-step guide to analyzing CAGE data using R/Bioconductor.F1000Research · 2019Article
- Unsupervised clustering and epigenetic classification of single cells.Nature communications · 2018Article
- Vitamin D Receptor Signaling and Cancer.Endocrinology and metabolism clinics of North America · 2017Review
- ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION.The annals of applied statistics · 2016Article
- csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows.Nucleic acids research · 2016Article
- Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.F1000ResearchArticle
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify the genomic binding sites for protein of interest. Most conventional approaches to ChIP-seq data analysis involve the detection of the absolute presence (or absence) of a binding site. However, an alternative strategy is to identify changes in the binding intensity between two biological conditions, i.e., differential binding (DB). This may yield more relevant results than conventional analyses, as changes in binding can be associated with the biological difference being investigated. The aim of this article is to facilitate the implementation of DB analyses, by comprehensively describing a computational workflow for the detection of DB regions from ChIP-seq data. The workflow is based primarily on R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, from alignment of read sequences to interpretation and visualization of putative DB regions. In particular, detection of DB regions will be conducted using the counts for sliding windows from the csaw package, with statistical modelling performed using methods in the edgeR package. Analyses will be demonstrated on real histone mark and transcription factor data sets. This will provide readers with practical usage examples that can be applied in their own studies.
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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.