How gedine-lab/garreau_2026 works
This repository contains research code and supplementary results for a study that builds a context-specific co-expression network and uses patient-wise network propagation to prioritize candidate genes in holoprosencephaly. The documented workflow covers expression and patient-variant processing, per-patient propagation and signal-gene analysis, then candidate-gene evidence rating and figure/table analyses. Edges reflect only roles and outputs stated in the README; source excerpts were unavailable, so undocumented calls and data transfers are omitted.
Main entry points: Suplementary_Tables Supplementary tables S1–S13 · PUBMED_query.R PubMed evidence queries · rwr.R Per-patient RWR · rwr_normalization_fct.R RWR profile normalization
Components 25
Data preparation
- Forebrain gene selection
scripts/scrna.R - Co-expression network
scripts/tprimrna.R - Patient variant filtering
scripts/patient_data_HPE_POI.R
Network propagation
- Per-patient RWR
scripts/rwr.R - RWR helpers
scripts/custom_fct.R - CDS-weighted permutation bank
scripts/cds_weighted_bank_generation.R - RWR profile normalization
scripts/rwr_normalization_fct.R - Signal gene analysis
scripts/signal_gene_fct.R
Candidate evidence
- PubMed evidence queries
scripts/PUBMED_query.R - Mouse phenotype ratings
scripts/MGI_query.R - Constraint metrics retrieval
scripts/loeuf_query.R
Analyses and results
- Over-representation analysis
scripts/ora_fct.R - Ancestry analysis
scripts/Figures/ethseq_analysis.R - Network topology and enrichment
scripts/Figures/network_analysis.R - Seed and seed-enrichment analysis
scripts/Figures/seeds_analysis.R - RWR results analysis
scripts/Figures/rwr_results_analysis.R - Cohort permutation analysis
scripts/Figures/rwr_cohort_permutations.R - Candidate subnetwork analysis
scripts/Figures/rwr_subnetwork_analysis.R - Supplementary tables S1–S13
Suplementary_Tables
Other components
- Early-forebrain atlas
- iPSC RNA-seq
- Patient exome variants
- PubMed
- MGI
- gnomAD constraint metrics
Connections 16
- Forebrain gene selection → Early-forebrain atlas: selects genes from
README.md - Co-expression network → iPSC RNA-seq: normalizes data
README.md - Patient variant filtering → Patient exome variants: filters variants
README.md - Per-patient RWR → RWR helpers: uses RWR functions
- RWR profile normalization → Per-patient RWR: normalizes profiles
- Signal gene analysis → RWR profile normalization: aggregates profiles
- PubMed evidence queries → PubMed: queries
README.md - Mouse phenotype ratings → MGI: retrieves phenotypes
README.md - Constraint metrics retrieval → gnomAD constraint metrics: retrieves metrics
README.md - Ancestry analysis → Supplementary tables S1–S13: produces S1
README.md - Network topology and enrichment → Supplementary tables S1–S13: produces S6–S7
README.md - Seed and seed-enrichment analysis → Supplementary tables S1–S13: produces S4, S8–S10
README.md - RWR results analysis → Supplementary tables S1–S13: produces S11
README.md - Candidate subnetwork analysis → Supplementary tables S1–S13: produces S12
README.md - PubMed evidence queries → Supplementary tables S1–S13: rates evidence for S13
- Cohort permutation analysis → Signal gene analysis: tests signal counts