differences between the no SI (a score of 0) and the high SI (a score of 2 and above) visits, using a powerful within-participant design, then an across-participants summation (Figure 1). We analyzed the data in two ways: an Absent-Present (AP) approach, and a differential expression (DE) approach, as in previous work by us on suicide biomarkers. The AP approach may capture turning on and off of genes, and the DE approach may capture gradual changes in expression. Analyses were performed as previously described, , and as described in detail in Supplementary Information. Gene Symbol for the probesets were identified using NetAffyx (Affymetrix) for Affymetrix HG-U133 Plus 2.0 GeneChips, followed by GeneCards to confirm the primary gene symbol. In addition, for those probesets that were not assigned a gene symbol by NetAffyx, we used GeneAnnot () to obtain gene symbol for these uncharacterized probesets, followed by GeneCard. Genes were then scored using our manually curated CFG databases as described below (Figure 1E). Step 2: Prioritization Convergent Functional Genomics (CFG) Databases. We have established in our laboratory (Laboratory of Neurophenomics, ) manually curated databases of the human gene expression/protein expression studies (postmortem brain, peripheral tissue/fluids: CSF, blood and cell cultures), human genetic studies (association, copy number variations and linkage), and animal model gene expression and genetic studies, published to date on psychiatric disorders. Only findings deemed significant in the primary publication, by the study authors, using their particular experimental design and thresholds, are included in our databases. Our databases include only primary literature data and do not include review papers or other secondary data integration analyses to avoid redundancy and circularity. These large and constantly updated databases have been used in our CFG cross validation and prioritization platform (Figure 1E). For this study, data from 454 papers on suicide were present in the databases at the time of the CFG analyses (Summer 2016) (genetic studies-170, brain studies-197, peripheral fluids- 87). Analyses were performed as previously described, , and as described in detail in Supplementary Information.
differences between the no SI (a score of 0) and the high SI (a score of 2 and above) visits, using a powerful within-participant design, then an across-participants summation (Figure 1). We analyzed the data in two ways: an Absent-Present (AP) approach, and a differential expression (DE) approach, as in previous work by us on suicide biomarkers. The AP approach may capture turning on and off of genes, and the DE approach may capture gradual changes in expression. Analyses were performed as previously described, , and as described in detail in Supplementary Information. Gene Symbol for the probesets were identified using NetAffyx (Affymetrix) for Affymetrix HG-U133 Plus 2.0 GeneChips, followed by GeneCards to confirm the primary gene symbol. In addition, for those probesets that were not assigned a gene symbol by NetAffyx, we used GeneAnnot () to obtain gene symbol for these uncharacterized probesets, followed by GeneCard. Genes were then scored using our manually curated CFG databases as described below (Figure 1E). Step 2: Prioritization Convergent Functional Genomics (CFG) Databases. We have established in our laboratory (Laboratory of Neurophenomics, ) manually curated databases of the human gene expression/protein expression studies (postmortem brain, peripheral tissue/fluids: CSF, blood and cell cultures), human genetic studies (association, copy number variations and linkage), and animal model gene expression and genetic studies, published to date on psychiatric disorders. Only findings deemed significant in the primary publication, by the study authors, using their particular experimental design and thresholds, are included in our databases. Our databases include only primary literature data and do not include review papers or other secondary data integration analyses to avoid redundancy and circularity. These large and constantly updated databases have been used in our CFG cross validation and prioritization platform (Figure 1E). For this study, data from 454 papers on suicide were present in the databases at the time of the CFG analyses (Summer 2016) (genetic studies-170, brain studies-197, peripheral fluids- 87). Analyses were performed as previously described, , and as described in detail in Supplementary Information.
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