Broad Enrich

Broad-Enrich: gene set enrichment testing for sets of broad genomic regions
Overview
Broad-Enrich tests sets of broad genomic regions (e.g., from ChIP-seq data for histone modifications or copy number variations) for enriched biological pathways, Gene Ontology terms, or other gene sets. The pre-defined gene sets are the same as used in LRpath, and can be browsed here. Using an input .bed, .narrowPeak or.broadPeak file, Broad-Enrich determines the proportion of each gene locus covered by a peak, using a chosen "gene locus definition". The "locus" of a gene is the region from which the gene is predicted to be regulated. Broad-Enrich uses a logistic regression model to test for association between the proportion of each gene locus covered by a peak and gene set membership. It empirically adjusts for the bias due to locus length using a binomial cubic smoothing spline 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 is also available as part of the Chip-Enrich R package: Broad-Enrich.zip
Vignette: pdf

Select input file

Input file should be a standard .bed,.narrowPeak or.broadPeak file containing at least three columns: (1) chromosome (of the form "chr3") (2) start position, and (3) end position. Additional columns will be ignored.

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

Email
Please provide your email address to be notified when the analysis is complete.

Supported Genomes



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

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".

Locus Definition
  • 1kb
    (only use peaks within 1kb of a transcription start site)
  • 5kb
    (only use peaks within 5kb of a transcription start site)
  • Exon
    (only use peaks that fall within an annotated exon)
  • 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)
  • User Defined
    (user can input their own locus definition)
Adjust for the mappability of the gene locus regions
  • True
  • False
 



Reference
Please reference the following publication when citing Broad-Enrich:

1 Cavalcante RG, Lee C, Welch RP, Patil S, Weymouth T, Scott LJ and Sartor MA. "Broad-Enrich: Functional interpretation of large sets of broad genomic regions." Bioinformatics. 2014; (accepted).

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Copyright 2013 The University of Michigan
Developed under the support of the NIH/NCI
Grant # R01-CA158286-01A1
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