Predicting Phenoconversion to Clinically Manifest ALS: Results of a Large-Scale Proteomic Study

Contents

• Overview

• Repo Contents

• System Requirements

• Installation Guide

• Figures

• Data

• License

• Citation

Overview

This study identifies plasma protein biomarkers for ALS and develops predictive models for phenoconversion. We analyze differentially regulated proteins, describe their longitudinal trajectories, and build models to predict disease onset and timing. Findings are replicated using UK Biobank data.

Repo Contents

figure/
R scripts and generated figures for each main figure panel

• Fig1–Fig5: Main figure scripts and results

• Supplement_Figure: Supplementary figure scripts and results

data/

• analysis_data: processed datasets (not included)

• fig_data: figure-specific summary data

  • individual_data: patient-level data (not included)

  • summary_data: summary statistics and aggregated results

analysis/
Additional analysis scripts

images/
Project schematics and figures

System Requirements

Hardware

Minimum:

• 4 GB RAM

• 2 CPU cores

Recommended:

• 16 GB RAM

• 4 CPU cores @ 3.0+ GHz

Supported Operating Systems

• Linux (Ubuntu 18.04 or newer)

• macOS (10.14 or newer)

• Windows 10 or newer

R Requirements

Tested on: R version 4.4.0 (2024-04-24) or newer

Key R packages used include:
arrow, cowplot, dplyr, extrafont, ggforce, ggnewscale, ggplot2, ggplotify, ggpubr, ggraph, ggrepel, ggsignif, ggtext, gprofiler2, gridExtra, here, igraph, jtools, kableExtra, knitr, lme4, lmerTest, OlinkAnalyze, patchwork, pheatmap, progress, purrr, RColorBrewer, scales, stringr, tibble, tidygraph, tidyr, tidyverse, UpSetR.

A full list is stored in the repository.

Installation Guide

Install R

Ubuntu:

sudo apt-get update
sudo apt-get install r-base r-base-dev

macOS / Windows:
Download from CRAN: https://cran.r-project.org/ (copy/paste manually; Zenodo cannot render links)

Install R Packages

Run in R:

install.packages(c('tidyverse', 'OlinkAnalyze', 'lme4', 'lmerTest',
                   'gprofiler2', 'igraph', 'tidygraph', 'pheatmap',
                   'ggplot2', 'dplyr', 'gridExtra', 'ggraph',
                   'RColorBrewer', 'ggpubr', 'cowplot'))

Some figures require additional dependencies; see individual scripts.

Figures

Scripts and results for each figure are located within the figure/ directory.

Main Figures

Figure 1 – Plasma marker differential regulation
Directory: figure/Fig1

• Fig_1A_volcano.png

• Fig_1B_up_enrichment.png

• Fig_1C_down_enrichment.png

• Fig_1D_ppi_network.png

• Fig_1E_heatmap.png

Figure 2 – Longitudinal trajectory of biomarkers
Directory: figure/Fig2

• Fig_2A_Temporal_Heatmap.png

• Fig_2B_Key_Protein_Trajectories.png

Figure 3 – Phenoconversion event prediction
Directory: figure/Fig3

• Fig_3A_ROC_LR.png

• Fig_3B_heatmap_single_protein_LR.png

• Fig_3C_upset_optimal_model_plot.png

Figure 4 – Time-to-phenoconversion estimation
Directory: figure/Fig4

• Fig_4_combined_tobit_model_prediction_vs_observed.png

Figure 5 – UK Biobank replication
Directory: figure/Fig5

• Fig_5A_Replication_vs_discovery_correlation.png

• Fig_5B_UKB_heatmap_1yr.png

• Fig_5C_UKB_pre_ALS_2yr_NEFL_EDA2R.png

• Fig_5D_UKB_DA_model.png

Supplementary Figures

Located in: figure/Supplement_Figure

• Sup_Fig1_NEFL_example.pdf

• Sup_Fig2A_Discovery_ALS_all_81.pdf

• Sup_Fig2B_Discovery_ALS_convert_pre_post_74.pdf

• Sup_Fig2C_Discovery_ALS_convert_pre_54.pdf

• Sup_Fig4_AUC.pdf

Data

Summary data
Stored in: data/fig_data/summary_data
These files are included and used for figure regeneration.

Individual-level data
Stored in: data/fig_data/individual_data (excluded from upload)

Analysis data
Stored in: data/analysis_data (excluded from upload)

License

See the LICENSE file included in this record.

Citation

If you use this code or data, please cite:

Ran, X., Wuu, J., Qin, Z. S., Cooper-Knock, J., Granit, V., Grignon, A.-L., Li, Y., Lin, E., Fernandez, M. C., Colato, D., Carberry, N., Lill, C. M., Piazza, P., Malaspina, A., & Benatar, M. (2025). Predicting Phenoconversion to Clinically Manifest ALS: Results of a Large-Scale Proteomic Study. Zenodo. https://doi.org/10.5281/zenodo.17834330

Please also cite the associated publication once available.