Table 2. Differentially expressed genes (FDR corrected p-value < 0.05 for three-group comparison, co-varied for age, race, sex, and batch effects) associated with the top-3 KEGG pathways identified by the DAVID software package.
Genes are listed separately for each pathway.
| a) T-cell receptor pathway genes | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| GENE SYMBOL |
p-value (Group) |
FDR corrected p-value |
p-value (AD vs. HD) |
Fold- Change (AD vs. HD) |
p-value (AD vs. MD) |
Fold- Change (AD vs. MD) |
p-value HD vs. MD) |
Fold- Change (HD vs. MD) |
REFSEQ_ID | DEFINITION |
| NFKBIE | 8.41E- 04 |
4.22E-02 | 1.92E- 04 |
1.38 | 4.59E-03 | 1.27 | 1.07E-01 (NS) |
−1.09 | NM_004556.2 | Homo sapiens nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon (NFKBIE), mRNA. |
| RASGRP1 | 1.76E- 04 |
1.99E-02 | 5.22E- 03 |
1.37 | 4.69E-05 | 1.64 | 1.80E-02 | 1.20 | NM_005739.2 | Homo sapiens RAS guanyl releasing protein 1 (calcium and DAG-regulated) (RASGRP1), mRNA. |
| ARHGAP12 | 1.17E- 03 |
4.80E-02 | 1.81E- 03 |
1.36 | 2.87E-04 | 1.45 | 3.28E-01 (NS) |
1.06 | NM_018287.5 | Homo sapiens Rho GTPase activating protein 12 (ARHGAP12), mRNA. |
| MAPK14 | 7.32E- 04 |
3.94E-02 | 3.87E- 01 (NS) |
1.05 | 4.92E-02 | −1.13 | 1.83E-04 | −1.19 | NM_001315.1 | Homo sapiens mitogen- activated protein kinase 14 (MAPK14), transcript variant 1, mRNA. |
| PAK1 | 7.09E- 05 |
1.57E-02 | 1.07E- 02 |
−1.29 | 2.86E-05 | −1.59 | 3.45E-03 | −1.23 | NM_002576.3 | Homo sapiens p21/Cdc42/Rac1- activated kinase 1 (STE20 homolog, yeast) (PAK1), mRNA. |
| PIK3CG | 5.01E- 04 |
3.15E-02 | 8.24E- 04 |
−1.43 | 1.21E-04 | −1.53 | 3.17E-01 (NS) |
−1.07 | NM_002649.2 | Homo sapiens phosphoinositide- 3-kinase, catalytic, gamma polypeptide (PIK3CG), mRNA. |
| PTPN6 | 1.85E- 04 |
2.02E-02 | 1.20E- 04 |
−1.56 | 7.06E-05 | −1.59 | 7.67E-01 (NS) |
−1.02 | NM_080548.3 | Homo sapiens protein tyrosine phosphatase, non-receptor type 6 (PTPN6), transcript variant 2, mRNA. |
| b) JAK-STAT signaling pathway genes | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| GENE SYMBOL |
p-value (Group) |
FDR corrected p-value | p-value (AD vs. HD) |
Fold- Change (AD vs. HD) |
p-value (AD vs. MD) |
Fold- Change (AD vs. MD) |
p-value (HD vs. MD) |
Fold- Change (HD vs. MD) |
REFSEQ_ID | DEFINITION |
| BCL2 | 9.08E- 04 |
4.34E-02 | 2.90E- 03 |
1.36 | 2.04E-04 | 1.50 | 1.64E-01 (NS) |
1.10 | NM_000633.2 | Homo sapiens B-cell CLL/lymphoma 2 (BCL2), nuclear gene encoding mitochondrial protein, transcript variant alpha, mRNA. |
| IL15 | 1.05E- 03 |
