1. Gene ID <---> Gene SYMBOL

Are you frustrated :confounded: always having to track down the conversion for ENSEMBL GENE ID and GENE SYMBOL in your dataset?! Try this trick :exploding_head: to convert GENE IDs and GENE SYMBOLs in the gastrulation dataset.

Conveniently, the gastrulation dataset has both the ENSEMBL GENE ID and the corresponding GENE SYMBOL already embedded in the sce object! Here is how to access it:

First check out the rowData to see for yourself. This is where all the information about the genes is listed.


now convert your gene of interest SYMBOL → ID

gene_name <- "Sox17"
rowData(sce)[which(rowData(sce)[,2] %in% gene_name),]

Or convert the ENSEMBL ID to its gene SYMBOL ← ID

gene_id <- "ENSMUSG00000025902"
rowData(sce)[which(rowData(sce)[,1] %in% gene_id),]

With this output, you can quickly plug in the ENSEMBL ID for plotting and google the GENE SYMBOL for exploration!

Happy Hunting! :bow_and_arrow:

1 Like