Correlation between protein-protein interactions and mRNA expression variation. (A) Definition of the three interaction datasets considered. PPI consists of all non-aneuploid chromosome genes coding for a protein with at least one interaction (348 genes out of 413 in the example considered here). Any genes with at least one protein interaction with a protein encoded on the aneuploid chromosome are in AneuPPI (36 here); all other members of PPI are placed in NonAneuPPI (312). (B) Plot of the frequency of the genes with increased or decreased mRNA expression (y-axis; 1.3-fold change, see Methods) coding for a protein interaction with a protein encoded either on an aneuploid chromosome, AneuPPI (green dots), or on a different chromosome, NonAneuPPI (blue dots), against the proportion of genes without interactions that showed changed mRNA expression for each aneuploidy microarray experiment (x-axis). (C) Scatter plot of protein abundance (protein molecules per cell) versus mRNA expression variation. High abundance proteins show low mRNA variation (Spearman rank correlation; P < 10-15). The number of protein-protein interactions is color-coded as illustrated by the legend at right. Proteins with a high degree of interaction are of both low abundance and low mRNA expression variation (Spearman rank correlations, P < 10-15).
Bekaert and Conant BMC Systems Biology 2011 5:62 doi:10.1186/1752-0509-5-62