1. Global Gene Expression Analysis Reveals Evidence for Decreased Lipid Biosynthesis and Increased Innate Immunity in Uninvolved Psoriatic Skin 
Johann E. Gudjonsson, Jun Ding, Xing Li, Rajan P. Nair, Trilokraj Tejasvi, Zhaohui S. Qin, Debashis Ghosh, Abhishek Aphale, Deborah L. Gumucio, John J. Voorhees, Goncalo R. Abecasis, James T. Elder 
Journal of Investigative Dermatology 
Volume 129, Issue 12, Pages (December 2009)
DOI: /jid
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions

2. Figure 1
Principal component analysis. The first and second principal components are shown. Two uninvolved samples (2/58) overlapped minimally with the lesional samples, whereas a large overlap was observed between the control and uninvolved samples.
Journal of Investigative Dermatology  , DOI: ( /jid )
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions

3. Figure 2
Progressive gene changes in NN versus PN versus PP skin. To analyze genes that show progressive change through all three sample groups, we used a threshold of equal or greater than 1.3-fold change and a nominal P-value of less than 0.05 between NN and PN samples, whereas a twofold change was used to compare lesional versus uninvolved and control skin with an FDR corrected P-value of less than The blue color indicates low expression, whereas the red color indicates high -expression.
Journal of Investigative Dermatology  , DOI: ( /jid )
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions

4. Figure 3
QRT-PCR analysis of selected transcripts in NN versus PN versus PP skin. QRT-PCR was performed as described in Materials and Methods. Error bars indicate SEM (n=25 in control, uninvolved, and lesional groups). P-values for various comparisons are indicated above the horizontal bars. On average, C10orf99 was upregulated by approximately 1.7-fold in uninvolved samples, whereas ALOX15B was downregulated by 2-fold, galanin (GAL) by 1.9-fold, and ELOVL3 by 2.4-fold. C10orf99 was 30-fold upregulated in lesional skin.
Journal of Investigative Dermatology  , DOI: ( /jid )
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions

5. Figure 4
Correlated expression of genes involved lipid metabolism. Genes shown fall under the GO term “lipid metabolic process,” the term subsuming the largest number of downregulated transcripts in our sample. We observed a strong correlation between all the genes within this GO category, except for CYP1B1 and CD74. CD74 is the invariant polypeptide associated with major histocompatibility complex Class II molecules and it has been shown to have a role in enhancing lipid antigen presentation on CD1d. CYP1B1 is a member of the cytochrome P450 family, which catalyzed many reactions involved in drug metabolism and synthesis of cholesterol, steroids, and other lipids. It has been implicated in arachidonic acid metabolism in the cornea (Schwartzman et al., 1987). The most likely reason that these two genes do not show the same correlation as the rest of the group is that these are only marginally associated with lipid metabolic processes.
Journal of Investigative Dermatology  , DOI: ( /jid )
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions

6. Figure 5
Bioinformatic analysis of promoter-binding sites. The transcription factors PPARA, ESR2, and SREBF were found to have an increased number of promoter-binding sites in the lipid metabolism group compared with three control groups consisting of genes with low, medium, and high expressions in our data set.
Journal of Investigative Dermatology  , DOI: ( /jid )
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions

7. Figure 6
Pathway analysis of lipid metabolic process genes. To interrogate the known interactions among the 25 lipid metabolic process genes that are co-regulated in PN and NN skin and the three transcription factors that show enriched numbers of binding sites in the promoters of these genes, we used Genomatix BiblioSphere to build gene interaction networks. Two of the enriched transcription factors, PPARA and ESR, connected most (17/25) of the genes in an extended network.
Journal of Investigative Dermatology  , DOI: ( /jid )
Copyright © 2009 The Society for Investigative Dermatology, Inc Terms and Conditions