Abstract
BackgroundFunction genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis. While tools have been developed to identify biological functions that are enriched in the genes sets, there remains a need for comprehensive tools that identify functional enrichment of genes for both model and non-model species from a different function classification perspective.ResultsWe developed AllEnricher, a tool that calculates gene set function enrichment, with user-defined updatable libraries backing up for both model and non-model species as well as providing comprehensive functional interpretation from multiple dimensions, including GO, KEGG, Reactome, DO and DisGeNET.ConclusionsAllEnricher incorporates up to date information from different public resources and provides a comprehensive resolution for biologists to make sense out of specific gene sets, making it an advanced open-source tool for gene set function analysis.
Highlights
Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis
We developed a user-defined updatable application, which could be integrated into pipelines of functional genomic studies (RNA-seq, ATAC, BS-seq, etc.) and can be incorporated into the five optimized public gene-function annotation collections (GO, Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, DISEASE, and DisGeNET)
The primary version of AllEnricher had been applied to several in house researches engaged in enrichment analysis of epigenetically modified gene sets and differentially expressed gene (DEG) sets of model species [19,20,21]
Summary
Command line application based on Unix Shell, perl, and R were utilized to develop an easy to use command line application based on Unix environment to calculate gene enrichment of a user-provided gene set. The primary version of AllEnricher had been applied to several in house researches engaged in enrichment analysis of epigenetically modified gene sets and differentially expressed gene (DEG) sets of model species [19,20,21]. We used another two gene sets from previous studies to test AllEnricher. When a DEG set is generated from samples of a specified tissue, where some parts of genes never expressed due to the high differentiation of cells, they should be excluded from the background gene list of enrichment analysis. AllEnricher provides flexible solutions to satisfy the application scenarios of the user-defined background gene list
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