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PAVIS: a tool for Peak Annotation and Visualization - PubMed

  • ️Tue Jan 01 2013

PAVIS: a tool for Peak Annotation and Visualization

Weichun Huang et al. Bioinformatics. 2013.

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.

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Figures

Fig. 1.
Fig. 1.

A pie chart example from PAVIS annotation report

Fig. 2.
Fig. 2.

Illustration of PAVIS visualization explorer. On the top is the navigation control panel with the legend indicating colors for query and comparison peaks. In the middle is the density overview bar of all query peaks on the chromosome, where the red line segment indicates the displayed peaks location. At the bottom are two display windows showing query peaks #177 and #178 and their comparison peaks, respectively

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