Loading custom geneset files¶

GMT (Gene Matrix Transposed) files are a format commonly used in bioinformatics and gene set enrichment analysis (GSEA).

Gene sets are collections of genes that share certain biological characteristics, such as being involved in the same biological pathway or having similar functions. GSEA is a computational method used to determine whether a particular gene set is significantly enriched in a given dataset of gene expression.

In a GMT file, the first column is the geneset name, followed by a description on the second column. Each subsequent column line represents a gene set and consists of a gene set name, and the list of genes belonging to that set. The gene names are typically represented using gene symbols or other identifiers. Each line in a GMT file will correspont to a different geneset.

Download here an example GMT file from genes activated by the transcription factor EGFR: EGFR_TARGET_GENES.v2023.1.Hs.gmt

Tip

If you want to create your own genesets, the easiest way is to download our example GMT file and open it in excel as tab-separated values. The first column is the geneset name (EGFR_TARGET_GENES), followed by any description (can be left empty) or the geneset source website in the second column. Then finally the genes should be listed on the third and following columns (ABCA7, ACTB, etc.). After editing, save the file as a tab-separated values file and change the extension to .gmt.

In Omics playground, GMT files are the backbone of several modules, where we aim to identify enriched gene sets associated with specific biological processes, diseases, or experimental conditions.

You can find the geneset availables in omicsplayground with the R package playbase. First, install playbase with devtools::install_github("omicsplayground/playdata") and then run the command playdata::GSET_INFO.

If you have your own geneset, or you want to include a GMT file from a database, you can upload directly in the Upload module under Options.

See also

If you are working in R, you can add your gmt file to the playbase::pgx.computePGX by providing the custom.geneset argument. custom.geneset argument. That should be a list where the first argument gmt is the gmt file (see playbase::EXAMPLE_GMT), and the second argument is the name of the gmt file.

Building on what we learned in the section Computing PGX , we can add our own geneset to the analysis with the followign call:

filePath <- getwd() # path to gmt file

custom.geneset <- list()

custom.geneset$gmt <- playbase::read.gmt(filePath)

# perform some basic checks
gmt.length <- length(custom.geneset$gmt)
gmt.is.list <- is.list(custom.geneset$gmt)

# clean genesets

custom.geneset$gmt <- list(CUSTOM = custom.geneset$gmt)

# convert gmt to OPG standard
custom.geneset$gmt <- playbase::clean_gmt(custom.geneset$gmt,"CUSTOM")

# compute custom geneset stats
custom.geneset$gmt <- custom.geneset$gmt[!duplicated(names(custom.geneset$gmt))]
custom.geneset$info$GSET_SIZE <- sapply(custom.geneset$gmt,length)

# pass the custom.geneset as argument to pgx.computePGX
pgx <- playbase::pgx.computePGX(
    pgx = pgx,
    custom.geneset = custom.geneset
)