Fig. 2
From: Cross-species gene modules emerge from a systems biology approach to osteoarthritis
Definition of co-expression modules in the rat. a Hierarchical cluster dendrograms in the rat, derived from gene expression data (n = 115 arrays and 5982 genes) show 20 modules. An alphanumeric code is provided to clarify references to specific modules (Supplementary Fig. 5a). Unassigned genes are colored gray; b top bar—modules are colored below the dendrogram and represent highly co-expressed genes. Key modules of interest (R5, R8, R9, R11, R18) are annotated. Some consensus modules are split across two or more rat network modules. Consensus modules, modules of co-expressed genes that are shared by two or more co-expression networks, are presented above the module bar; consensus module colors and codes are comparable between species and can be related to those in Fig. 1b and Supplementary Fig. 5b; bands 2–4—selected trait groups showing positive or negative correlation with genes enriched in each module (see figure key—red corresponds to positive correlation). Complete module–trait associations are provided in Supplementary Fig. 5a. Whole-cartilage samples derived from neonate and adult rat cartilage show reciprocal correlations with some modules. Whole-cartilage samples derived from in vivo intervention studies (“Intervention Group 1–2”) also show reciprocal correlations with rat modules that contribute to the C4 and C5 consensus modules; c Module eigengene expression (y-axis) is defined for two consensus modules (C4 and C5, right-hand vertical bars) across selected samples (x-axis, “Condition”) relative to all other samples (“Other”). Across sample groups both module eigengenes, using a non-parametric Kruskal–Wallis chi-square test, are found to be significantly differentially expressed with high expression found in “Intervention Group 2” relative to other selected traits (C4—p = 4e−05; C5—p = 2.8e−08) including “Intervention Group 1” and “Adult” rat cartilage. Overall, subsets of rat whole-cartilage samples derived from in vivo joint intervention studies demonstrate heterogenous gene expression and differ in their association with network modules
