Help / Tutorial

Overview

This visualizer has two main panels:

• Plots (Right Panel): Contains two subplots:
  • Activity Data Plot — displays MPRA activity data in different formats based on selections in the left panel.
  • Genome Plot — shows the genome region with a range slider for exploration, zooming, and panning.

  You can zoom and pan using mouse scroll or built-in controls. Activity values may be positive or negative depending on the strand of each tile, to improve visualization clarity.

• Panel of Options (Left Panel): Used to customize the visualizations and filter data.

Panel of Options (Left Panel)

Virus Selection

Select one dsDNA virus from the following families:

• Adenovirus
• Papillomavirus (HPV-5 not available yet)
• Polyomavirus
• Herpesvirus (largest genomes)

Multibutton Selections

Plot Options

Tile Plot Type

Select one of three visualization types:

• Line: Connects tiles according to the "Connect By" option. Shows activity on the y-axis aligned with genomic positions. Note: "Color By" is disabled for this view.
• Bar: Represents each tile as a 200 nt wide bar. Bars are stacked in tracks to avoid overlap and improve readability.
• Dot: Displays tiles as scatter points positioned by genome location and activity value.

Connect By

Available only for the Line plot. Determines how tiles are connected:

• Strand (default): connects tiles at the top or bottom depending on the strand.

• Cell Line: connects tiles grouped by selected cell lines.

Color By

Available for Bar and Dot visuals. Tiles are colored according to:

• Cell Line
• CREs Class
• Strand
• Activity (only for Bar plot): uses a continuous color scale representing activity values.

Scale

Choose the scale for activity values:

• Linear
  
• Log₂(activity + 1) — useful to compress large value ranges and highlight subtle differences.
  

Filter by Activity

Set a threshold value and click "Apply Filter" to display only tiles with activity values meeting the criteria.

Before (0)

After (3)

Genes Strand Annotation

Toggle this checkbox to display genes from the + strand at the top and genes from the − strand at the bottom of the genome plot.

Before

After

Additional Notes

• Hovering over any tile shows detailed information: ID, Cell line, genome position, strand, and activity value.
• Clicking a tile from the K562 cell line opens a panel with:
  • A sequence logo plot from mutagenesis assay data.
  • The tile's nucleotide sequence, which can be copied manually or using the copy-to-clipboard button.