Research Paper Volume 16, Issue 19 pp 12726—12768
A proteomics approach to study mouse long bones: examining baseline differences and mechanical loading-induced bone formation in young-adult and old mice
Figure 3. A single age-related module with perfect separation was identified using weighted gene co-expression network analysis (WGCNA) of the RNA-seq data. (A) Gene counts across all samples were clustered into 44 modules and correlated with age status. Three modules (black and orange) were significantly different between ages using a Bonferroni correction (p = 0.0011 = 0.05/44). (B) Only Module 40 (orange) displayed perfect separation using hierarchical clustering. (C, D) COMPBIO analysis of the subset of 1055 genes from Module 40 that had an FDR <0.05 between young-adult and old samples identified TGF-beta signaling and Wnt signaling as the top themes. (E, F) PANTHER Pathway and KEGG analyses of all 2452 genes in Module 40 also revealed Wnt signaling and TGF-beta signaling, among other pathways. Examination of the fold-changes of the genes from the PANTHER analysis showed that all 9 pathways are reduced with aging. Abbreviation: FE: fold-enrichment.