Figure 4

Hybridizations of orthopedic samples (patients 1 to 7). (a) Results of hierarchical clustering (HCL) performed on the raw data after normalization. On average, 26,111 features were used per array. Cophenetic (coph) correlation coefficient = 0.9. (b) HCL analysis of the 2,285 genes that were found to vary between biopsies and were present in one or more comparisons; coph = 0.92. Color codes: red, upregulated genes; green, downregulated genes; yellow, genes showing no change; white, missing values. For patients 1 to 3, the coding of samples in (a) and (b) is as follows: Pt2 1.BA refers to patient 2, biopsy 1, sub-biopsy B, technical replicate A. For patients 4 to 7, the coding of samples in (a) is as follows: Pt6 2.A refers to patient 6, biopsy 2, technical replicate A. (c) Volcano plot of the comparison between the adipose-enriched samples versus all other biopsies. Biopsies 1 and 3 of patient 1, and biopsy 1 of patient 4, were tested for differentially expressed genes against all other orthopedic biopsies. Genes with a B-score of more than 20 are shown in blue. Genes with highly significant differences in expression levels that were upregulated in the samples with an overrepresentation of adipose cells in comparison with other biopsies can be seen in the upper left corner.