Additional file 5 of Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications

Table S4. Eigengenes. The eigengenes computed for all gene modules are available as part of the online supplementary materials. Each row reports the values for a sample and columns correspond to modules. The first sheet was computed using moduleEigengenes function from WGCNA package, which applied PCA on the gene expression in the MILE dataset. The second sheet shows the inferred expression of these 33 eigengenes in the BCCA dataset (Methods). Module zero contains the set of “outlier” genes that did not correlated with each other or with the rest of the genome. WGCNA could not confidently assign them to any module and we did not use them in our analysis. (XLS 334 kb)