Figure 6. Loss of UBP6 Function Preferentially Affects Proteins Overproduced in Disome V and Disome XIII Cells Relative to Wild-type.
(A) Comparison of the means of the log2 ratios of relative abundance of proteins. Proteins are binned based on their relative levels in disome V cells. Bin 1 (left bars) contains proteins whose levels are lower than one SD of the mean (ratio < −0.49, n = 141). Bin 2 (middle bars) contains proteins whose levels fall within one SD of the mean (−0.49 < ratio < 0.49, n = 1947) and Bin 3 (right bars) contains proteins whose levels are greater than one SD (ratio > 0.49, n = 264). Only proteins that were detected in all four experiments were used for this analysis: Disome V compared to wild-type (black bars), disome V ubp6Δ compared to wild-type (dark grey), ubp6Δ compared to wild-type (light grey) and the wild-type/wild-type comparison (white bars) are shown.
(B) RNA levels of the same genes analyzed in (A).
(C) The same analysis as in (A) was performed for proteins encoded by genes located on chromosome V. The SD was that of the distribution of chromosome V encoded proteins. The bins are: ratio < 0.24, n = 16; 1.44 > ratio > 0.24, n = 105; and ratio > 1.44, n = 15. Nomenclature is as in (A).
(D) RNA levels of the same proteins analyzed in (C).
(E) Comparison of the means of the log2 ratios of relative abundance of proteins. Proteins are binned based on their relative levels in disome XIII cells as described for disome XIII cells. Bin 1 (left bars) ratio < −0.51, n = 112; Bin 2 (middle bars) −0.51 < ratio < 0.51, n = 2,171; Bin 3 (right bars) ratio > 0.51, n = 371. Only proteins that were detected in all four experiments were used for this analysis: Disome XIII compared to wild-type (black bars), disome XIII ubp6Δ compared to wild-type (dark grey), ubp6Δ compared to wild-type (light grey) and the wild-type/wild-type comparison (white bars) are shown.
(F) RNA levels of the same proteins analyzed in (E).
(G) The same analysis as in (E) was performed for proteins encoded by genes located on chromosome XIII. The SD was that of the distribution of chromosome XIII encoded proteins. The bins are: ratio < 0.36, n = 16; 1.55 > ratio > 0.36, n = 190; and ratio > 1.55, n = 23. Nomenclature is as in (E).
(H) RNA levels of the same proteins analyzed in (G).
Error bars represent +/− S.E.M. P = p value paired Student’s t test.