ArticleNucleic acids research2014
Optimization of transcription factor binding map accuracy utilizing knockout-mouse models.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- CRISPR-PITA: An Imaging-Based CRISPR/dCas9 Assay to Determine Recruitment Directionality of Nuclear Proteins.Bio-protocol · 2026Article
- Selecting ChIP-seq normalization methods from the perspective of their technical conditions.Briefings in bioinformatics · 2025Article
- Tissue-specific localization of the ING4 targeting subunit of the HBO1 histone acetyltransferase in the cytoplasm and nucleus of secretory cells.Histochemistry and cell biology · 2025Article
- Article
- Motif elucidation in ChIP-seq datasets with a knockout control.Bioinformatics advances · 2023Article
- Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages.The Journal of experimental medicine · 2022Article
- The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
- Gawky modulates MTF-1-mediated transcription activation and metal discrimination.Nucleic acids research · 2021Article
- Genome-Wide Profiling of Protein-DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq ).Methods in molecular biology (Clifton, N.J.) · 2021Article
- Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression.Genome research · 2019Article
- HOT or not: examining the basis of high-occupancy target regions.Nucleic acids research · 2019Article
- A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.Scientific reports · 2017Article
- Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae.Journal of visualized experiments : JoVE · 2017Article
- A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata.Frontiers in microbiology · 2016Article
- Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments.Nucleic acids research · 2015Article
- BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.Epigenetics & chromatin · 2015Article
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
Abstract
Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify 'hyper ChIPable regions' as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.
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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.