Figure 1.
PID-related proteins in B cell maturation pathway.
Defects in proteins and genes important for maturation cause PIDs and block the maturation on certain stage. The PID-related proteins and stages where diseases affect the development are shown on top. The cell lines (RS4;11, 380, REH, 697, Nalm-1, Nalm-6, Ramos and U-266) are marked inside the corresponding cells representing their normal B cell counterparts.
Figure 2.
Reference 2D-DIGE map of Cy2-labelled internal standard.
The 233 identified proteins are numbered in the gel and listed in Table S2.
Figure 3.
Unsupervised clustering of B cell samples on the basis of protein profiles.
IM-B Ramos samples clustered according to time after anti-IgM stimulation (1–120 h) and were distinctive from early pre-B (RS4;11, 380 and REH), pre-B (697, Nalm-1 and Nalm-6) and plasma cell U-266 samples. The degree of similarity in profiles is shown by colour (base-two logarithmical scale below the figure). Red and green indicate high and low levels of protein expression in relative to internal standard. The average protein abundance of the 175 identified proteins (labelled with Cy3 and Cy5 dyes) is calculated relative to internal standard (labelled with Cy2 dye). Cluster numbers (1–19) are shown to the right and refer to those in Table 1, Table 2, Table 3, Table S2 and Table S4.
Figure 4.
Unsupervised clustering of proteins affected by anti-IgM stimulation.
The heat map shows the comparison between anti-IgM stimulated and control Ramos samples during the time course 1–120 h. Protein abundance difference is calculated between stimulated and corresponding control samples for the 69 identified proteins, which passed the significance criteria (student’s t-test p≤0.05). Red and green colours indicate up- and down-regulation in response to anti-IgM stimulation (base-two logarithmical scale below the figure). Cluster numbers (1R-11R), short protein names and SSP are shown to the right and refer to those in Table 1, Table 2, Table 3, Table S2 and Table S4.
Figure 5.
Differences in proteome profiles between IM-B and early pre-B cell stages.
Early pre-B 380 and IM-B Ramos (120 h time point) proteome samples were labelled with Cy5 and Cy3 dyes, respectively, and separated in a 2D-DIGE gel (nonlinear pH gradient 3–10) with internal standard sample labelled with Cy2 dye. Triple image overlay shows proteins highly expressed in Ramos (red) and 380 (green) samples in relative to internal standard sample (blue). Protein identities are indicated for those proteins with major changes in expression profile. IgM chains, ER and membrane bound vesicle proteins were highly expressed in Ramos cells, whereas cytoskeleton and immunity related proteins were expressed in 380 cells.
Table 1.
Biological process GO terms and their p-values for co-expressed proteins.
Table 2.
Molecular function GO terms and their p-values for co-expressed proteins.
Table 3.
Cellular component GO terms and their p-values for co-expressed proteins.