ArticleGenome biology2014
MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Altered Chromatin States Drive Cryptic Transcription in Aging Mammalian Stem Cells.Nature aging · 2021Article
- Multi-Omics Model Applied to Cancer Genetics.International journal of molecular sciences · 2021Review
- A flexible ChIP-sequencing simulation toolkit.BMC bioinformatics · 2021Article
- Genome-wide shifts in histone modifications at early stage of rice infection with Meloidogyne graminicola.Molecular plant pathology · 2021Article
- F-Seq2: improving the feature density based peak caller with dynamic statistics.NAR genomics and bioinformatics · 2021Article
- WACS: improving ChIP-seq peak calling by optimally weighting controls.BMC bioinformatics · 2021Article
- Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements.BMC bioinformatics · 2021Article
- RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data.Quantitative biology (Beijing, China) · 2020Article
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3 authors.
Funding
Abstract
We present MUSIC, a signal processing approach for identification of enriched regions in ChIP-Seq data, available atmusic.gersteinlab.org. MUSIC first filters the ChIP-Seq read-depth signal for systematic noise from non-uniformmappability, which fragments enriched regions. Then it performs a multiscale decomposition, using median filtering, identifying enriched regions at multiple length scales. This is useful given the wide range of scales probed in ChIP-Seq assays. MUSIC performs favorably in terms of accuracy and reproducibility compared with other methods.In particular, analysis of RNA polymerase II data reveals a clear distinction between the stalled and elongating forms of the polymerase.
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