FunChIP: An R/Bioconductor package for functional classification of ChIP-seq shapes

Alice C.L. Parodi, Laura M. Sangalli, Simone Vantini, Bruno Amati, Piercesare Secchi, Marco J. Morelli

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein- DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: After approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a kmean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity.

Original languageEnglish
Pages (from-to)2570-2572
Number of pages3
JournalBioinformatics
Volume33
Issue number16
DOIs
Publication statusPublished - Jan 1 2017

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Transcription factors
Chromatin Immunoprecipitation
Chromatin
Fibroblasts
Clustering algorithms
Splines
Sequencing
Cluster Analysis
DNA
Visualization
Pipelines
Genes
Inspection
Proteins
Cubic B-spline
Transcription Factors
K-means
Genome
Transcription Factor
Clustering Algorithm

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Parodi, A. C. L., Sangalli, L. M., Vantini, S., Amati, B., Secchi, P., & Morelli, M. J. (2017). FunChIP: An R/Bioconductor package for functional classification of ChIP-seq shapes. Bioinformatics, 33(16), 2570-2572. https://doi.org/10.1093/bioinformatics/btx201

FunChIP : An R/Bioconductor package for functional classification of ChIP-seq shapes. / Parodi, Alice C.L.; Sangalli, Laura M.; Vantini, Simone; Amati, Bruno; Secchi, Piercesare; Morelli, Marco J.

In: Bioinformatics, Vol. 33, No. 16, 01.01.2017, p. 2570-2572.

Research output: Contribution to journalArticle

Parodi, ACL, Sangalli, LM, Vantini, S, Amati, B, Secchi, P & Morelli, MJ 2017, 'FunChIP: An R/Bioconductor package for functional classification of ChIP-seq shapes', Bioinformatics, vol. 33, no. 16, pp. 2570-2572. https://doi.org/10.1093/bioinformatics/btx201
Parodi, Alice C.L. ; Sangalli, Laura M. ; Vantini, Simone ; Amati, Bruno ; Secchi, Piercesare ; Morelli, Marco J. / FunChIP : An R/Bioconductor package for functional classification of ChIP-seq shapes. In: Bioinformatics. 2017 ; Vol. 33, No. 16. pp. 2570-2572.
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