Upload Files for Analysis

Welcome to the Epromoter Clustering Tool

A tool to predict gene clustering regulation by Epromoters.

Upload your data files and configure analysis parameters.

Clustering Method
This name will be used to identify your analysis in results and dashboard
Required Files
Choose the appropriate genome version for your data
TSV/CSV format file, max 100MB
BED, BEDGraph, narrowPeak, broadPeak, GFF, or GTF format file, max 100MB
Analysis Parameters
Recommended: 1000 bp
Recommended: 1000 bp
Recommended: 100000 bp
Help & Guidelines

Distance-based Clustering

Groups genes based on their genomic distance. Suitable for identifying local gene clusters.

TAD-based Clustering

Uses Topologically Associating Domains to group genes. Better for capturing 3D genome organization.

Sample Files
Distance-based Example:
TAD-based Example:
Recommended Parameters
  • RefSeq Version: hg19
  • TSS Upstream: 1000 bp
  • TSS Downstream: 1000 bp
  • Cluster Distance: 100000 bp
  • Induced Condition: TNFa

These sample files contain ChIP-seq and expression data from a TNFα stimulation study in endothelial cells. You can use them to test the analysis pipeline with the recommended parameters.

RefSeq File (BED)
chr1  1000  2000  gene1
Expression File (TSV)
geneID  log2FC
gene1  2.50
gene2  1.21
Peak File (BED/BEDGraph/narrowPeak/broadPeak/GFF/GTF)
chr1  1000  2000  (peak1)

Supports multiple genomic formats including BED, BEDGraph, narrowPeak, broadPeak, GFF, and GTF

TAD File (BED/BEDGraph/GFF/GTF)
chr3  5639  5705  (tad1)

Supports BED, BEDGraph, GFF, and GTF formats

TSS Region

Define the region around the Transcription Start Site (TSS) to be analyzed.

  • Upstream: 1000 bp recommended
  • Downstream: 1000 bp recommended
Cluster Distance

For distance-based clustering, determines maximum distance between genes in a cluster.

  • 100000 bp recommended
  • Smaller values: tighter clusters
  • Larger values: broader clusters