Multi-omics and pathway analyses of genome-wide associations implicate regulation and immunity in verbal declarative memory performance

Table 5 Differential expression analysis of significant component genes from verbal declarative memory-associated pathways

GEO_ID	PUBMED_ID	Organism	Tissue	N_genes	Contrast	p-value
GDS4135	21705112	Human	Astrocytes	13	Braak stage I-II, III-IV, V-VI	0.006
GDS4231	21909266	Human	Brain tissues	13	HIV cognitive impairment vs uninfected control	3.28E − 08
GDS4358	23049970	Human	Basal ganglia	13	Trend I	3.33E − 05
			Basal ganglia	13	Trend II	8.83E − 05
			Frontal cortex	13	Trend I	0.74
			Frontal cortex	13	Trend II	0.99
			White matter	13	Trend I	0.03
			White matter	13	Trend II	0.50
GDS2082	15169854	House mouse	Hippocampus	12	15-month-old mice with age-related cognitive deficit vs 2-month-old normal mice	0.03
GDS2639	17376971	Norway rat	Hippocampus	6	Impaired vs. unimpaired cognition	0.016
GDS520	12736351	Norway rat	Hippocampus	5	Age 4, 14, and 24 months	0.015

This table contains results for the differential expression analysis (mean-rank test) of genes in memory-associated pathways by cognitive status in human and rodent samples. GEO_ID is the curated Gene Expression Omnibus data set identifier; PUBMED_ID is the PUBMED publication identifier. N_genes is the number of component genes that have expression measured in the given dataset (refer to Supplementary Tables S4 and S5 for the gene lists). Contrast indicates the cognitive function groups across which we contrasted the differential expression of component genes. p-value is the p-value from the gene-set differential analysis. The trend I test assessed differential expression across control, HIV-only, HIV-NCI, and HIV-NCI-HIVE statuses. The trend II test compared expression across the HIV-only, HIV-NCI, and HIV-NCI-HIVE statuses

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