Summary of GO cluster analysis results for the lists of differentially expressed genes with known direct relationships.

<p>Enrichment score is a –Log10 of a geometric mean of individual <i>p</i> reported for individual GO terms within cluster. Only top 5 clusters that exceed enrichment score cut-off of 2 (corresponds to geometric mean of <i>p</i> = 0.01) are listed. The listed terms present in cluster are the most representative of the main themes of all GO terms included in cluster.</p

Summary of GO cluster analysis results for the lists of all differentially expressed genes.

<p>Enrichment score is a –Log10 of a geometric mean of individual <i>p</i> reported for individual GO terms within cluster. Only the top two clusters that exceed enrichment score cut-off of 2 (corresponds to geometric mean of <i>p</i> = 0.01) are listed. The listed terms that are present in cluster are the most representative of the main themes of all GO terms included in cluster.</p

Functional annotation analysis demonstrates that differentially expressed probe sets represent true biological difference between control and depressed suicide subject groups.

<p>Comparison of functional annotation analysis of differentially expressed probe sets generated at different <i>p</i> and FC cut-offs and randomly generated probe sets lists of the same size. Note the shift of the experimental curve to the right.</p

Coordinated gene expression is greatly reduced in suicide/MDD cohort.

<p>Pearson’s correlation-based gene network for differentially expressed genes for depressed suicide class. Red nodes represent genes up-regulated in depressed suicide class, blue nodes represent genes down-regulated in depressed suicide class, graphs - correlation of gene expression. Network contains 21 genes connected by 80 correlation relationships higher than 0.8.</p

Comparison of complexity of relationship networks generated for the DEG’s list and 100 random probe set lists of the same size.

<p>Total number of entities and relationships present in the largest network generated for a list were used to construct the graph. Circles represent random probe set lists, yellow square represents the average for 100 random list networks and the red diamond represents the DEG list. The red triangle shows the value of entities versus relationships found from our gene list. The Z score for this value in relation to average (yellow square) was 12.5 (p<0.01).</p

Gene relationship network generated for differentially expressed genes based on known direct relationships.

<p>For detailed description of various types of relationships see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047581#pone.0047581.s001" target="_blank">Table S1</a>.</p

Heat Map and dendrogram of all Control and depressed/suicide samples show both up and down-regulation and clustering of 238 differentially expressed genes.

<p>Relative Expression values were normalized across all samples within each data set. Rows represent probes while columns represent individual samples. Grey bars indicate no difference in expression, whereas blue and red indicate more and less expression, respectively.</p

PCA demonstrates separation of control and depressed suicide subject groups. PCA

<p>of microarray expression data based on complete data set. Red nodes represent control subjects, blue nodes - depressed suicide victims. Variable shading indicates distance from a viewer in 3D space.</p

Relationship between Fold Change (FC) reported in microarray and QPCR experiments.

<p>Pearson’s correlation r = 0.86 and <i>p</i><0.01. Circles represent individual genes. If more than one probe set was present in microarray dataset for a particular gene, an average FC was used for this gene as a “MAS5 FC”.</p

Summary of the known functions of genes that were found to be “hubs” in the pathway analysis network of DEGs’.

<p>Summary of the known functions of genes that were found to be “hubs” in the pathway analysis network of DEGs’.</p