Some scripts to prepare ontology long table for enrichment and GSEA analysis.

This pipeline requires these dependencies.

python3 -m pip install pandas owlready2 retrying openpyxl

following data require manually download.

• Sitalica_312_v2.2.annotation_info.txt: from JGI Sitalica annotation
• ATH_GO_GOSLIM.txt: from TAIR Download GO_and_PO_Annotations

For TAIR gene search results, in TAIR Gene Search page, use different chromosome as filter, after clicking "Submit Query" bottom and search results displayed, click "Download All" bottom to download result tsv file.

A example of enrichment analysis using clusterProfiler.

install.packages("readxl")
install.packages("BiocManager")
BiocManager::install("clusterProfiler")

term_to_gene = readr::read_tsv("results/oryzabase.RAP_GO.term_to_gene.tsv.gz", col_names=F)
term_to_description = readr::read_tsv("results/oryzabase.RAP_GO.term_to_description.tsv.gz", col_names=F)

gene = c("Os01g0118100", "Os01g0549700", "Os02g0710800", "Os03g0108600", "Os03g0158200", "Os03g0746500")
universe = NULL

enrich_res = clusterProfiler::enricher(
    gene=gene,
    universe=universe,
    TERM2GENE=term_to_gene,
    TERM2NAME=term_to_description
)

write.csv(as.data.frame(enrich_res), "enrich_res.csv")

svg("demo_dotplot.svg")
clusterProfiler::dotplot(enrich_res)
dev.off()