EnhancerAtlas 2.0 is a comprehensive database based on 12 independent high throughput experimental technologies from nine species. Here is a brief guide for six advanced search options.
1. Search enhancers by region: By providing a cell/tissue type and a genome region, users are able to identify the enhancers in the region. A graphic presentation will be shown. The “consensus” track summarizes all the information, while the other tracks are the independent experimental datasets for the chosen cell type and the given region.
2. Search enhancers by gene: If users are interested in the enhancers that are associated with a particular gene, users can provide a gene name and a cell type. All the enhancers associated with the gene will be presented in a graph. By clicking “show the details” below the figure, a summary table will be provided. If the gene name provided by the users is ambiguous, several choices will be shown to let users select the right gene of interest.
3. Compare enhancers across cells: Users can also compare the enhancers across multiple cell/tissue types in a given genomic region. Using this search option, users are able to identify conserved or cell type-specific enhancers. If users click on individual cell type in the graph, detailed experimental evidences will be shown for a particular cell type (similar to the first search option).
4. Compare enhancers of gene across cells: Users can also compare the enhancers associated with one gene across various cell types. Using this search option, users are able to identify conserved or cell type-specific enhancers associated with a particular gene.
5. Generate enhancer-gene network: We will also provide cytoscape network presentation between enhancers and associated genes in a given genomic regions and cell type. The interactions that are specific to the cell type or conserved in other cell types are marked with different colors.
6. Predict target genes for genomic regions: If users identify a set of potential cis-regulatory regions (e.g. peaks identified by ChIP-seq of a TF), they could upload the regions in bed format and select cell types that are most relevant to the cell type of interest. The database will compare uploaded regions with the enhancers in the selected cell types and obtain the target genes of the enhancers in these cell types. If some of the uploaded regions are in promoters, the database will also provide the flanking target genes of the regulatory regions.
Tianshun Gao, Bing He, Sheng Liu, Heng Zhu, Kai Tan and Jiang Qian. EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw495.
For any questions about enhancer annotation and database construction, please contact Jiang Qian and Tianshun Gao. For questions about enhancer target gene prediction, please contact Kai Tan and Bing He.