Handout for WashU EpiGenome Browser Tutorial

Bold blue text represents browser functions, such as facet table or matplot.

Bold purple text represents browser buttons, Tracks, and Apps.    


       Bold gray text represents browser menus accessed by right-click on a track, track name, or colormap block, such as Configure or Information.

Topics and definitions are numbered or bulleted. To follow along with the demo, follow the instructions at the ➽ arrows.

Follow the demo as depicted in the screen shots. Places to click are marked with red circles. Circled numbers (e.g.      ) denote the order to click. Screen shots are ordered by bracketed letters (e.g. [A] and [B]) as necessary.

To start again at any point, load the saved session status for the section just completed, indicated by the ✰ and green highlighted-text.

This tutorial has 12 demos:

[1-3] Loading the EpiGenome Browser and public data hubs

[4-5] Exploring Metadata

[6] Genome navigation

[7] Sessions

[8-9] Track visualization & customization

[10] Adding new tracks

[11] Using EpiGenome Browser apps

[12] Loading human genetic variation tracks

Loading the EpiGenome Browser and public data hubs

  1. To access the Browser, go to epigenomegateway.wustl.edu/browser. Browse the menu to select the genome you want to use.

  1. Load the public data hub.

  1. Orientation to the Wash U Epigenome browser view.

Exploring Metadata

  1. Use the colormap panel and information box to find metadata terms associated with tracks.
  1. The information box for each track displays metadata terms associated with that track and information about the experiment that generated that track.


[A]                                                                                  [B]

  1. The colormap organizes metadata terms for quick display.


[A]                                              [B]                                             [C]

  1. The facet table is an intuitive way to browse large amounts of data by using metadata to stratify datasets.

Genome navigation

  1. Genome navigation in the Wash U EpiGenome browser.


  1. The sessions app allows you to save a browsing status to revisit later. Each session can have several versions.


[A]                                                                      [B]


Track visualization & customization

  1. Track navigation & customization is processed by right-clicking a track to enter the Configure menu.


[A]                                                                             [B]

  1. Use the matplot feature to compare two numerical tracks on the same y-axis scale.


[A]                                                                      [B]

Adding new tracks

  1. Use the dataset search box to find data sets using keywords.


[A]                                                               [B]

Using EpiGenome Browser apps

  1. Use applications found in the browser’s Apps menu to generate quantitative tests of our hypothesis.
  1. The Gene set app allows the user to submit a list of genes or genomic positions to the browser for analysis.



[C] Configure the gene set region:



  1. To test the hypothesis that the DNase hypersensitivity regions are proximal enhancers, we will use the Scatterplot app to plot DNase vs H3K4me1 signal in the keratinocyte sample.




  1. Last use the Gene plot app to quantify the RNA signal over SPRR genes in both cell types.







Loading human genetic variation tracks

  1. View human genetic variation tracks in the EpiGenome Browser.



[B]                                                                   [C]