parentalNapaVsDMSOEnrichment: The result of an enrichment analysis has been done using the...

In adeschen/gprofiler2cytoscape: From functional enrichment results to biological networks

The result of an enrichment analysis has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.

Description

The enrichment analysis was done with gprofile2 package (Kolberg L et al 2020) with database version 'e109_eg56_p17_1d3191d' and g:SCS multiple testing correction method applying significance threshold of 0.05 (Raudvere U et al 2019). All tested genes were used as background.

Usage

data(parentalNapaVsDMSOEnrichment)

Format

a list created by gprofiler2 that contains the results from the enrichment analysis:

• "result": a data.frame with the significantly enriched terms

• "meta": a list with the meta-data information

Details

The object is a named list with 2 entries. The 'result' entry contains a data.frame with the enrichment analysis results and the 'meta' entry contains metadata information.

The dataset used for the enrichment analysis is associated to this publication:

Froeling F.E.M. et al.Bioactivation of Napabucasin Triggers Reactive Oxygen Species–Mediated Cancer Cell Death. Clin Cancer Res 1 December 2019; 25 (23): 7162–7174

The enrichment analysis has been done with gprofile2 package (Kolberg L et al 2020) with database version 'e109_eg56_p17_1d3191d' and g:SCS multiple testing correction method applying significance threshold of 0.05 (Raudvere U et al 2019). All tested genes were used as background.

Value

a list containing 2 entries:

• "result": a data.frame with the significantly enriched terms

• "meta": a list with the meta-data information

Source

The original RNA-sequencing data is available at the Gene Expression Omnibus (GEO) under the accession number GSE135352.

See Also

• createNetwork for transforming functional enrichment results from gprofiler2 into a Cytoscape network

• createEnrichMap for transforming functional enrichment results from gprofiler2 into an enrichment map

Examples

## Loading dataset containing the results of the enrichment analysis 
## done on a differentially expressed 
## analysis between 2-hour treatment with 0.5 uM napabucasin and 
## DMSO vehicle control parental MiaPaCa2 cells
data(parentalNapaVsDMSOEnrichment)

## Create an enrichment map for the GO:CC terms
createEnrichMap(gostObject=parentalNapaVsDMSOEnrichment, 
    query="parental_napa_vs_DMSO", source="GO:CC")

adeschen/gprofiler2cytoscape documentation built on Nov. 4, 2024, 3:16 p.m.