Supplementary Materials: The molecular landscape of premature aging diseases defined by multilayer network exploration

This dataset contains supplementary materials related to study "The molecular landscape of premature aging diseases defined bymultilayer network exploration" (Beust C., Valdeolivas A., Baptista A., Brière G., Lévy N., Ozisik O., Baudot A.)

Supplementary Figures:  Supplementary Figure S1: Clustering of the premature aging disease communities obtained with 50 iterations of  itRWR  Supplementary Figure S2: Clustering of the premature aging disease communities obtained with 150 iterations of  itRWR  Supplementary Figure S3: Clustering of the premature aging disease communities obtained with 100 iteration of  itRWR, with a cutoff value at 0.5 on the dendrogram  

Supplementary Tables:  Supplementary Table S1: Premature Aging HPO phenotypes  Supplementary Table S2:Tthe 67 PA diseases and their 132 associated genes from ORPHANET  Supplementary Table S3: Number of nodes, edges, and densities of the 4 network layers composing the multilayer  biological network  Supplementary Table S4: Parameters used for MultiXrank  

Supplementary Files:  Supplementary File S1: Csv file containing the enrichment analysis results computed using the genes associated with  physiological aging  Supplementary File S2: Excel file containing the gene nodes belonging to each of the 67 communities  Supplementary File S3: Excel file containing the gene nodes belonging to each cluster (i.e., the union of the genes belonging to the set of communities composing the cluster)  Supplementary File S4: Csv file containing the diseases belonging to each cluster  Supplementary File S5: Excel file containing the enrichment of clusters using lists of physiological aging genes  Supplementary File S6: Csv file containing the lists of genes differentially expressed in human blood, skin, brain, muscle and breast during aging, from the study of Irizar et al.  Supplementary File S7: Excel file containing the enrichment analysis results of the 67 communities, using GO Biological Processes and Cellular Components, and Reactome pathways functional annotations  Supplementary File S8: Excel file containing the enrichment analysis results of the 6 clusters, using GO Biological Processes and Cellular Components, and Reactome pathways functional annotations. The last 2 columns contain  the seed nodes of the cluster annotated for the corresponding function and their corresponding diseases. Supplementary File S8bis: Excel file containing the enrichment analysis results of the 8 clusters obtained with an alternative cutoff of 0.5 in the dendrogram, using GO Biological Processes and Cellular Components, and Reactome pathways functional annotations.Supplementary File S9: Excel file containing enrichment analysis results of the 6 clusters, using HPO phenotypes  

Supplementary Text:  Supplementary Text S1: Comparison with alternative network exploration strategies, including classical (non- iterative) Random Walk with Restart, Multilayer network partitioning, and computation of network distances with shortest paths.