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[Preprint]. 2023 Aug 30:2023.08.28.555198.
doi: 10.1101/2023.08.28.555198.

RichPathR: a gene set enrichment analysis and visualization tool

Binod Regmi  1 , Stephen R Brooks  1 , Andrew J Uhlman  1 , Hong-Wei Sun  1
Affiliations

RichPathR: a gene set enrichment analysis and visualization tool

Binod Regmi et al. bioRxiv. .

Abstract

Gene set enrichment analysis (GSEA) is an important step for disease and drug discovery. Genomic, transcriptomics, proteomics and epigenetic analysis of tissue or cells generates gene lists that need to be further investigated in the known biological context. The advent of high-throughput technologies generates the vast number of gene lists that are up or down regulated together. One way of getting meaningful insights of the relationship of these genes is utilizing existing knowledge bases linking them with biological functions or phenotypes. Multiple public databases with annotated gene sets are available for GSEA, and enrichR is the most popular web application still requiring custom tools for large-scale mining. richPathR package is a collection of R functions that helps researchers carry out exploratory analysis and visualization of gene set enrichment using EnrichR.

Keywords: Jacard’s similarity index; adjacency matrix; heat map; network plot; pathway analysis.

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Figures

Figure 1:
Figure 1:
Pathways/terms presented in the gene sets and libraries.
Figure 2:
Figure 2:
Signifincat pahways/terms extracted for the gene lists.
Figure 3:
Figure 3:
Significant pathways/terms extracted for the gene lists and libraries
Figure 4:
Figure 4:
Hub (high frequency) genes presented in one or multiple gene sets and libraries.
Figure 5:
Figure 5:
Interaction network among terms and genes for the selected terms
See this image and copyright information in PMC

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