Supplementary materials for "Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations"

This repository contained supplementary materials in the study named: "<strong>Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations.</strong>" For extracting all files from the downloaded tar.gz file, the following commanda could be used: <pre><code>tar -xf supplementary_materials.tar.gz </code></pre> The supplementary_materials/data diretcory contains the following sections: eqtm_predictions: This contains the training and testing datasets for the eQTM prediction procedures public_methylation_data_and_pca: This contains the harmonized public DNA methylation dataset and its first 100 PCA components cca_data: This contains the CCA components for the public DNA methylation and gene expression datasets for the negative eQTMs, and the input datasets for the functional gene pair prediction analylsis. gene_enrichment_results_for_cca: This contains the gene enrichment results for the CCA components for negative and positive eQTMs The supplementary_materials/model directory contains the following sections: disease_tissue_predictions: This contains the models trained for tissue prediction and disease prediction based on the PCA components from the public DNA methylation data eqtm_predictions: This contains models trained for eQTM prediction cca_transformations: This contains CCA transformation models and models for STRING gene pair predictions