Colorectal-cancer cell-line glycosphingolipid glycans

Relative glycosphingolipid-glycan abundances across 22 human colorectal-cancer cell lines spanning unassigned, undifferentiated and colon-like transcriptional subtypes.

Usage

glyhub_GPST000239_GSL(
  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 94 features and 22 observations. The abundance assay is in relative abundance (%). rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000239. S-5. Study: https://doi.org/10.1016/j.mcpro.2022.100239. Repository: https://glycopost.glycosmos.org/entry/GPST000239.

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

Supplementary Table S5 supplies 94 chromatographically distinguished glycan features and cell-line aggregate abundance values. Cell-line origin, tumour stage, differentiation and microsatellite status are joined from Table S1 when the source identifier matches exactly. Original antigen, glycan-family and linkage annotations are retained. Typed structures are transcribed from the same-row SNFG diagrams with all unspecified linkages left unknown; repeated compositions remain separate isomer features. Values are cell-line summaries, not individual biological-replicate measurements.

Source-derived compositions and original labels are retained. 94 source-supported structures are typed; unspecified bonds remain unknown. Unresolved or conflicting structures remain missing with source provenance.

Access

Use glyhub_load("glyhub_GPST000239_GSL") to load this dataset.