ArticlePloS one2012
ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 44 citations in OpenAlex.
- Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer.Artificial intelligence in medicine · 2025Article
- Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.Genome biology · 2022Article
- CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.BMC bioinformatics · 2021Article
- Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer.Frontiers in genetics · 2021Article
- Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2021Article
- S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data.Nucleic acids research · 2020Article
- IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.Computational and structural biotechnology journal · 2020Article
- Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.Nucleic acids research · 2018Article
- Retrotransposons Are the Major Contributors to the Expansion of theG3 (Bethesda, Md.) · 2017Article
- Epimetheus - a multi-profile normalizer for epigenomic sequencing data.BMC bioinformatics · 2017Article
- HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics.Nucleic acids research · 2017Article
- NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data.BMC genomics · 2017Article
- Statistical challenges in analyzing methylation and long-range chromosomal interaction data.Statistics in biosciences · 2016Article
- Article
- A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.Bioinformatics (Oxford, England) · 2015Article
- Is this the right normalization? A diagnostic tool for ChIP-seq normalization.BMC bioinformatics · 2015Article
- Identifying differential transcription factor binding in ChIP-seq.Frontiers in genetics · 2015Article
- dCLIP: a computational approach for comparative CLIP-seq analyses.Genome biology · 2014Article
- BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data.BMC bioinformatics · 2014Article
- Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit different patterns of histone enrichment. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, because of the significant level of noise in ChIP-seq data. In this paper we propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that the ChIPnorm method removes most of the noise and bias in the data and outperforms other normalization methods. We correlate the histone marks with gene expression data and confirm that histone modifications H3K27me3 and H3K4me3 act as respectively a repressor and an activator of genes. Compared to what was previously reported in the literature, we find that a substantially higher fraction of bivalent marks in ES cells for H3K27me3 and H3K4me3 move into a K27-only state. We find that most of the promoter regions in protein-coding genes have differential histone-modification sites. The software for this work can be downloaded from http://lcbb.epfl.ch/software.html.
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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.