Additional file 1: of Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes

Abstract

Text S1. Materials and data collection. Text S2. Details of smoothing and Feature Topology Plots (FTP). Text S3. Simulation setting to evaluate iPF. Text S4. Comprehensive validation scheme for iPF. Figure S5. (A) An illustration of integrated omics data sets, (B) A workflow to generate future topology plot (FTP). Figure S6. Flowchart of validation scheme for Integrative phenotyping framework for multiple omics data sets. Figure S7. An example of iPF that utilizes fused multiple data sets at the stage (vi). Figure S8. Examples of iPF using various combinations of the omics data sets (pooled analysis). Figure S9A. The gap statistics and its scree plot to choose the optimal number of clustering (clinical and miRNA data). Figure S9B. The gap statistics and its scree plot to choose the optimal number of clustering (mRNA and miRNA data). Figure S9C. The gap statistics and its scree plot to choose the optimal number of clustering (mRNA and clincal data). Figure S9D. The gap statistics and its scree plot to choose the optimal number of clustering (clincal data and combined data of mRNA and miRNA). Figure S10. The best choice of the number of feature modules. Figure S11. Simulation study shows robust true feature discovery in “Feature Fusion”. The x-axis represents multiplication levels of noise features. The y-axis represents average ARIs from 100 simulations. Each figure is generated based on simulation scenarios of the different number of true features (e.g., 200, 400, and 600, respectively). Figure S12. Immunomodulating drugs target overexpressed genes in module two. Table S13. The description of mRNA and miRNA lung disease data. Table S14. Various correlation types depending on variable attributes. Table S15. The demographic summary of clinical features in each sub-cluster. Table S16. Target gene enrichment analysis (via Fisher exact test) related to twelve. Table S17. Regression analysis on target miRNA features, and coefficient of determination significant miRNA features. Table S18. The top disease or functional annotations associated with genes in module two in Cluster E patients. Figure S19. Basic consensus clustering using only gene expression data. (DOCX 6398 kb