Overview Link Genomic Regions to Target Genes Genomic Region Enrichment Gene Expression Enrichment Reverse Enrichment Testing Combined Enrichment Genomic Regions + Expression

Gene Set Enrichment Suite

Enrichment testing methods for ChIP-seq, RNA-seq, and other sets of genomic regions

Recognizing that gene set enrichment (GSE) for gene regulatory data should not be a one-size-fits-all task, GSEsuite offers a variety of methods, resources, and regulatory definitions to choose from. Don’t know what’s best for you? We’ll help determine that based on properties of your data and your goals.


Link Genomic Regions to Target Genes

Just want to find the target genes for your genomic regions? Upload your set of genomic regions to assign them to target genes based on the selection of regulatory regions, including enhancers, promoters, whole genome, exons, introns, etc. For enhancer to target gene assignments, we use human genome version hg19, however, multiple species and multiple reference genome versions are available for all other regulatory regions. The human enhancer to target gene assignments can be generated by selecting data from a variety of sources and methods.

Genomic Region Enrichment

Upload a set of genomic regions to find out which GO terms, pathways, etc are being regulated. Go through each step to choose the most appropriate enrichment testing method, most appropriate type(s) of regulatory regions (e.g., promoters, enhancers, etc), and the desired gene set databases. If desired, the software will use properties of your data and diagnostic plots to help identify your optimal choices.

Gene Expression Enrichment

Identify enriched pathways, GO terms, etc, from gene expression data. Choose from a number of different methods and gene set databases, and save your results to compare with others. Visualize multiple experimental results together. Includes optional adjustment for read count level with RNA-seq data.

Reverse Enrichment Testing

Query a pathway, GO term or MeSH term to find the set of factors and cell types under which its regulated. We will use the most appropriate method for the queried gene set. Output includes a table and visualizations of the experiments, binding proteins, cell types, enrichment results, and list of genes and locations that are significantly associated with the queried term.

Combined Enrichment Genomic Regions + Expression

If you have gene expression and ChIP-seq data for the same transcription factor or other binding protein, this allows you to do a combined enrichment analysis. The results will tell you which pathways are: bound by the protein and differentially expressed, bound but not differentially expressed (i.e. poised for regulation), differentially expressed only (secondary effects), or neither.

Genomic Region Enrichment

Upload a set of genomic regions to find out which GO terms, pathways, etc are being regulated. Go through each step to choose the most appropriate enrichment testing method, most appropriate type(s) of regulatory regions (e.g., promoters, enhancers, etc), and the desired gene set databases. If desired, the software will use properties of your data and diagnostic plots to help identify your optimal choices. Use "Narrow" for transcription factor data or other regions up to several hundred bps. Use "Broad" for regions multiple kb or larger in length (e.g. for histone ChIP-seq data).

Gene Expression Enrichment

Identify enriched pathways, GO terms, etc, from gene expression data. Choose from a number of different methods and gene set databases, and save your results to compare with others. Visualize multiple experimental results together. Includes optional adjustment for read count level with RNA-seq data.

Visit site



Reverse Enrichment Testing

Query a pathway, GO term or MeSH term to find the set of factors and cell types under which its regulated. We will use the most appropriate method for the queried gene set. Output includes a table and visualizations of the experiments, binding proteins, cell types, enrichment results, and list of genes and locations that are significantly associated with the queried term.

Coming Soon

Combined Enrichment Genomic Regions + Expression

If you have gene expression and ChIP-seq data for the same transcription factor or other binding protein, this allows you to do a combined enrichment analysis. The results will tell you which pathways are: bound by the protein and differentially expressed, bound but not differentially expressed (i.e. poised for regulation), differentially expressed only (secondary effects), or neither.

Coming Soon