Genes and pathways underlying regional and cell type changes in Alzheimer's disease

Table 3 Top genes differentially expressed by disease and region

Gene	Fold change	P-value
Genes regionally DE in control only
CA1-specific
*SPARCL1*	-1.44 (-1.42)	7.0E-08
CYP1B1	-1.42	4.7E-07
PPP1R16B	-1.49	4.2E-06
KCNH3	-2.07	5.2E-06
EPHB1	-1.47	5.8E-06
STOX1	-1.56	5.8E-06
MT1M	-1.58	1.1E-05
ID2	-1.49	1.4E-05
SOX2	-1.49	1.7E-05
GPAM	-1.53	1.9E-05
CA3-specific
*NRIP3*	2.14 (2.52)	7.4E-08
*ABHD12*	1.54 (1.60)	9.0E-07
TMEM158	1.72	2.0E-06
*TSPAN18*	4.00 (4.07)	2.9E-06
TOMM34	1.85	4.2E-06
CCDC109A	1.52	6.7E-06
HOMER2	1.57	6.8E-06
CPNE4	3.18	7.5E-06
LINGO1	1.65	7.8E-06
HMGCR	1.65	8.8E-06
Genes changing with AD in CA1 only
Down with AD
SEPT5	-1.59	2.8E-05
CSPG5	-1.82	6.9E-05
WFDC1	-1.47	8.2E-05
KCNIP1	-1.77	1.0E-04
*CXCL14*	-1.96 (-2.09)	1.1E-04
ANKRD20A1	-1.81	1.6E-04
*SEC14L5*	-1.43 (-1.25)	3.0E-04
LOC648639	-1.71	3.1E-04
ARPP-21	-1.92	3.9E-04
ADRA1B	-2.11	6.3E-04
Up with AD
*S100A6*	1.59 (1.83)	4.6E-07
*GEM*	1.64 (2.05)	5.9E-06
PFKFB3	1.44	4.5E-05
SERPINA3	2.11	6.7E-05
TPST1	1.63	1.5E-04
SPARC	1.71	1.6E-04
CAB39L	1.46	1.9E-04
RCN1	1.42	2.0E-04
DMN	1.73	2.9E-04
BCL2	1.45	3.1E-04

Top ten CA1-specific genes in control (top list), CA3-specific genes in control (second list), genes down with AD in CA1 (third list), and genes up with AD in CA1 (bottom list) with fold change >1.4. For each list, the left column is the gene, the second column is the fold change of differential expression, and the right column is the associated P-value as measured by a t-test (Materials and methods). For genes that were validated using qRT-PCR (in bold), fold changes from the validations are presented in parentheses in the 'Fold change' column. All genes are still significant after accounting for cell type composition using a linear model. DE, differentially expressed.

ISSN: 1756-994X