Massive epigenome mapping projects have led to a deluge of data that eager epigeneticists can’t wait dive into, but it’s not quite that simple. It’s no easy feat to learn about the best places to download, view or manipulate epigenomic data, much less understand the tidal wave of information once you’ve found it. It’s all a little like trying to sip water from a fire-hose, which is why we got together with Lisa Chadwick at NIH, who helped us put together a list of online tools available for browsing epigenomes, in order to make selecting the right one an easier job.
Each of the different resources was compared based on various features (summarized in a table below), take a look.
Downloading Epigenome Data to Your Server
In almost all cases, this option is available. But there are several different methods (ftp or htp) and file formats ( .wig, .bed, .bam ) that the data may come in, so you’ll want to be sure that you’re equipped to deal with that before you begin.
Epigenomic Data Browsing
Each of the tools employs a different data matrix that allows users to select the data set they want to look at by experiment, sample type or other classifications. A couple of sites use UCSC or ENCODE style interfaces, which may be familiar to some scientists.
Viewing the Epigenomes
To view the actual data tracks, most of these sites are using a NCBI Epigenome viewer and/or the UCSC browser, which has been en-vogue in genomics circles for a while now. There are a few other types out there as well, so it’s just a matter of finding one that let’s you do what you need.
Frequency of Epigenetic Data Updates
You definitely don’t want to get stuck crunching through data from some bygone era. Luckily, a few online tools are updated continuously and the rest are refreshed whenever they have a “data freeze”, or an epigenome atlas release, which according to Chadwick currently happens about every 3 months.
Uploading Your Own Epigenomic Datasets
Some, but not all, of these systems will let you submit your own data so that you can view and analyze it, and a handful of others have plans to make that available. Make sure to double-check the site you’re using.
Epigenome Browser Bells and Whistles
These online epigenomics browsers all have nearly identical basic functions, but they also distinguish themselves from each other by including such a wide range of different apps it makes Apple jealous. You can all sorts of features like protocols and publications, sample comparisons, quality metrics, and even GoogleMaps-style pan and zoom viewing.
Summary of Epigenome Browsers
Check out this summary table to find your favorite browser:
||Download Data?||Browse Data||View Data||Updates
||Other Features||Upload Data?|
|Reference Epigenome Mapping Consortium Homepage||Links to data download||Clickable data matrix or visual data browser||Links to UCSC browser mirror (Epigenome Browser)||Data: At each data freeze (4x/year)||Protocols, publications, quality metrics, project and center/group information||No (but linked Epigenome Browser supports upload)|
|NCBI Epigenomics Hub||.wig||Sample (i.e. cell/tissue type) browser, experiment (i.e. epigenetic feature) browser, text search||NCBI epigenomics viewer or UCSC browser mirror||Continuously||“Compare Samples” tool to identify regions of greatest chromatin differences, suggests GO terms and pathways most associated.||Being implemented|
|NCBI Gene Expression Omnibus||.bed, .wig, .bam and SRA||By sample, study, or data matrix||NCBI Epigenomics viewer||Continuously||N/A|
|The Human Epigenome Atlas (on Genboree)||.bed, .wig by ftp or http||By sample, assay, or clickable data matrix||UCSC browser, Atlas Gene/Pathway browser (read densities across single genes or pathways)||At each data freeze||Info on metadata, data flow, data quality. Tools for analysis via Genboree workbench (Independent tools and Galaxy pipelines). Data & functionality exposed via HTTP REST APIs for programmatic use and extension|
|Roadmap Epigenomics Visualization Hub and Load Track Hub||No||ENCODE style data matrix||UCSC browser mirror, or remote display at UCSC main site (load track hub)||At each data freeze||UCSC mirror hosts integrative analysis tracks and summary tracks, tracks viewable at UCSC main site||Being implemented|
|Human Epigenome Browser at Wash U||Yes||Expandable data selection matrix and metadata matrix||Next generation epigenome browser||At each data freeze||Google map style zoom and pan, genomic data and metadata viewer, data collation view, pathway/gene set view, statistical analysis||Yes|
|Epigenome Browser UCSC mirror||.bed, .wig through Table Browser. Individual reads not available||UCSC data selection matrix (ENCODE style)||UCSC browser mirror||At each data freeze||High-utility UCSC mirror tracks||Yes|