Metabolite Protein Network Construction

---
name: metabolite-protein-network-construction
description: Use when after generating metabolite-disease correlation data and protein
  association predictions from a deep learning metabolomics module (e.g., DeepMSProfiler's
  feature extraction step).
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3083
  edam_topics:
  - http://edamontology.org/topic_0121
  - http://edamontology.org/topic_3520
  tools:
  - DeepMSProfiler
  - Python (networkx, igraph, matplotlib/seaborn)
  techniques:
  - LC-MS
  license_tier: open
  provenance_tier: literature
derived_from:
- doi: 10.1038/s41467-024-51433-3
  title: DeepMSProfiler
evidence_spans: []
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_deepmsprofiler_cq
    doi: 10.1038/s41467-024-51433-3
    title: DeepMSProfiler
  dedup_kept_from: coll_deepmsprofiler_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1038/s41467-024-51433-3
  all_source_dois:
  - 10.1038/s41467-024-51433-3
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# metabolite-protein-network-construction

## Summary

Construct and visualize bipartite network graphs linking metabolites to proteins, weighted by association strength and disease class, to reveal disease-specific metabolic–proteomic relationships from LC-MS data. This skill transforms raw correlation and prediction outputs into interpretable network topology suitable for publication.

## When to use

Apply this skill after generating metabolite-disease correlation data and protein association predictions from a deep learning metabolomics module (e.g., DeepMSProfiler's feature extraction step). Use it when you need to communicate multi-disease metabolite–protein associations as a unified graph rather than as separate heatmaps or lists, or when the research question requires visual exploration of network topology, hub metabolites, or disease-specific connectivity patterns.

## When NOT to use

- Input is already a publication-ready network image or has been manually curated for display — construction is unnecessary.
- No protein association predictions are available; network would be unipartite metabolite-only, which may be better served by alternative metabolite correlation network workflows.
- The research question focuses on statistical testing or quantitative comparison of correlations rather than visual network topology discovery.

## Inputs

- metabolite-disease correlation matrix (numpy array or table)
- protein association prediction scores (array or dataframe)
- disease class labels (categorical array matching samples or metabolite groups)
- association strength metadata (edge weights, confidence scores)

## Outputs

- bipartite network graph object (networkx or igraph format)
- network visualization image (PNG, SVG, or PDF file)
- node and edge coordinate data (optional, for reproducibility)

## How to apply

Load the metabolite-disease correlation matrix and protein association predictions generated by the deep learning module. Construct a bipartite graph where metabolites and proteins form two distinct node sets, with edges weighted by correlation strength or prediction confidence and colored/stratified by disease class. Apply a force-directed or hierarchical layout algorithm (e.g., Fruchterman–Reingold) to position nodes for interpretability and minimize edge crossing. Render the network with disease-type color coding on nodes, node size scaled proportionally to association strength, and edge transparency or width reflecting confidence scores. Export the finalized network as a high-resolution vector or raster image (PNG, SVG, PDF) suitable for publication.

## Related tools

- **DeepMSProfiler** (generates metabolite-disease correlations and protein association predictions as upstream inputs to network construction) — https://github.com/yjdeng9/DeepMSProfiler
- **Python (networkx, igraph, matplotlib/seaborn)** (libraries for graph construction, layout algorithms, and visualization rendering)

## Examples

```
# After DeepMSProfiler feature extraction:
from DeepMSProfiler import run_feature, show_feature
run_feature(job_dir='../jobs/jobs007')
show_feature(job_dir='../jobs/jobs007', mode='ensemble')
```

## Evaluation signals

- Verify bipartite structure: metabolite and protein nodes are in separate, non-overlapping sets; edges only cross between sets, never within.
- Check node scaling: node size correlation with association strength is monotonic and visually discriminable across at least 3–5 magnitude tiers.
- Confirm disease stratification: nodes or edges exhibit clear, consistent color or visual clustering by disease class; disease-specific subnetworks should be visually separable.
- Validate layout stability: run the layout algorithm 2–3 times with different random seeds; node positions should be qualitatively similar (same neighbor relationships preserved), indicating deterministic convergence.
- Confirm export quality: high-resolution output (≥300 DPI if raster, or vector format) is readable at publication size; edge labels and node IDs are not occluded.

## Limitations

- Network layout algorithms (force-directed, hierarchical) are stochastic and sensitive to initialization; reproducibility requires fixed random seeds.
- Large networks (>1000 nodes) become visually cluttered; subgraph extraction or interactive visualization may be required for interpretability.
- Edge transparency and color encoding are limited to ~5–7 visually distinct categories; disease classes >7 or continuous confidence scores require binning or alternative encoding (e.g., edge width).
- DeepMSProfiler's protein association predictions are computed post-hoc from metabolite features; direct protein measurement data is not incorporated, potentially inflating apparent protein-metabolite relationships.

## Evidence

- [other] Construct a bipartite network graph with metabolites and proteins as nodes, weighted by association strength and disease class.: "Construct a bipartite network graph with metabolites and proteins as nodes, weighted by association strength and disease class."
- [other] Apply network layout algorithm (force-directed or hierarchical) to position nodes for interpretability.: "Apply network layout algorithm (force-directed or hierarchical) to position nodes for interpretability."
- [other] Render the network plot with disease-type color coding, node size scaled by association strength, and edge transparency reflecting confidence.: "Render the network plot with disease-type color coding, node size scaled by association strength, and edge transparency reflecting confidence."
- [readme] Disease-associated metabolite-protein network plots: "Disease-associated metabolite-protein network plots"
- [other] Export the finalized network plot as a high-resolution image file suitable for publication.: "Export the finalized network plot as a high-resolution image file suitable for publication."