Figure 1.

Comparison of gp100 expression normalized by different endogenous reference genes. Candidate endogenous reference genes were selected among those in Table 1. The gp100 probe (Cy3) was co-hybridized with one endogenous reference gene probe (Cy5) at the time to the transcriptome array. The transcriptome array included 235 cDNA libraries derived from samples of melanocytic lineage (maroon bar) and 594 cDNA libraries from samples of non melanocytic lineage (green bar). Melanocytic samples consisting in the overwhelming majority of melanoma metastases or melanoma cell lines while non-melanocytic libraries included a large collection of esophageal, kidney, colon and other cancers and several normal tissues or circulating mononuclear cells. The complete list of samples is available upon request. The expression of gp100 normalized with different endogenous reference genes was compared by unpaired two-tailed student t test and the endogenous reference genes were ranked according to the level of significance in their ability to discriminate between melanocytic and non-melanocytic lesions (data presented as the _Log10 p₂-value (shown in the boxes associated with individual graphs; for details see Figure 2). The distribution of the _Log2 ratios for each individual cDNA library is shown for each gp100 / endogenous reference gene combination. In addition, results compiled using the average of the _Log2 ratios for all the endogenous reference genes, the 5 and the 3 with the lowest p₂-value are presented (orange bar graphs).