Additional file 3 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 S1. Module assignments. The module assignments for all of the 9,166 genes are available as part of the online supplementary materials. The columns of the table include:   • Symbol: The gene name.   • ENTREZ ID: The gene ID in the Global Query Cross-Database Search System.   • Probe representative: The representative probe mapped to this gene.   • Adjusted p-value: For the null hypothesis that expression is similar in AML and MDS (Supplementary Note 2).   • Module ID: The assigned module.   • IMC: Intramodular connectivity.   • EMC: Extramodular connectivity.   • Rank: The rank of the gene in the module based on its intramodular connectivity.   • # of references The number of studies that reported the gene being relevant to AML according to Miller et al,. survey [81]. Intramodular and extramodular connectivities were computed by intramodularConnectivity() function from WGNCA package. They measure the overall correlation of the gene with other genes within and outside the module, respectively. The genes with the most connectivity in a module are considered as the “hubs” of that module [82]. See WGNCA manual for more information. (XLS 1618 kb)