Overview

New ! Human enhancer to target gene assignments (hg19 and hg38): We now include distal enhancer to target gene assignments by combining multiple spatial and in silico approaches for defining enhancer locations and linking them to their target genes, aggregated across >500 cell types. In a comprehensive comparison, this approach was shown to significantly outperform the simple nearest TSS approach. PolyEnrich method is required with these new enhancer to target gene links.
ChIP-Enrich and Poly-Enrich test ChIP-seq peak data for enrichment of biological pathways, Gene Ontology terms, and other types of gene sets. Using an input .BED file, ChIP-Enrich and Poly-Enrich assign peaks to genes based on a chosen "locus definition". The "locus" of a gene is the region from which the gene is predicted to be regulated. ChIP-Enrich uses a logistic regression model to test for association between the presence of at least one peak in a gene and gene set membership, while Poly-Enrich uses a negative binomial regression model to test the association between the number of peaks in a gene and gene set membership. They empirically adjust for the relationship between the length of the loci (and optionally mappability) and the outcome using a cubic smoothing spline term within the logistic model. Detailed methods are provided here. Output includes summary plots, peak to gene assignments,and enrichment (and depletion) results including odds ratio, p-value, and FDR for each gene set.
Broad-Enrich: If your data set consists of broad genomic regions or covers a significant portion of the total genome, we recommend using Broad-Enrich instead.

Run Analysis

Select input file

The following formats are fully supported via their file extensions: .bed, .broadPeak, .narrowPeak, .gff3, .gff2, .gff, and .bedGraph or .bdg. BED3 through BED6 files are supported under the .bed extension. Files without these extensions are supported under the conditions that the first 3 columns correspond to 'chr', 'start', and 'end' and that there is either no header column, or it is commented out.

Analysis Name
Please provide a meaningful name for this analysis (used to name output files).

Email
Please provide your email address if you wish to be notified when the analysis has been completed.

Supported Genomes



Annotation Databases
Selecting multiple, or a large, annotation database may require several minutes of computation time. For approximate Chip-Enrich running times against different databases view this table.

Method
  • Poly-Enrich
    (usually best for >40,000 of genomic regions. This is recommended method to use with distal enhancer-gene target links)
  • Chip-Enrich
    (usually best for 1000's to 10,000's of genomics regions)
  • Hybrid Test
    (get the best of both! ...but longer runtime)
  • ProxReg
    • (This is a proximity test, not an enrichment method
  • Fisher's exact test
    • We recommend using Fisher's Exact test only with the 1kb or 5kb locus definition. Using it with any of the other locus definitions may result in biased enrichment results.

  • Weight peaks by peak strength?
    Input must be .narrowpeak file to use this option. Only available for Poly-Enrich and Hybrid
Which peaks to use and how to link them to target genes (Choose one)
    Promoter regulation choices
  • < 1kb
    (only use peaks within 1kb of a transcription start site)
  • < 5kb
    (only use peaks within 5kb of a transcription start site)
  • < 10kb
    (only use peaks within 10kb of a transcription start site)
    • Gene distal regulation choices
  • > 5kb upstream
    (only use peaks greater than 5kb upstream of a transcription start site)
  • > 10kb upstream
    (only use peaks greater than 10kb upstream of a transcription start site)
  • Distal enhancer-gene target links (> 5kb from TSS)
    (Uses enhancer-target links from from the selected ChIA-PET data, Thurman data and FANTOM5 where available, and gene with nearest TSS for unassigned distal regions. This has been shown to outperform the simple >5kb upstream in most case
    • Regulation from across the whole genome
  • Nearest Gene
    (use all peaks; assign peaks to the nearest gene defined by transcription start and end sites)
  • Nearest TSS
    (use all peaks; assign peaks to the gene with the closest TSS)
  • Distal enhancer-gene target links (> 5kb from TSS) plus 5kb locus definitions
    Use distal peaks (> 5kb from TSS): assign distal enhancer peaks to the target genes or distal non-enhancer peaks to the nearest TSS; and use peaks within 5kb of a TSS (5kb) and assign them to the nearest TSS
    • Other
  • Exon
    (only use peaks that fall within an annotated exon)
  • Intron
    (only use peaks that fall within an annotated itron)
  • User Defined
    (user can input their own locus definition)
Filter Only test gene sets with less than the following number of genes:
Filter value should be numeric and greater than 30.It can be used to remove large, vague gene sets such as "binding".

Adjust for the mappability of the gene locus regions
  • True
  • False
Peak Threshold Number
Number of peaks a gene must have assigned to it before getting coded as 1 (having a peak) in the test. Typically, this should be set to 1.

 


Please reference the following publication when citing Chip-Enrich:
  1. R.P. Welch, C. Lee, R.A. Smith,S. Patil, T. Weymouth, P. Imbriano, L.J. Scott, M.A. Sartor. "ChIP-Enrich: Gene set enrichment testing for ChIP-seq data." NAR. 2014;42(13):e105.
  2. Lee CT, Cavalcante RC, Qin T, Patil S, Wang S, Lee C, Sartor MA. "Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions" NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, link
  3. Lee CT, Wang K, Qin T, Sartor MA. "Testing proximity of genomic regions to transcription start sites and enhancers complements gene set enrichment testing." Front Genet. 2020; 11: 199.
  4. Qin T, Lee C, Cavalcante R, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. “Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.” link

Contact: chipenrich@umich.edu