PAVIS: a tool for Peak Annotation and Visualization

Bioinformatics. 2013 Dec 1;29(23):3097-9. doi: 10.1093/bioinformatics/btt520. Epub 2013 Sep 4.


We introduce a web-based tool, Peak Annotation and Visualization (PAVIS), for annotating and visualizing ChIP-seq peak data. PAVIS is designed with non-bioinformaticians in mind and presents a straightforward user interface to facilitate biological interpretation of ChIP-seq peak or other genomic enrichment data. PAVIS, through association with annotation, provides relevant genomic context for each peak, such as peak location relative to genomic features including transcription start site, intron, exon or 5'/3'-untranslated region. PAVIS reports the relative enrichment P-values of peaks in these functionally distinct categories, and provides a summary plot of the relative proportion of peaks in each category. PAVIS, unlike many other resources, provides a peak-oriented annotation and visualization system, allowing dynamic visualization of tens to hundreds of loci from one or more ChIP-seq experiments, simultaneously. PAVIS enables rapid, and easy examination and cross-comparison of the genomic context and potential functions of the underlying genomic elements, thus supporting downstream hypothesis generation.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Chromatin Assembly and Disassembly
  • Chromatin Immunoprecipitation*
  • Gene Expression Regulation
  • Genomics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Internet
  • Oligonucleotide Array Sequence Analysis / methods*
  • Sequence Analysis, DNA / methods*
  • Software*