Genotype frequencies of investigated SNPs/haplotypes.

<p>HWE: Hardy-Weinberg equilibrium; NA: not applicable.</p

Crosstalk analysis of enriched pathways/GO terms.

<p>Panel A shows the connections among the enriched pathways/GO terms. Blue squares are enriched KEGG pathways, green squares are their connected pathways from KEGG, red squares are enriched GO terms. Panel B shows the shared genes between the first group of enriched pathways. Panel C shows the shared genes between four groups of enriched pathways/GO terms. The genes in groups with more than one pathway/GO term were combined for the shared gene analysis.</p

Protein-protein interaction network involving all merged module genes.

<p>Square nodes denote the reported genes associated with schizophrenia or bipolar disorder. The color of the node was proportioned with the <i>P</i>-value of gene. The width of the edge was proportioned with the No. of repeats of the edge in the modules. The purple edges, green edges and blue edges were interactions from MGS, Affy6 and Affy500K respectively.</p

Crosstalk analysis of enriched pathways/GO terms.

<p>Panel A shows the connections among the enriched pathways/GO terms. Blue squares are enriched KEGG pathways, green squares are their connected pathways from KEGG, red squares are enriched GO terms. Panel B shows the shared genes between the first group of enriched pathways. Panel C shows the shared genes between four groups of enriched pathways/GO terms. The genes in groups with more than one pathway/GO term were combined for the shared gene analysis.</p

Enriched KEGG pathways and GO terms by module genes.

<p>^a Merged denotes all genes of the merged modules from MGS, Affy6 and Affy500K.</p><p>^b N is total number of genes in the pathway or GO term. X is number of input genes which is mapped to the pathway. Only pathways or GO terms with N < 350 were shown.</p><p>^c FDR is the Benjamini & Hochberg-adjusted <i>P</i>-value. Only pathways or GO terms with FDR < 0.05 were shown.</p><p>CC: cellular component; BP: biological process.</p><p>Enriched KEGG pathways and GO terms by module genes.</p

Characteristics of the included studies.

<p>PGC(CATIE): data from samples in Clinical Antipsychotic Trials of Intervention Effectiveness of Psychiatric Genomics Consortium; SNPs: single nucleotide polymorphisms; DSM: diagnosis and statistical manual of mental health disorders; NA:not available; ^aCases after excluding overlapping samples with study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090407#pone.0090407-Peng1" target="_blank">[23]</a>.</p

Schizophrenia GWAS datasets used for this analysis.

<p>^a The controls of Cardiff UK were from WTCCC [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133404#pone.0133404.ref069" target="_blank">69</a>].</p><p>^b The number of cases, controls and SNPs after quality control were labeled in parentheses.</p><p>Schizophrenia GWAS datasets used for this analysis.</p

Flow chart of study selection.

<p>Flow chart of study selection.</p

Results of meta-analysis.

a<p>studies with Caucasian samples were included; ^bstudies with Asian samples were included; NA: not available; OR: Odds ratio; CI: confidence interval; significant results of pooled ORs are presented in bold.</p

MK4MDD: A Multi-Level Knowledge Base and Analysis Platform for Major Depressive Disorder

<div><h3>Background</h3><p>Major depressive disorder (MDD) is a complex neuropsychiatric syndrome with high heterogeneity. There are different levels of biological components that underlie MDD and interact with each other. To uncover the disease mechanism, large numbers of studies at different levels have been conducted. There is a growing need to integrate data from multiple levels of research into a database to provide a systematic review of current research results. The cross level integration will also help bridge gaps of different research levels for further understanding on MDD. So far, there has been no such effort for MDD.</p> <h3>Descriptions</h3><p>We offer researchers a Multi-level Knowledge base for MDD (MK4MDD) to study the interesting interplay of components in the pathophysiological cascade of MDD from genetic variations to diagnostic syndrome. MK4MDD contains 2,341 components and 5,206 relationships between components based on reported experimental results obtained by diligent literature reading with manual curation. All components were well classified with careful curation and supplementary annotation. The powerful search and visualization tools make all data in MK4MDD form a cross-linked network to be applied to a broad range of both basic and applied research.</p> <h3>Conclusions</h3><p>MK4MDD aims to provide researchers with a central knowledge base and analysis platform for MDD etiological and pathophysiological mechanisms research. MK4MDD is freely available at <a href="http://mdd.psych.ac.cn">http://mdd.psych.ac.cn</a>.</p> </div