In most of the EP-Atlas pages, there is a search bar on the top.

Search by gene symbol or ENSEMBL ID

The search bar can be filled in with gene symbol or ENSEMBL IDs.

Click search to view the example.

By clicking on a gene symbol, users can initiate a query, which leads to a detailed results page where cell-specific enhancer-promoter RNA interactions can be observed.

This image showcases an interactive gene analysis interface designed to investigate the interactions between enhancers and promoters for specific genes across various cell types.

The bar plot shows the bulk tissue gene expression for target gene.

Search by enhancer name

The search bar can be filled in with custom enhancer ID defined in this database.

Click search to view the example.

This figure displays the information of genes regulated by the enhancer after querying by enhancer name.

Search by enhancer region

Users can search using the location information of the enhancer.

Click search to view the example.

This figure shows the enhancer which overlap with the input region and the extension region, with an upstream and downstream extension of 10kb.

By clicking the enhancer name, we could find tissue-specific enhancer interacts with promoter and regulates gene transcription.

We construct the interaction network. See the detailed information on the next table.

We performed an overlap analysis between our identified enhancers and those annotated in the GeneHancer database to assess concordance and validate the enhancer regions.

Concurrently, we incorporated genome-wide association study (GWAS) data to map putative genetic variants located within the enhancer regions and to retrieve trait associations corresponding to these variants.

To explore post-transcriptional regulatory interactions, we analyzed CLIP-seq data from the ENCODE database and identified RBP binding sites overlapping enhancer and promoter regions.

The Statistics interface displays key summary statistics of the dataset, helping users understand the overall data distribution and trends.

Here, we show the counts of typical enhancers, super-enhancers, and promoters identified across different cell lines.

Here we compare our identified enhancers with those from other databases to highlight the consistency and reliability of our results.

We first quantified the distribution of enhancers based on the number of associated promoters.

We then quantified the distribution of promoters based on the number of associated enhancers.

All interaction data can be freely downloaded, from the Download & API page .

We also offered the enhancer and promoter region used in this database.

The EP-Atlas database offered the API interface to search.

The detailed information can be viewed on the Download & API page.

The author's contact information and address are on the contact page.