Figure 1

Cluster map analysis of 118 genes identified by PAM of 15 different specimens resulting in two classes (9 neoplastic skin lesions and 6 normal skin). Prediction Analysis of Microarrays (PAM) using nearest shrunken centroids was performed with 22,283 genes, which were present on the microarray platform (Affymetrix) to identify genes best characterizing normal skin, actinic keratosis (AK), and squamous cell carcinoma (SCC). Hierarchical clustering was performed with 118 genes identified by PAM (CHI3L1 was detected with two independent Affymetrix probes and are included twice, marked with an asterisk). Thirteen genes verified by quantitative real-time RT-PCR are marked in bold. Each color patch represents the normalized expression level of one gene in each group, with a continuum of expression levels from dark blue (lowest) to dark red (highest). The minimal set of informative genes is given by HUGO Gene Nomenclature Committee (HGNC) symbols. Group (1–9) are non-melanoma skin cancer AK (1, 5, 6, and 8), and SCC (2–4, 7, and 9) showing different expression levels compared with six cases of normal skin (10–15). Numbers 6 and 10 were specimens with pooled RNAs.