Figure 4.

A co-expression network of the Environmental Response 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 ER dataset. (B) A drawn network of gene co-expression from the ER dataset. 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 [20]. 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) Correlation plots showing the relationship between gene group connectivity and essentiality for rRNA processing, protein synthesis and ubiquitin from the ER 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: 317/929 = 34.1 (C), 98/323 = 30.3 (D), 18/37 = 48.6 (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.

Carlson et al. BMC Genomics 2006 7:40   doi:10.1186/1471-2164-7-40
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