Table 1.
Overview of frontomedial cortex enriched genes analysed in this study.
Table 2.
Overview of temporal cortex enriched genes analysed in this study.
Table 3.
Overview of occipital cortex enriched genes analysed in this study.
Figure 1.
Schematic overview of the method.
SNP markers from GWAS data were assigned to single genes in a process termed “gene binning”, by implementing a novel LD-based tool (LDsnpR, Christoforou et al. under revision). Modified Sidak's P-values were extracted for each gene (“gene bin”) in the GWAS data sets. Single gene-based analysis of the differentially expressed cortical genes was performed by extracting the modified Sidak's P-values for the candidate genes from the NCNG GWAS. Gene set-based analysis of the differentially expressed cortical genes was performed by extraction of the modified Sidak's P-values, followed by GSEA of GWAS data on cognition, psychiatric disorders and non-psychiatric phenotypes. GSEA: Gene set enrichment analysis, GWAS: Genome-wide association study.
Table 4.
Gene-based analysis of frontomedial cortex enriched genes for association to cognitive abilities.
Table 5.
Gene-based analysis of temporal cortex enriched genes for association to cognitive abilities.
Table 6.
Gene-based analysis of occipital cortex enriched genes for association to cognitive abilities.
Table 7.
GSEA of differentially expressed cortical genes in neurocognitive traits.
Table 8.
GSEA of differentially expressed cortical genes in psychiatric disorders and non-psychiatric phenotypes.
Figure 2.
Functional characterisation of the human homologues to the rat regionally enriched cortical genes.
Search for over- and under-represented biological processes and molecular functions was performed by using Panther [35], [36]. The significance of over- and under-represented Panther classification categories in the complete list of candidate genes (i.e. all the cortical regions, column 2), the FMCx enriched genes (column 3), TCx enriched genes (column 4) and OCx enriched genes (column 5), is illustrated by a heat map. The statistical significance of each gene set (negative log P-value) is illustrated by colour intensity (red: over-represented, blue: under-represented, white: as expected). Number of genes in each gene set is listed. The OCx gene HTR5B was not represented in Panther. The percentage of genes within a gene set that map to the given category is indicated on the heat map, e.g. 59% of the 61 enriched genes map to the biological process “cellular process”. The first column states the overall distribution of a term among the 19,911 genes from the default human reference gene list, e.g. 31% of the 61 regional genes were expected to map to ‘“cellular process”, hence this category is significantly over-represented among the regional genes. Exp: expected (based on default human reference gene list), FMCx: frontomedial cortex, TCx: temporal cortex, OCx: occipital cortex, #: number of genes in each gene set, %: percentage of genes.