Work

Multi-Layer Network Integration for Colorectal Cancer Patient Stratification

Year: 2026

Type: software

Abstract: The pipeline stratifies 600 colorectal cancer (CRC) patients by integrating three microbiome layers: species, enzyme and MetaCyc pathway abundance from shotgun metagenomics. It compares three network-integration strategies: multiplex (MolTi/Leiden), CROSSIM diffusion fusion and iNet consensus fusion. It then: detects communities with CmmD over a resolution sweep clusters patients with Ward's linkage assesses cluster significance by multiscale bootstrap and SigClust identifies per-subtype biomarkers with MaAsLin2, against both the other CRC patients and 662 controls validates the biomarkers against cross-layer EC coherence, curated CRC markers, Disbiome and PubMed Input data is public and is not included. download_inputs.py downloads the abundance tables and metadata from Beghini et al. 2021 (eLife 10:e65088, Supplementary Files 5 and 10) and builds the three input tables.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.23120342

Authors: Erkantarcı, Betül, Bakir-Gungor, Burcu, Cirillo, Davide, Coskun, Mustafa

Institutions: Abdullah Gül University, Barcelona Supercomputing Center, Ankara University

Language: English

Topic: Bioinformatics and Genomic Networks

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

OpenAlex ID: W7219040128

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