Overall analytical strategy.

<p>In step I, 50 co-regulation modules were generated using meta-clustering of gene clusters identified by the “penalized K-medoids” method across 11 transcriptome MDD and matched controls studies. In step II, modules enriched from most of the selected GWAS studies related to MDD, neuropsychiatric disorder and traits, including systemic disease linked to psychiatric disorders were identified. In step III, the biological functions represented by genes included in each module were defined by pathway analysis from 2,334 gene sets of MSigDB (<a href="http://www.broadinstitute.org/gsea/msigdb" target="_blank">www.broadinstitute.org/gsea/msigdb</a>). In step IV, SNPs from the Catalog of GWAS were organized into three categories: cancer GWAS, human body indices GWAS and GWAS for common diseases and medial illnesses unrelated to MDD or other brain function. Three additional categories were defined as non-MDD-related negative control gene sets. (Note: In order to increase the performance of the heatmap in module #35, we first performed the hierarchical clustering with “complete” agglomeration method to aggregated samples with similar expression among all 88 genes, and the genes were sorted by the correlation from high to low of selected genes in the top.).</p

Consistent association of genes in module #35 with MDD-related gene categories.

<p>(<b>a</b>) Heatmap of log₁₀-transformed p-values from Fisher’s exact test for 50 modules obtained from MDD cases and matched controls and 8 MDD related GWAS and 3 negative controls. (<b>b</b>) Heatmap of log₁₀-transformed p-values from Fisher’s exact test for 50 modules obtained from controls and 8 MDD related GWAS and 3 negative controls. The green rectangle identifies module #35.</p

Histograms of the –log₁₀(p) of the Stouffer statistic from 50 modules of meta-analysis of 11 MDD studies and each single study.

<p>Module #35 with 88 genes (red arrow and double-cross) have largest –log₁₀ transformed p-value of Stouffer’s statistic 4.4. The other four blue arrows and double crosses indicated that these four modules in all single studies have more than 14 (15% of the 88 genes in module #35) overlapped with module #35. See detailed description in text.</p

Top 15 enriched pathways in module #35.

<p>Top 15 enriched pathways in module #35.</p

Description of cohorts in 11 MDD microarray platforms.

<p>ACC, anterior cingulate cortex; AMY, amygdala; DLPFC, dorsolateral prefrontal cortex, OFC, orbital ventral prefrontal cortex.</p

Functional groups of 88 gene in module #35<b>.</b>

<p>Annotations are based on Gene Ontology. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090980#pone-0090980-t003" target="_blank">Table 3</a> for a separate analysis of pathway enrichment.</p