Download & API

Download

All the enahncer RNA-promoter RNA interaction data in EP-Atlas database can be downloaded.

File name Enhancer Promoter Whole Enhancer-Promoter RNA Interactome
H1 hESC H1-hESC_enhancer H1-hESC_promoter H1-hESC_interactome
A549 A549_enhancer A549_promoter A549_interactome
HeLa HeLa_enhancer HeLa_promoter HeLa_interactome
GM12878 GM12878_enhancer GM12878_promoter GM12878_interactome
HT29 HT29_enhancer HT29_promoter HT29_interactome
IMR90 IMR90_enhancer IMR90_promoter IMR90_interactome
HepG2 HepG2_enhancer HepG2_promoter HepG2_interactome
K562 K562_enhancer K562_promoter K562_interactome
hNPC hNPC_enhancer hNPC_promoter hNPC_interactome
HEK293T HEK293T_enhancer HEK293T_promoter HEK293T_interactome

Download file formats

The following are the details of each column. Here is the detailed information of enhancer RNA and promoter RNA interactome:

  • 1
    Chr: The name of the chromosome.
  • 2
    Start: The zero-based starting position of the interacting region on chromosome.
  • 3
    End: The one-based ending position of interacting region on chromosome.
  • 4
    ENSG: Ensembl Gene ID.
  • 5
    Gene_id: Gene symbol.
  • 6
    Gene type: Genomic context of the interaction region.
  • 7
    Strand: The strand for the gene. Either '+' or '-'.
  • 8
    Promoter chr: The name of the chromosome.
  • 9
    Promoter chr start: The zero-based starting position of promoter.
  • 10
    Promoter chr end: The one-based ending position of promoter.
  • 11
    Promoter_id: Promoter ID used in this database.
  • 12
    Enhancer chr: The name of the chromosome.
  • 13
    Enhancer chr start: The zero-based starting position of enhancer.
  • 14
    Enhancer chr end: The one-based ending position of enhancer.
  • 15
    Enhancer_id: Enhancer ID used in this database.
  • 16
    Reads count: Through Monte Carlo simulation, obtained the high confidence reads.
  • 17
    P-value: Statistical significance of the interaction.
  • 18
    Cell line: Cell line of the detected interaction.
  • 19
    Methods: The method for detecting this interaction.
API usage

Search by gene symbol

  https://epatlas.cn/search/%3F?geneSymbol=SOX2

  • geneSymbol = The gene symbol that the user wants to search, also support the ENSEMBL ID.

Search by enhancer name

  https://epatlas.cn/search_enhancer_name/%3F?cell_line=GM12878&enhancer_type=TE&enhancer_number=9310

  • Cell line = 10 different cell lines above.
  • Enhancer type = Typical enhancer (TE) or super enhancer (SE).
  • Enhancer number = The enhancer serial number in this database.

Search by enhancer region

  https://epatlas.cn/search_enhancer_region/%3F?enhancer_chr=chr6&enhancer_start=116406458&enhancer_end=116412470

  • Enhancer chromosome
  • Enhancer start
  • Enhancer end