O-glycan profiles in HEK293 glycosylation-knockout cells

Complete Table S4_1 O-glycan relative-abundance block from Global mapping of glycosylation pathways in human-derived cells, comparing wild-type HEK293 with seven glycosylation knockout conditions.

Usage

glyhub_GPST000125_O_HEK293(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Format

A glyexp::GlycomicSE with 14 features and 16 observations. The abundance assay is in percent relative abundance. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000125. Table S4_1, O block. Study: https://doi.org/10.1016/j.devcel.2021.02.023. Repository: https://glycopost.glycosmos.org/entry/GPST000125. Quantitative source: https://pmc.ncbi.nlm.nih.gov/articles/instance/8086148/bin/NIHMS1683936-supplement-5.xlsx.

Arguments

kind: "curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.
cache_dir: Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.
refresh: Download the pinned resource again, even if cached.
offline: Prohibit downloads; require a verified local resource.

Details

All source-numbered features and both experiment columns for all eight conditions are retained. The article methods explicitly call these two biological replicates. Average/error columns are retained only in source cell records and are not sample observations. Quantitative zeros become NA without renormalization; original numeric measurements remain in raw_matrix. Same-composition source rows are not collapsed. Five conflicting source compositions are supported by the original name and diagram; one unresolved row remains NA. All conflicting registry IDs and quantitative rows are preserved.

Composition counts are from source Component IDs resolved through the official GlyTouCan WURCS registry. Generic base-composition residues are counted directly from explicit WURCS residue indices; full structures are parsed with glyparse 0.8.1 and glyrepr 1.1.0. A single, non-conflicting source Structure ID is eligible for typed structure. Candidate lists remain lists; no representative is chosen from a mixture. Five previously conflicting compositions are supported by original names and native-vector diagrams; N feature 17 remains unresolved because its source drawing also disagrees. Registry identifiers and all conflicting evidence remain intact. No mass-derived structure or sample identity is inferred.

Access

Use glyhub_load("glyhub_GPST000125_O_HEK293") to load this dataset.