Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Quality control (QC) parameters for RNA. The relationships between RNA QC (determined by the average of the 5′/3′ signal ratios of β-actin and glyceraldehyde-3-phosphate dehydrogenase across U133A and U133B chips) and the postmortem interval (PMI) in Brodmann area (BA) 4, BA11, and BA8/9 show no effect of the PMI on the QC measurements. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Results of principal component analysis. Analysis was based on the approximately genes on the HG-U133A chip from control samples in 3 cortical regions (Brodmann area [BA] 11, BA4, and BA8/9) and the cerebellum. The first 3 components accounted for 31.7% of the total variance. Components 1, 2, and 3 accounted for 14.1%, 10.7%, and 7.0% of the variances, respectively. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Venn diagrams show the number of genes identified as differentially expressed and the overlap of genes between the different comparisons in the motor cortex (Brodmann area [BA] 4), the dorsolateral prefrontal cortex (BA8/9), and the orbital cortex (BA11). Each circle represents a single contrast. Upward and downward arrows indicate the number of up- and down-regulated genes. The numbers of genes that are differentially expressed in a single contrast are shown in parentheses. The intersections of the circles indicate the number of genes common between contrasts. The between-region Venn diagram shows the differentially expressed genes in BA4, BA8/9, and BA11. The numbers of genes that are differentially expressed in a single brain region are shown in parentheses. The intersections of the circles indicate the number of genes differentially expressed between brain regions. C indicates control subjects; DSC, depressed suicide completers; and SC, suicide completers. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Hierarchical cluster analysis of the 375 genes identified as being differentially expressed in Brodmann area (BA) 11. Both expression patterns in individuals and genes were clustered. A, Clustered image map. The color and intensity indicate direction and level of change. Blue spectrum colors indicate down-regulated expression; red spectrum colors, up-regulated expression. C indicates controls; DSC, depressed suicide completers; and SC, suicide completers. B, Cluster set plots display the average expression profile (light green line) of all genes in each of the clusters, along with the minimum and maximum deviation around the mean (black vertical lines). C, Principal component analysis based on the differentially expressed genes. The first 3 components accounted for 63.3% of the total variance (components 1, 2, and 3 accounted for 41.9%, 15.9%, and 5.5% of the variance, respectively). The DSC, SC, and C groups show separation on the first component. D, Graphical representation of the percentage of the most common gene ontology terms within each of the clusters in BA11. ATP indicates adenosine triphosphate. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Motor cortex (Brodmann area [BA] 4) analysis. A, Clustered image map of the hierarchical cluster analysis of the 163 genes identified as being differentially expressed genes in BA4. Both expression patterns in individuals and genes were clustered. The color and intensity indicate direction and level of change. Blue spectrum colors indicate down-regulated expression; red spectrum colors, up-regulated expression. Most of the genes (99 or approximately 60%) were misregulated in the depressed suicide completers (DSC) in relation to controls (C). Of these, 63 were up-regulated and 36 were down-regulated in relation to the C group. SC indicates suicide completers. B, Cluster set plots display the average expression profile (light green line) of all genes in each of the clusters, along with the minimum and maximum deviation around the mean (black vertical lines). C, Principal component analysis based on the differentially expressed genes. The first 3 components accounted for 61.2% of the total variance. Components 1, 2, and 3 accounted for 36.4%, 20.0%, and 4.9% of the variance, respectively. The DSC, SC, and C groups show separation on the first component. D, Graphical representation of the percentage of the most common gene ontology terms within each of the clusters. ATP indicates adenosine triphosphate. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Dorsolateral prefrontal cortex (Brodmann area [BA] 8/9) analysis. A, Clustered image map of the hierarchical cluster analysis of the 282 genes identified as being differentially expressed genes in the BA8/9. Both expression patterns in individuals and genes were clustered. The color and intensity indicate direction and level of change. Blue spectrum colors indicate down-regulated expression; red spectrum colors, up-regulated expression. Most of the genes were misregulated in suicide completers (SC) in relation to controls (C) (140 or approximately 50%) and depressed suicide completers (DSC) (75 or approximately 25%). B, Cluster set plots display the average expression profile (light green line) of all genes in each of the clusters, along with the minimum and maximum deviation around the mean (black vertical lines). C, Principal component analysis based on the differentially expressed genes. The first 3 components accounted for 65.6% of the total variance. Components 1, 2, and 3 accounted for 43.6%, 17.2%, and 4.7% of the variance, respectively. The DSC, SC, and C groups show separation on the first component. D, Graphical representation of the percentage of the most common gene ontology terms within each of the clusters. ATP indicates adenosine triphosphate; GTP, guanosine triphosphate. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Graphic representations of the observed changes in spermidine/spermine N 1 -acetyltransferase gene (SSAT) expression. Raw Affymetrix data (Microarray Analysis Suite version 5.0; available at: illustrate the differential expression of SSAT in Brodmann area (BA) 4, BA8/9, and BA11. C indicates controls; DSC, depressed suicide completers; and SC, suicide completers. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Spermine/spermidine N 1 -acetyltransferase gene (SSAT) and β-actin polymerase chain reaction (PCR) products after reverse transcription and PCR amplification. A, Agarose gel stained by ethidium bromide. Bands illustrated as an example are from Brodmann area (BA) 4. C indicates controls; DSC, depressed suicide completers; and SC, suicide completers. B, Distribution of the SSAT342A/C locus in a sample of SC (n = 181) and matched controls (n = 80). CI indicates confidence interval; OR, odds ratio. C, Graphical representation of the relative SSAT messenger RNA (mRNA) levels in C, SC, and DSC groups (percentage of β-actin). The semiquantitative analysis by reverse transcription–PCR of SSAT mRNA levels was performed in the motor cortex (BA4), dorsolateral prefrontal cortex (BA8/9), and orbital cortex (BA11). Asterisks indicate significant differences compared with the C group. Figure Legend:

Date of download: 6/25/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression Arch Gen Psychiatry. 2006;63(1): doi: /archpsyc Confirmation of the spermine/spermidine N 1 -acetyltransferase gene (SSAT) expression differences at the protein level. A, Immunohistochemical staining photomicrographs of adjacent brain sections using an anti-SSAT polyclonal antibody (1:75) in the motor cortex (Brodmann area [BA] 4), the dorsolateral prefrontal cortex (BA8/9), and the orbital cortex (BA11) of a control subject (C), a suicide completer (SC), and a suicide completer with major depression (DSC). Arrows indicate examples of positive immunohistochemical staining. B, Western blot analysis using an anti-SSAT polyclonal antibody (1:1000) in the motor cortex (BA4), dorsolateral prefrontal cortex (BA8/9), and orbital cortex (BA11). Asterisks indicate significant differences in comparisons with the control group. Figure Legend: