MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework

Genome Biol. 2014;15(10):474. doi: 10.1186/s13059-014-0474-3.

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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Chromatin Assembly and Disassembly
  • Chromatin Immunoprecipitation / methods*
  • Gene Expression
  • Humans
  • K562 Cells
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • Reproducibility of Results
  • Sequence Analysis / methods

Substances

  • RNA Polymerase II