Transcriptional Profiling of Epidermal Keratinocytes: Comparison of Genes Expressed in Skin, Cultured Keratinocytes, and Reconstituted Epidermis, Using Large DNA Microarrays  Alix Gazel, Patricia Ramphal, Martin Rosdy, Bart De wever, Carine Tornier, Nadia Hosein, Brian Lee, Marjana Tomic-Canic, Miroslav Blumenberg  Journal of Investigative Dermatology  Volume 121, Issue 6, Pages 1459-1468 (December 2003) DOI: 10.1111/j.1523-1747.2003.12611.x Copyright © 2003 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 1 Scatterplots of individual versus individual microarrays, individual arrays versus medians, and the medians. Scatterplots compare the expression of all genes in two experiments; the identically expressed genes fall on the diagonal. The thin lines offset from the diagonals mark the 2-, 3-, 10-, and 30-fold differences in expression. The top row shows representative comparisons of two individual microarrays from each sample type. The middle row shows comparisons of one microarray with the median of all five. In the comparison with the medians, points fall much closer to the diagonal. The bottom row shows comparisons of the medians. The wider scattering of the points between different samples indicates an abundance of differentially expressed genes, including many differentially expressed 10-fold or more. K'cyt, cultured keratinocytes; REp, reconstituted epidermis. Journal of Investigative Dermatology 2003 121, 1459-1468DOI: (10.1111/j.1523-1747.2003.12611.x) Copyright © 2003 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 2 Functional classes of genes identified in the scatterplots. Groups of functionally related genes can be selected from the gene annotations, identified and highlighted within the scatterplots. Here we show genes whose annotations contain the words “mitochondrial” (top) or “growth factor” (bottom). Journal of Investigative Dermatology 2003 121, 1459-1468DOI: (10.1111/j.1523-1747.2003.12611.x) Copyright © 2003 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 3 Identification of keratin genes in scatterplots. Individual genes containing the word “keratin” are highlighted and identified in the scatterplot comparing medians of skin and cultured keratinocytes microarrays. Note that the keratin differentiation markers, 1, 2e, and 10, are expressed at higher levels in skin, whereas the simple-epithelia keratins, 8, 18, and 19, are expressed more in cultured cells. Several hair keratin genes appear expressed at low levels and are marked with “h” KGFR is the gene for keratinocyte growth factor, and a represents a gene annotated as “cloned from a keratinocyte cDNA library”; both contain the string of letters “keratin” in their annotations. In the scatterplot of reconstituted epidermis versus cultured keratinocytes, we identified the same differentially expressed keratins (arrows), and in the scatterplot of skin versus reconstituted epidermis, most keratin genes fall at or close to the diagonal. Journal of Investigative Dermatology 2003 121, 1459-1468DOI: (10.1111/j.1523-1747.2003.12611.x) Copyright © 2003 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 4 Clustering of differentially expressed genes. (A) Self-organizing maps distributing the genes into 24 bins of a 6×4 grid. Of the 15 microarrays, the first 5 are cultured keratinocytes, the middle 5 skin, and the last 5 from reconstituted epidermis, as shown in the top left cluster. The lines represent the medians of relative expression of the genes in each cluster. Whereas many clusters contain genes specifically highly expressed in just one microarray, e.g., the top left, or bottom right clusters, and are presumably outlier artifacts, other clusters contain genes differentially induced or suppressed in cultured keratinocytes, skin, and reconstituted epidermis. (B) Correlation coefficient clustering. A set of 6 selected clusters of the 28 obtained is chosen to demonstrate similarities with the self-organizing maps. Journal of Investigative Dermatology 2003 121, 1459-1468DOI: (10.1111/j.1523-1747.2003.12611.x) Copyright © 2003 The Society for Investigative Dermatology, Inc Terms and Conditions