Background
- g:GOSt
- performs functional enrichment analysis on an input gene list. It
maps genes to known functional information sources and detects
statistically significantly enriched terms. Data is regularly retrieved
from Ensembl database and fungi, plants or metazoa specific versions of
Ensembl Genomes, and parasite specific data from WormBase ParaSite. In
addition to Gene Ontology, pathways from KEGG Reactome and WikiPathways
are included; miRNA targets from miRTarBase and regulatory motif matches
from TRANSFAC; tissue specificity from Human Protein Atlas; protein
complexes from CORUM and human disease phenotypes from Human Phenotype
Ontology. g:GOSt supports close to 500 organisms and accepts hundreds of
identifier types.
- GO hierarchy
- MF = molecular function
- BP = biological process
- CC = celular component
Setup
# load package
library(gprofiler2)
# read gene list
up <- read.table("../../results/meninges_1CPM_in_12_samples/DEGs/metascape_input_upregulated_FDRq_0.05.tsv")
up <- up$V1
down <- read.table("../../results/meninges_1CPM_in_12_samples/DEGs/metascape_input_downregulated_FDRq_0.05.tsv")
down <- down$V1
Gene list functional enrichment
Up-regulated genes
# query
gost.up <- gost(query = up,
organism = "hsapiens",
ordered_query = TRUE)
# plot
gostplot(gostres = gost.up, capped = FALSE)
# save results
#publish_gosttable(gostres = gost.up)
Down-regulated genes
gost.down <- gost(query = down,
organism = "hsapiens",
ordered_query = TRUE)
gostplot(gostres = gost.down, capped = FALSE)