A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae

Abstract

The relationship between the similarity of expression patterns for a pair of genes and interaction of the proteins they encode is demonstrated both for the simple genome of the bacteriophage T7 and the considerably more complex genome of the yeast Saccharomyces cerevisiae. Statistical analysis of large-scale gene expression and protein interaction data shows that protein pairs encoded by co-expressed genes interact with each other more frequently than with random proteins. Furthermore, the mean similarity of expression profiles is significantly higher for respective interacting protein pairs than for random ones. Such coupled analysis of gene expression and protein interaction data may allow evaluation of the results of large-scale gene expression and protein interaction screens as demonstrated for several publicly available datasets. The role of this link between expression and interaction in the evolution from monomeric to oligomeric protein structures is also discussed.

Figure 1

Protein–protein interaction matrix for the phage T7. Rows and columns correspond to individual genes, scored positive in yeast two-hybrid screens (3). Genes are arranged left to right and top to bottom according to their position in the genome; class boundaries are shown. Gene expression is coupled to the genome position in T7, since class members are co-expressed. Genes not detected in interaction screens are given in the row labelled ‘other’, also grouped by class. An interaction between two proteins i and j is presented in the (i,j) and the symmetrical (j,i) elements of the matrix as + (an empty cell indicates no detected interaction). A positive yeast two-hybrid result likely caused by intramolecular associations only (3) is shown as × and interactions known from other studies but missed in yeast two-hybrid screens are marked as *. Distinction between baits and targets is not taken into account so the matrix is symmetrical. Shaded rectangles correspond to the different gene classes and inter-class mRNAs are shown schematically as grey boxes at the bottom (see text).

Figure 2

Distributions of the pairwise correlation coefficients of gene expression profiles for interacting proteins in the MIPS and ITO-NONCORE datasets and for all ORF pairs.