CEpBrowser (Comparative Epigenome Browser) is a gene-centric genome browser that visualize the genomic features of multiple species with color-coded orthologous regions, aiding users in comparative genomic research. The genome browser is adapted from UCSC Genome Browser and the orthologous regions are generated from cross-species lift-over pairs.
To use Comparative EpiGenome Browser, just select the wanted species and look the gene in interest up in the gene query panel. CEpBrowser will try to automatically complete your entry if possible. If there are more than one genes that match the query, the location, gene name and all other genes in the ortholog group will be shown in gene information panel and can be visualized via the button.
In visualization of genes, a split vision of all the selected species is shown and regions that are orthologous within a gene contextual region will be shaded in color. A "gene context" is defined by a region including gene body and the flanking regions with a length of 10kbp or 100% of gene body (whichever is larger). There are a total of 16 colors in the shades and the regions with the same color (lighter and darker colors are different) are within the same orthologous group. The visualization can be navigated in synchronization for all the species via the navigation panel.
In the cases when there are more than 16 distinct orthologous regions within one gene context, a track named "Multi-species Alignment Track" will display the name of every orthologous region group to identify the orthologs across species. The track will also show the direction of orthologous regions.
Click here to read a detailed manual.
CEpBrowser now has incorporated ENCODE data to help facilitate in-depth research. Please visit http://encode.cepbrowser.org/ to enable ENCODE data. Click here for a demonstration of CEpBrowser with ENCODE data.
Feedback and Citation
Your support is very important to this project and we welcome your feedback! Please tell us how you think about CEpBrowser, what feature you would like to have, or any other thoughts by clicking here and filling the feedback form. You may contact us by sending an email to Xiaoyi Cao (x9cao at ucsd dot edu). We appreciate your support very much!
Also, if you find CEpBrowser helpful in your project, please cite the following publication to support future development:
Cao X, Zhong S. (2013) Enabling Interspecies Epigenomic Comparison with CEpBrowser. Bioinformatics, 29(9): 1223-1225.
(Older release notes)