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Table 3 Top genes differentially expressed by disease and region

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

Gene Fold change P-value
Genes regionally DE in control only   
    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
    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
  1. 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.