The Comparative Epigenome Browser

Landing page

The WashU Comparative Epigenome Browser is a valuable resource for scientists studying comparative genomics and epigenomics. The browser is available at http://comparativegateway.wustl.edu/. It allows users to easily select and compare multiple assemblies from different species.

  • Click “select genomes” on the page to begin. A few examples are available as “showcases”, and video tutorials are available on the “tutorials” page:

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Select a reference genome and one or more secondary genomes

After clicking “select genomes”, the species selection tool will become available for users to choose a reference genome. Next, users can select one or multiple species to compare to the reference. For species with multiple assemblies available, we marked one assembly with a “>” as the recommended assembly based on genome completeness and genome-alignment availability.

  • The WashU Comparative Epigenome Browser uses a selected reference genome to compare other genomes. Available assemblies can be found in the dropdown menu:

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  • After selecting the reference genome, users can select available secondary genome(s). In the following example, after selecting hg38 as the reference genome, both mm10 and panTro6 are selected as secondary genomes:

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  • With all the desired genomes selected, click “save selection” and a temporary datahub link will be generated. Once it is ready, click the datahub link under “OPEN IN WASHU EPIGENOME BROWSER” and a new browser view will be opened in a new tab:

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Organizing tracks on the WashU Epigenome Browser

The new browser tab contains basic annotation tracks of the reference genome and the selected genome-align tracks that connects the syntenic regions from the reference genome to the secondary genomes. In the example, hg38-mm10 and hg38-panTro6 genome-align tracks are attached to the hg38 reference genome tracks:

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To add annotations to the secondary genomes, click “Tracks” -> “Annotation tracks” and the available annotation tracks will be listed in a dropdown menu. Click the checkbox to add a particular track to the browser view:

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Here, we added Refseq gene annotations for both mm10 and panTro6, and both gene annotation tracks will be added to the bottom of the browser view. To change the order of the tracks, click the “Reorder tool” icon on the tools menu:

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Now drag the tracks up and down to the desired position, as shown here:

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Add data tracks to the Comparative Epigenome Browser

Add new tracks to the Comparative Epigenome Browser

With genome-align track loaded, we can start loading additional data tracks onto it and perform analysis. Here, we have human genome hg38 as the reference genome, mouse mm10 as the secondary genome. We also have gene and repeat annotations mapped to both genomes:

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Now, we can start loading our data. We can load our data from the local file system or from a URL. Let’s start by loading our data from the URL. Click Tracks -> remote Tracks: We are using a human liver RNA-seq data from ENCODE (https://www.encodeproject.org/files/ENCFF861FSP/@@download/ENCFF861FSP.bigWig) in the demo. We will specify the “Track type” as “bigWig”, enter the URL in the “Track file URL” entry, name the track using “Track label” entry, and select “hg38” as the assembly to map to.

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Next, let’s load our data from the local file system. Click Tracks -> Local Tracks: The track file is downloaded from ENCODE (https://www.encodeproject.org/files/ENCFF798FMB/@@download/ENCFF798FMB.bigWig) and renamed MouseLiverRNA-seq.bigWig. We will choose “bigWig” as the track file type, and choose “mm10” as the assembly it will map to. Click “Choose Files” to select the file.

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Now, we have liver RNA-seq data from both human and mouse, mapped to hg38 and mm10 respectively, loaded at the bottom of the window ready to compare:

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Organizing all the tracks in the browser

To better compare the data, we can reorder the tracks. Here, we will group the tracks by species and have them separated by the genome-align track. Click the “Reorder tool”, and drag the “Human liver RNA-seq” track above the genome-align track:

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After reordering, the human track is between the human repeatMasker track and the hg38-mm10 genome-align track:

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Using tools to zoom in and out

We built a “tools” bar at the top of the browser window to allow users to perform some basic operations within the browser. There are different buttons to zoom in or out with different resolutions or pan left/right. For example, to zoom out one time, click the “-1” button:

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It is possible to zoom into a selected region using the “Zoom-in tool”. Click the “Zoom-in tool”, then click and drag over the region you want to zoom to:

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To zoom into the SPP2 gene’s promoter region, click and drag over the regions that covers the promoter and the first extron of SPP2:

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Now, the browser displays the comparison between human SPP2 gene’s promoter region with the orthologous Spp2 gene promoter in mouse, with gene annotation, repeat annotation and liver RNA-seq data tracks from both species mapped to the hg38 and mm10, respectively:

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