ArticleNucleic acids research2011
EpiChIP: gene-by-gene quantification of epigenetic modification levels.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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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Who cites it
26 citing papers in PubMed, 42 citations in OpenAlex.
- Epigenetic targets in B- and T-cell lymphomas: latest developments.Therapeutic advances in hematology · 2023Review
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- Regulation of the JMJD3 (KDM6B) histone demethylase in glioblastoma stem cells by STAT3.PloS one · 2017Article
- Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.PLoS genetics · 2015Article
- An atlas of mouse CD4(+) T cell transcriptomes.Biology direct · 2015Article
- The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection.PLoS neglected tropical diseases · 2015Article
- ChIP-seq profiling of the active chromatin marker H3K4me3 and PPARγ, CEBPα and LXR target genes in human SGBS adipocytes.Genomics data · 2014Article
- Heterochromatin controls γH2A localization in Neurospora crassa.Eukaryotic cell · 2014Article
- Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.Nucleic acids research · 2014Article
- Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems.Frontiers in cell and developmental biology · 2014Article
- Two histone deacetylases, FfHda1 and FfHda2, are important for Fusarium fujikuroi secondary metabolism and virulence.Applied and environmental microbiology · 2013Article
- HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.Bioinformatics (Oxford, England) · 2013Article
- Gene dysregulation by histone variant H2A.Z in bladder cancer.Epigenetics & chromatin · 2013Article
- The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters.PLoS genetics · 2013Article
- Article
- Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements.Aging cell · 2013Article
- Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.PLoS pathogens · 2013Article
- Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes.Nature communications · 2013Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The combination of chromatin immunoprecipitation with next-generation sequencing technology (ChIP-seq) is a powerful and increasingly popular method for mapping protein-DNA interactions in a genome-wide fashion. The conventional way of analyzing this data is to identify sequencing peaks along the chromosomes that are significantly higher than the read background. For histone modifications and other epigenetic marks, it is often preferable to find a characteristic region of enrichment in sequencing reads relative to gene annotations. For instance, many histone modifications are typically enriched around transcription start sites. Calculating the optimal window that describes this enrichment allows one to quantify modification levels for each individual gene. Using data sets for the H3K9/14ac histone modification in Th cells and an accompanying IgG control, we present an analysis strategy that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal. Curve fitting permits false discovery rate-based classification of genes as modified versus unmodified. We have developed a software package called EpiChIP that carries out this type of analysis, including integration with and visualization of gene expression data.
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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.