PAVIS: a tool for Peak Annotation and Visualization

Abstract

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.

Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation

“…ChIP-seq signal track was visualized by the Integrative Genomics Viewer (IGV) (32,33). Peak location data was annotated by PAVIS (34). …”

Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9

“…All datasets were aligned to human reference sequence GRCh37/hg19 and annotated with corresponding UCSC genes (RRID:SCR_005780) and Ensembl genes/transcripts (RRID:SCR_002344) (Huang et al, 2013; Rosenbloom et al, 2015; Yates et al, 2016; Yu et al, 2015). Statistically significant overlap between gene sets were calculated using the Fisher’s exact test based on the hypergeometric distribution through the R package GeneOverlap (Shen, 2013).…”

FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis

“…Samples were sequenced using Illumina HiSeq, and raw reads were mapped to human reference genome (hg19). Peaks were selected using MACS in Galaxy and annotated with PAVIS (Huang et al, 2013; Langmead et al, 2009; Zhang et al, 2008). Datasets were analyzed in Galaxy and mapped to genes using PAVIS, with −5000 to +1000 TSS windows.…”