RegRegSEA

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Upload your differential analysis results (DMRs or ATAC peaks) and configure parameters to run regulatory region set enrichment analysis.

Upload Data File

Select your data file Accepted formats: CSV, TSV, TXT, BED, Excel (.xlsx, .xls)

Required Columns

Your file must contain the following information:

Genomic Coordinates: Chromosome, start position, end position for ALL tested regions (background)
Effect Size: Measure of difference (log fold change, beta coefficient, mean difference)
Statistical Significance: Raw p-values (not FDR-adjusted)

Example formats:

DMR analysis: chr, start, end, stat, pval
ATAC-seq: seqnames, start, end, log2FoldChange, pvalue

Analysis Configuration

Column Mapping

Select which columns in your file correspond to each required field:

Chromosome Column e.g., chr, chromosome, seqnames

Start Position e.g., start, pos

End Position e.g., end

Effect Size e.g., stat, log2FoldChange, beta, diff

P-value e.g., pvalue, pval, p_value

Regulatory Region Set Databases

Reference Genome

Select the genome build your input coordinates are based on

Coordinate liftover: Your coordinates will be automatically lifted to (UCSC chain) before analysis. Regions that cannot be mapped are dropped; multi-mapping regions keep their first hit.

Databases

UniBind TFBSs

Robust Collection

Permissive Collection

LOLA Region Databases

Select collections to include:

ENCODE TFBS Transcription Factor Binding Sites from ENCODE

CODEX CODEX database

Cistrome ChIP-seq data of TFs and other DNA-binding proteins

Cistrome Epigenome ChIP-seq data of histone modifications

Sheffield DNase Tissue-clustered DNase hypersensitive sites

UCSC Features CpG islands, etc.

ENCODE TFBS Transcription Factor Binding Sites from ENCODE

CODEX CODEX database

UCSC FeaturesCpG islands, etc.

JASPAR Motif Matches

Select databases and collections for RegRegSEA

Analysis Parameters

Genomic Coordinate Indexing

BED -> probably 0-based, R -> probably 1-based

Minimum Overlap (bp)

Minimum base pairs overlap required to count a DB hit

Upload a file to begin

Configuration options will appear after file upload and validation

OR

View Example Results Download Example Input Data

Using the WGBS-seq data from Laufer et al., 2019