Flowchart for (1) detection and replication of schizophrenia associated pathways and (2) identification of the most informative genes, and (3) functional annotation of single nucleotide polymorphisms in the genes of interest.

<p>Flowchart for (1) detection and replication of schizophrenia associated pathways and (2) identification of the most informative genes, and (3) functional annotation of single nucleotide polymorphisms in the genes of interest.</p

Comparisons of FDRs (BH) and p-values (P) for the BOMA-UTR and the GAIN-MGS data sets for the replicated pathways.

<p>* - Significant pathways identified by more than one pathway analysis method within the BOMA-UTR data set. The test statistics obtained using the alternative algorithms are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345.s004" target="_blank">Table S1B</a>.</p><p>Note: FDR – False Discovery Rate; BH – Benjamini-Hochberg.</p

Description of individual samples.

a<p>Platforms are: I5, Illumina HumanHap 550; I6Q, Illumina Human610 Quad; IWQ, Illumina Human660W-Quad; A6, Affymetrix Genome-Wide Human SNP Array 6.0.</p>b<p>Publication reporting individual sample level genotypes for Schizophrenia is listed.</p><p>Discovery set: single nucleotide polymorphisms (SNPs) before pruning – 491,393; after pruning – 419,267.</p><p>Replication set: SNPs before pruning – 669,059; after pruning – 552,988.</p

RegulomeDB functional annotation for SNPs in CTCF and its regulatory regions.

<p>Notes: * genotyped in the BOMA-UTR data set and sorted by their genomic coordinates. SNPs are within or 20 kb upstream and downstream of <i>CTCF</i>. ** <i>AR FOXA1 USF1 CDX2 HNF4A TRIM28 USF2 TCF4 HDAC2 SP1 BHLHE40</i>. *** <i>KROX SP4 SP1:SP3 HIC1 Zif268 Sp4 Sp1 SP1 Egr</i>. § RegulomeDB score: [1f] - likely to affect binding and linked to expression of a gene target; [2b] - likely to affect binding; <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345-Herold1" target="_blank">[4]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345-Wang1" target="_blank">[5]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004345#pgen.1004345-Ramanan1" target="_blank">[6]</a> - minimum binding evidence.</p

StoichFun_SEM_Richness

StoichFun_SEM_Richnes

StoichFun_SEM_Evenness

StoichFun_SEM_Evennes

Readme_StoichFun

Readme_StoichFu

Results of the INRICH pathway analysis.

<p>Results of the INRICH pathway analysis are shown in bar plot format. The x-axis shows negative logarithmic enrichment p-values for all nominally associated pathways containing two and more genes prior to- (gray) and after- (blue) correction for multiple testing. The red horizontal line indicates a p-value of 0.05.</p

Results of the Ingenuity Pathway Analysis.

<p>Results of the Ingenuity Pathway Analysis (IPA) are shown in bar plot format. The x-axis shows negative logarithmic enrichment p-values for all associated pathways containing two and more genes prior to- (gray) and after- (blue) Benjamini Hochberg correction for multiple testing. The red horizontal line indicates a p-value of 0.05.</p

IPA pathway synaptic long term potentiation.

<p>Results of the Ingenuity pathway analysis (IPA) for the pathway “Synaptic Long Term Potentiation” are shown. Shared schizophrenia-bipolar disorder associated genes (<i>GRIN2A</i>, <i>GRM3</i>, <i>CACNA1C</i>) are highlighted in purple.</p