ArticleNucleic acids research2011
Efficiently identifying genome-wide changes with next-generation sequencing data.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.Genome biology · 2022Article
- AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.Scientific reports · 2021Article
- Global transcriptomic profiling of microcystin-LR or -RR treated hepatocytes (HepaRG).Toxicon: X · 2020Article
- Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching.Communications biology · 2020Article
- Characterization of the Fundulus heteroclitus embryo transcriptional response and development of a gene expression-based fingerprint of exposure for the alternative flame retardant, TBPH (bis (2-ethylhexyl)-tetrabromophthalate).Environmental pollution (Barking, Essex : 1987) · 2019Article
- Mediator complex component MED13 regulates zygotic genome activation and is required for postimplantation development in the mouse.Biology of reproduction · 2018Article
- Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels.Data in brief · 2016Article
- ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences.BMC genomics · 2016Article
- Deficiency of the placenta- and yolk sac-specific tristetraprolin family member ZFP36L3 identifies likely mRNA targets and an unexpected link to placental iron metabolism.Development (Cambridge, England) · 2016Article
- Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.Epigenetics & chromatin · 2016Article
- Post-transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans.Molecular microbiology · 2015Article
- Identifying differential transcription factor binding in ChIP-seq.Frontiers in genetics · 2015Article
- The Drosophila Tis11 protein and its effects on mRNA expression in flies.The Journal of biological chemistry · 2014Article
- Modeling Expression Plasticity of Genes that Differentiate Drug-sensitive from Drug-resistant Cells to Chemotherapeutic Treatment.Current genomics · 2014Article
- High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.Nature · 2013Article
- PAVIS: a tool for Peak Annotation and Visualization.Bioinformatics (Oxford, England) · 2013Article
- Mobility of the native Bacillus subtilis conjugative plasmid pLS20 is regulated by intercellular signaling.PLoS genetics · 2013Article
- Reconstructing regulatory networks from the dynamic plasticity of gene expression by mutual information.Nucleic acids research · 2013Article
- Posttranscriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in Schizosaccharomyces pombe.Molecular and cellular biology · 2012Article
- Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We propose a new and effective statistical framework for identifying genome-wide differential changes in epigenetic marks with ChIP-seq data or gene expression with mRNA-seq data, and we develop a new software tool EpiCenter that can efficiently perform data analysis. The key features of our framework are: (i) providing multiple normalization methods to achieve appropriate normalization under different scenarios, (ii) using a sequence of three statistical tests to eliminate background regions and to account for different sources of variation and (iii) allowing adjustment for multiple testing to control false discovery rate (FDR) or family-wise type I error. Our software EpiCenter can perform multiple analytic tasks including: (i) identifying genome-wide epigenetic changes or differentially expressed genes, (ii) finding transcription factor binding sites and (iii) converting multiple-sample sequencing data into a single read-count data matrix. By simulation, we show that our framework achieves a low FDR consistently over a broad range of read coverage and biological variation. Through two real examples, we demonstrate the effectiveness of our framework and the usages of our tool. In particular, we show that our novel and robust 'parsimony' normalization method is superior to the widely-used 'tagRatio' method. Our software EpiCenter is freely available to the public.
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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.