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Filter enzymes using RNA-seq expression

enzymes_from_rnaseq.Rd

enzymes_from_rnaseq() selects built-in enzymes whose genes are expressed at or above a TPM threshold. When mat contains multiple columns, the mean TPM across columns is used for each gene.

Usage

enzymes_from_rnaseq(mat, threshold = 1)

Arguments

mat

A numeric matrix of TPM values with gene symbols as unique row names and samples or replicates as columns.

threshold

A non-negative numeric scalar giving the minimum mean TPM for a gene to be considered expressed. The default follows Huang et al. (2021): genes with TPM below 1 are treated as not expressed or rarely expressed, whereas genes with TPM at least 1 are treated as expressed.

Value

A named list of enzyme() objects. Genes not represented in the built-in enzyme database are ignored.

References

Huang, Y.-F., Aoki, K., Akase, S., et al. (2021). Global mapping of glycosylation pathways in human-derived cells. Developmental Cell, 56, 1195-1209. doi:10.1016/j.devcel.2021.02.023 .

Examples

tpm <- matrix(
  c(0.2, 1, 3),
  ncol = 1,
  dimnames = list(c("FUT8", "ST3GAL3", "MOGS"), "sample")
)
enzymes_from_rnaseq(tpm)
#> $MOGS
#> 
#> ── Enzyme: MOGS ────────────────────────────────────────────────────────────────
#> ℹ Type: "GH" (Glycoside hydrolase)
#> ℹ Species: "human"
#> ℹ Glycan type: "N"
#> 
#> ── Rules (1) ──
#> 
#> → Rule 1: whole alignment
#> Acceptor:
#> "Glc(a1-2)Glc(a1-3)Glc(a1-3)Man(a1-2)Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"
#> Product:
#> "Glc(a1-3)Glc(a1-3)Man(a1-2)Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"
#> 
#> $ST3GAL3
#> 
#> ── Enzyme: ST3GAL3 ─────────────────────────────────────────────────────────────
#> ℹ Type: "GT" (Glycosyltransferase)
#> ℹ Species: "human"
#> ℹ Glycan type: "lipid" and "free"
#> 
#> ── Rules (4) ──
#> 
#> → Rule 1: terminal alignment
#> Acceptor: "Gal(b1-3)GlcNAc(b1-"
#> Product: "Neu5Ac(a2-3)Gal(b1-3)GlcNAc(b1-"
#> Rejects:
#> "Gal(b1-3)[Fuc(a1-4)]GlcNAc(b1-"
#> → Rule 2: terminal alignment
#> Acceptor: "Gal(b1-4)GlcNAc(b1-"
#> Product: "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-"
#> Rejects:
#> "Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-"
#> → Rule 3: core alignment
#> Acceptor: "Gal(b1-3)GalNAc(a1-"
#> Product: "Neu5Ac(a2-3)Gal(b1-3)GalNAc(a1-"
#> → Rule 4: terminal alignment
#> Acceptor: "Gal(b1-4)Glc(b1-"
#> Product: "Neu5Ac(a2-3)Gal(b1-4)Glc(b1-"
#>