Reaction-order

Analyzing Diamonds in the Biosynthetic Network to Show Preferred Reaction Order

This repository contains code and data for analyzing diamond-shaped motifs within biosynthetic networks derived from glycans, using all available glycomics datasets within glycowork.

Diamond-shaped motifs were specifically chosen to capture contexts where two added monosaccharides are not directly linked in the network, thereby enabling the evaluation of alternative reaction orders.
Each motif represents two possible reaction sequences — A-then-B and B-then-A — leading to a common glycan structure.

An illustration of a diamond motif example is shown below:

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Workflow Summary

Motif Extraction

• Diamond-shaped network motifs are extracted using the find_diamonds function available in the network_biosynthesis module of glycowork.

Reaction and Abundance Extraction

• The extract_diamond_reactions function is defined to:
  • Extract reactions stored in motif edges.
  • Couple intermediate abundances with each diamond motif.

Reaction Order Preference Analysis

• The collect_reaction_preferences_data function was implemented to assess preferred reaction paths by:
  • Collecting abundance differences for the two reaction orders.
  • Performing pairwise Welch’s t-tests + Benjamini-Hochberg multiple testing correction to evaluate statistical significance.

Visualization and Interpretation

• Data are summarized in tables and visualized through boxplots, highlighting:
  • Forward vs. reverse path preferences.
  • Distribution of datapoints.
  • Statistical significance indications.

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Applications

Glycan Class-Specific Analysis

Reaction order preferences were analyzed for different glycan classes:

• N-glycans
• O-glycans
• Glycosphingolipids (GSLs)
• Milk oligosaccharides (MOs)

Physiological Condition Comparison

Reaction preferences were compared between:

• Control samples
• Tumor samples

This enabled the evaluation of how physiological conditions may influence biosynthetic reaction order.