A co-expression network of the DNA Damage dataset. For all panels in the figure: blue color represents members of the rRNA processing module, yellow color represents members of the protein synthesis module and red color represents members of the ubiquitin pathway. (A) A hierarchical clustering of the topological overlap matrix for the DD dataset. (B) A drawn network of gene co-expression from the DD dataset. Edges were computed from the Pearson correlation coefficients. Network structure was drawn in Pajek . Each gene is represented as a dot. Edges are drawn as grey lines. Colored dots belong to the module that their color indicates and grey dots indicate all other genes in the network. (C-E) Scatter plots showing the relationship between gene group connectivity and essentiality for rRNA processing, protein synthesis and ubiquitin from the DD network respectively. On the y axis of these plots is the percentage of genes determined to be essential in yeast. The number of essential genes in each module/total number of genes in each module was: 196/390 = 50.3 (C), 122/441 = 27.7 (D), 50/222 = 22.5 (E). (F-H) Relationship between the average blastp score of a node and k for the same module members listed in C-E. On the y axis of these plots is the average log(e score) of genes within that bin. For plots C-H, the connectivity within each module for each gene was determined and each gene rank ordered by connectivity. 20 equal sized bins for each of the expression datasets were formed and the average connectivity of the genes in each bin plotted on the X axis.
Carlson et al. BMC Genomics 2006 7:40 doi:10.1186/1471-2164-7-40