ArticleGenes to cells : devoted to molecular & cellular mechanisms2013
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
Article in Genes to cells : devoted to molecular & cellular mechanisms, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans.BMC genomics · 2023Article
- Heterochronic development of pelvic fins in zebrafish: possible involvement of temporal regulation ofFrontiers in cell and developmental biology · 2023Article
- HSF1 phosphorylation establishes an active chromatin state via the TRRAP-TIP60 complex and promotes tumorigenesis.Nature communications · 2022Article
- Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation.Nature communications · 2022Article
- HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data.Briefings in bioinformatics · 2022Article
- Highly rigid H3.1/H3.2-H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells.Genes & development · 2022Article
- Modern epigenetics methods in biological research.Methods (San Diego, Calif.) · 2021Review
- The Aflibercept-Induced MicroRNA Profile in the Vitreous of Proliferative Diabetic Retinopathy Patients Detected by Next-Generation Sequencing.Frontiers in pharmacology · 2021Article
- Preparation of optimized concanavalin A-conjugated Dynabeads® magnetic beads for CUT&Tag.PloS one · 2021Article
- TET repression and increased DNMT activity synergistically induce aberrant DNA methylation.The Journal of clinical investigation · 2020Article
- Bioinformatical dissection of fission yeast DNA replication origins.Open biology · 2020Article
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells.Epigenetics & chromatin · 2019Article
- Cux2 refines the forelimb field by controlling expression ofBiology open · 2019Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) can identify genomic regions that bind proteins involved in various chromosomal functions. Although the development of next-generation sequencers offers the technology needed to identify these protein-binding sites, the analysis can be computationally challenging because sequencing data sometimes consist of >100 million reads/sample. Herein, we describe a cost-effective and time-efficient protocol that is generally applicable to ChIP-seq analysis; this protocol uses a novel peak-calling program termed DROMPA to identify peaks and an additional program, parse2wig, to preprocess read-map files. This two-step procedure drastically reduces computational time and memory requirements compared with other programs. DROMPA enables the identification of protein localization sites in repetitive sequences and efficiently identifies both broad and sharp protein localization peaks. Specifically, DROMPA outputs a protein-binding profile map in pdf or png format, which can be easily manipulated by users who have a limited background in bioinformatics.
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