USAGE

scEnhancer is a single-cell database with enhancer/gene annotation from 735 clustered tissue/cell types in three species. Based on the features of single cell enhancers or enhancer-gene interactions, a user-friendly platform with six useful modules for searching, visualizing, and browsing are designed.

1. Search single cell enhancers by region: By providing a cell/tissue type and a genome region, users are able to identify the enhancers in the region.

2. Search single cell 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 table. By clicking single enhancer, 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 single cell enhancers across tissue/cell types: 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 tissue/cell types: 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. Predict target genes for genomic regions in single cell level: We will provide a table to present identified enhancers and promoters of genes in tissue/cell types. .

6. Display the differences among tissue/cell types by enhancer clustering: If users select some tissue/cell types that are most relevant to the cell type of interest in the platform, the database will display the differences among selected tissue/cell types .

6. Identification of tissue/cell type-specific enhancers at the single-cell level: If users select a main cell type where the specific enhancers will be identified and the reference cell types to be compared with, the database will search and give the results. Moreover, it will display the specificity of the top three enhancers. .