Fig. 3

Cellular proteome of HeLa clones. A, B Two exemplary 2D gels showing identified differentially expressed protein spots, upregulated (circled in red) or downregulated (circled in blue) in mutant clones relative to WT. A KD mutant vs. WT: 157 spots differentially expressed, of which 94 spots upregulated and 63 spots downregulated. B BD mutant vs WT, 198 spots differentially expressed, of which 111 upregulated and 87 downregulated. C Principal component analysis (PCA) performed with all protein spots detected and matched. The score plot shows experimental maps; for more details see Material and Methods. D, E Heatmap clusters showing the relative changes of differentially expressed proteins within the two main identified functional groups related to metastasis (D) and mitochondrial dysfunction and oxidative stress (E); proteins were identified by IPA software, some mitochondrial proteins were further selected through annotation by UniProt. Color code for proteins: red, up-regulation; green, down-regulation; grey, no significant change; color saturation indicates the degree of change (see also Additional file 10: Table S1). For clone abbr. see Fig. 1; two clones of the same type (e.g., CTR1, CTR2) were analyzed in triplicate. In D, comparison of KD vs. WT yielded 22 proteins with altered expression (16 up- and 6 down-regulated). Comparison of BD vs. WT yielded 23 differentially expressed proteins (16 up- and 7 down-regulated), of which 21 are common with the previous one