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Ulisse - An R package to go beyond the boundaries of gene-sets

Omics assay results in long gene lists whose biological interpretation is a major challenge. Pathway enrichment analysis is used to test whether a pathway is richer in genes of a gene list than what is expected by chance. However, there are no clear boundaries between pathways, such that gene products interact within and between pathways, in a phenomenon called cross-talks. Cross-talks between pathways are relevant to dissect regulatory mechanisms, identify effective drug combinations and investigate complex disease phenotypes. As molecular interactions go beyond cell boundaries, cross-talks (or communication) between different cell-types can be studied thanks to single-cell RNA sequencing technologies.

Ulisse provide the tools to perform:

  • Cross-talk analysis:
    • Gene-set cross-talk
    • Gene-set connected components
    • Gene-Set Topological-Module cross-talk
    • Functional relevance analysis to reconstruct gene role in Gene-set cross-talk analysis in terms of number of interactor genes and processes/cell types involved
  • Gene-set enrichment analysis:
    • ORA (Over Representation Analysis)
    • GSEA (Gene set enrichment analysis)
    • Enrichment map to help interpretation of ORA or GSEA results

Typical application of Ulisse include:

  • Pathway cross-talk analysis of omics data obtained from bulk or single-cell samples
  • Communication analysis between clusters or cell-type in single-cell samples
  • Pathway enrichment analysis of omics data obtained from bulk or single-cell samples

Source code: https://github.com/emosca-cnr/Ulisse

Installation

Ulisse requires R >= 4.0.0, and some Bioconductor packages.

To successfully install Ulisse firstly run

```{r, include=TRUE, eval=FALSE} if (!require(“BiocManager”, quietly = TRUE)){ install.packages(“BiocManager”) } BiocManager::install(c(“DOSE”, “qvalue”, “TCGAbiolinks”, “ComplexHeatmap”, “pander”, “kableExtra”))

devtools::install_github(“emosca-cnr/NPATools”, build_vignettes = TRUE)


The other dependencies, if missing, should be automatically installed using the following command:

```{r, include=TRUE, eval=FALSE}
devtools::install_github("emosca-cnr/Ulisse", build_vignettes = TRUE)

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