GlycoMaple

GlycoMaple maps glycan biosynthesis pathways and predicts glycan structures from gene expression data to enable analysis of glycosylation variation across tissues, cell lines, and tumors.

Key Features:

• Gene Expression Integration: Integrates gene expression profiles with global glycan metabolic pathways using an informatically selected set of 950 genes associated with glycosylation and its regulation.
• Pathway Mapping: Maps gene expression onto comprehensive glycan-related pathways to connect gene-level changes to pathway activity.
• Predictive Analysis: Predicts glycan structures through computational analysis of pathway-mapped gene expression.
• Experimental Validation: Predictions were validated using glycomic techniques and by constructing 40 knockout HEK293 cell lines to observe resulting changes in glycan structures.
• Comparative Analysis: Estimates and compares glycan structures across 64 cell lines, 37 tissues, and primary colon tumor tissues using data from publicly available databases.

Scientific Applications:

• Glycan analysis and engineering: Supports analysis and engineering of glycosylation in mammalian cells by linking gene expression to predicted glycan structures.
• Cancer glycomics: Enables investigation of glycosylation patterns in cancer research, including assessment of associations with tumor progression and therapy response.
• Comparative glycomics: Facilitates comparative studies of glycan structures across cell lines, tissues, and tumor samples using public datasets.

Methodology:

Integrates gene expression with global glycan metabolic pathways using an informatically selected set of 950 glycosylation-associated genes, maps expression onto glycan-related pathways, and applies computational analysis to predict glycan structures.