Hierarchical clustering analysis of 34 microarray experiments on PBMC total RNA derived from 9 normal males, 10 normal females, one 46,XY-male with CAH and 14 individuals with DSD [see additional files 2, 3, 4, 5]. (A) Transcript levels of 157 transcripts identified by SAM as differing significantly between PBMC from 9 normal males and 10 normal females. Transcripts are grouped by hierarchical cluster analysis and displayed in rows while experiments are displayed in columns. Expression values per gene are centered by the mean log2 Cy5/Cy3 normalized ratio across the arrays. Increasing blue intensity in the heat map corresponds to higher relative transcript levels compared to the mean expression level across all 34 array experiments. Increasing yellow intensity corresponds to relatively decreased transcript levels compared to the mean. Dark grey corresponds to missing data. Examples taken from these gene clusters are marked by color within the gene tree on the left of the heat map. The red gene tree corresponds to the enlarged gene cluster D, the blue gene tree corresponds to F, the pink gene tree corresponds to G, and the green gene tree corresponds to E, respectively. Gene symbols of the named transcripts are shown on the right. (B) Enlarged cluster dendrogram of the PBMC samples demonstrating the degree of relatedness (Pearson correlation) between the expression patterns of the 157 transcripts. The length of the arms of the dendrogram reflects the degree of correlation between experiments. Samples are color coded to reflect the degree of external genital virilization according to Prader that had been applied to both XX and XY individuals to enable comparability of genital phenotypes independent of the sex chromosomes. The dark grey bar below the experiment cluster represents individuals with an XX karyotype, light grey represents an XY karyotype. The major subdivison of the individuals corresponds strictly to the karyotype. The second level of subdivision in each of the major arms reflects mostly the phenotype of external genital virilization independent of the karyotype. (C) Schematic representation of the Prader stages of external genital virilization. (D) X-chromosome gene cluster (E) Y-chromosome gene cluster (F) Genes with predominantly higher transcript levels in the phenotypic females and the normal females independent of the karyotype (G) Genes with higher transcript levels in the strongly virilized individuals and the normal males independent of the karyotype.