Figure 1

Rationale behind the study. The relative number of a specific cell type or activity of certain pathways will vary across a collection of individual tumours. For example, the macrophage content (Φ) will differ in every tumour and so therefore will the mRNA level of macrophage specific genes (in blue). Similarly in every tumour at the point it is sampled the number of cells in mitosis (the mitotic index) will differ and this will be reflected in different levels of expression of cell cycle genes (in red). As a result the expression level of genes specifically expressed by those cells or associated specifically with the pathways will vary accordingly. By calculating the correlation coefficient between every gene on the array and every other gene on the array it is possible to calculate a correlation matrix that includes all these correlation coefficients. Graphs are then used to visualise relationships above a given correlation threshold and clustering used identifying groups of co-expressed genes.