Fig. 1

Colorectal carcinoma classification based on gene expression profiling. a Heat map analysis of genes deregulated in colorectal carcinoma (CRC) as compared to normal tissue (NT). Representation of the log₂-transformed fold-change values from 111 cellular genes identified as significantly deregulated in colorectal carcinoma (CRC), compared to normal tissue (NT), with an absolute fold-change >1.7 and a q-value <0.05 (Student-t-test adjusted by FDR) using Heat Map analysis (median centered data performed in Cluster and TreeView) [63]. Deregulated genes were shown according to the type of specific PCR array and ranging from decreasing fold-change (red color for up-regulated genes and green color for down-regulated genes): Apoptosis: 14 genes, Cancer pathway: 33 genes, Lipoprotein signaling and cholesterol metabolism: 29 genes, Drug metabolism: 23 genes, Wnt pathway: 18 genes. The mean fold-change expression obtained from paired samples analysis (n = 17 paired CRC and NT) and all samples (n = 95 CRC versus n = 19 NT) analysis is indicated on the right of each graphic. Percentage of CRC showing an absolute fold-change superior to 1.7 and superior to 2 is also indicated on the right of each graphic. A blue color for gene names indicates a deregulation (> 1.7-fold) observed in more than 75% of tumor samples. A (−) sign and a green font refer to down-regulation; a red font refers to up-regulation. b Hierarchical clustering of colorectal carcinoma and normal colon tissue based on the expression profile of 47 genes. Log₂-transformed fold-change values from 47 genes fulfilling the criteria of deregulation in more than 75% of CRC samples (fold-change >1.7 and q < 0.05) were subjected to treatment by Cluster and Treeview using uncentered correlation and average linkage [63]. Red and green colors indicate transcript levels above and below the median values, respectively. NT, normal colon tissue (n = 19) and CRC, colorectal carcinoma (n = 95). Tumor samples are identified by a number followed by the Tumor Bank running number (S0, S1, S2, S3, S4) corresponding to a grading stage according to the pathological classification. Samples names above the dendrogram were colored according to stages: orange: 0 and I, red: II, purple: III and blue: IV. Genes identified by their gene symbol appear on the right side of each panel. Each column gives the gene expression profile of a sample, and each line indicates the variations in the level of expression of a given gene among tissue samples. The length of the branches on the trees forming the dendrograms on the top of each panel reflects the degree of similarity between samples; the longer the branch, the larger the difference in gene expression