ArticlePloS one2011
An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.
Article in PloS one, 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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Who cites it
26 citing papers in PubMed.
- The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes.BMC bioinformatics · 2024Article
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Nucleic acids research · 2024Article
- CRMnet: A deep learning model for predicting gene expression from large regulatory sequence datasets.Frontiers in big data · 2023Article
- Dynamic transcriptome analysis reveals signatures of paradoxical effect of vemurafenib on human dermal fibroblasts.Cell communication and signaling : CCS · 2021Article
- MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs.Bioinformatics (Oxford, England) · 2020Article
- The Identification and Interpretation ofHigh-throughput · 2018Review
- Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.Nucleic acids research · 2018Article
- Integrated analysis of motif activity and gene expression changes of transcription factors.Genome research · 2018Article
- Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production.Frontiers in bioengineering and biotechnology · 2018Review
- Maser: one-stop platform for NGS big data from analysis to visualization.Database : the journal of biological databases and curation · 2018Article
- Shifting transcriptional machinery is required for long-term memory maintenance and modification in Drosophila mushroom bodies.Nature communications · 2016Article
- Evaluating tools for transcription factor binding site prediction.BMC bioinformatics · 2016Article
- Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis.BMC bioinformatics · 2016Article
- Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.Epigenetics & chromatin · 2016Article
- Article
- Jmjd3-Mediated H3K27me3 Dynamics Orchestrate Brown Fat Development and Regulate White Fat Plasticity.Developmental cell · 2015Article
- Differential effects of STAT proteins on growth hormone-mediated IGF-I gene expression.American journal of physiology. Endocrinology and metabolism · 2014Article
- HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.BMC bioinformatics · 2014Article
- DNA methylation contributes to natural human variation.Genome research · 2013Article
- Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
ChIP-Seq has become the standard method for genome-wide profiling DNA association of transcription factors. To simplify analyzing and interpreting ChIP-Seq data, which typically involves using multiple applications, we describe an integrated, open source, R-based analysis pipeline. The pipeline addresses data input, peak detection, sequence and motif analysis, visualization, and data export, and can readily be extended via other R and Bioconductor packages. Using a standard multicore computer, it can be used with datasets consisting of tens of thousands of enriched regions. We demonstrate its effectiveness on published human ChIP-Seq datasets for FOXA1, ER, CTCF and STAT1, where it detected co-occurring motifs that were consistent with the literature but not detected by other methods. Our pipeline provides the first complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip 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.