4.66E-02 | 2.42E- 04 |
1.35 | 2.45E-03 | 1.27 | 2.42E-01 (NS) |
−1.06 | NM_000585.2 | Homo sapiens interleukin 15 (IL15), transcript variant 3, mRNA. |
| IL21R | 1.24E- 04 |
1.85E-02 | 3.80E- 04 |
1.13 | 2.67E-05 | 1.16 | 1.79E-01 (NS) |
1.03 | NM_181078.1 | Homo sapiens interleukin 21 receptor (IL21R), transcript variant 2, mRNA. |
| CSH1 | 4.96E- 04 |
3.15E-02 | 2.10E- 04 |
−1.16 | 2.64E-04 | −1.16 | 9.30E-01 (NS) |
1.00 | NM_022640.2 | Homo sapiens chorionic somatomammotropin hormone 1 (placental lactogen) (CSH1), transcript variant 2, mRNA. |
| IFNAR2 | 4.32E- 04 |
3.03E-02 | 1.78E- 02 |
−1.21 | 1.49E-04 | −1.39 | 1.30E-02 | −1.15 | NM_207585.1 | Homo sapiens interferon (alpha, beta and omega) receptor 2 (IFNAR2), transcript variant 1, mRNA. |
| PIAS1 | 8.78E- 05 |
1.66E-02 | 4.47E- 04 |
−1.26 | 1.79E-05 | −1.35 | 1.08E-01 (NS) |
−1.07 | NM_016166.1 | Homo sapiens protein inhibitor of activated STAT, 1 (PIAS1), mRNA. |
| MKNK1 | 5.19E- 04 |
3.17E-02 | 4.47E- 03 |
−1.35 | 1.20E-04 | −1.53 | 6.20E-02 (NS) |
−1.14 | NM_003684.3 | Homo sapiens MAP kinase interacting serine/threonine kinase 1 (MKNK1), transcript variant 1, mRNA. |
| STAT5A | 9.72E- 05 |
1.75E-02 | 2.22E- 04 |
−1.42 | 2.20E-05 | −1.52 | 2.41E-01 (NS) |
−1.07 | NM_003152.2 | Homo sapiens signal transducer and activator of transcription 5A (STAT5A), mRNA. |
| PIK3CG | 5.01E- 04 |
3.15E-02 | 8.24E- 04 |
−1.43 | 1.21E-04 | −1.53 | 3.17E-01 (NS) |
−1.07 | NM_002649.2 | Homo sapiens phosphoinositide- 3-kinase, catalytic, gamma polypeptide (PIK3CG), mRNA. |
| TNFRSF1A | 2.11E- 04 |
2.12E-02 | 1.05E- 03 |
−1.46 | 4.44E-05 | −1.65 | 1.09E-01 (NS) |
−1.13 | NM_001065.2 | Homo sapiens tumor necrosis factor receptor superfamily, member 1A (TNFRSF1A), mRNA. |
| PTPN6 | 1.85E- 04 |
2.02E-02 | 1.20E- 04 |
−1.56 | 7.06E-05 | −1.59 | 7.67E-01 (NS) |
−1.02 | NM_080548.3 | Homo sapiens protein tyrosine phosphatase, non-receptor type 6 (PTPN6), transcript variant 2, mRNA. |
| PLCB2 | 1.73E- 04 |
1.99E-02 | 2.84E- 04 |
−1.86 | 4.23E-05 | −2.06 | 3.28E-01 (NS) |
−1.11 | NM_004573.2 | Homo sapiens phospholipase C, beta 2 (PLCB2), mRNA. |
| c) Pentose Phosphate shunt pathway genes | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| GENE SYMBOL |
p-value (Group) |
FDR corrected p-value | p-value (AD vs. HD) |
Fold- Change (AD vs. HD) |
p-value (AD vs. MD) |
Fold- Change (AD vs. MD) |
p-value (HD vs. MD) |
Fold- Change (HD vs. MD) |
REFSEQ_ID | DEFINITION |
| PRPS2 | 5.68E- 05 |
1.57E-02 | 1.79E- 04 |
1.38 | 1.21E-05 | 1.49 | 1.76E-01 (NS) |
1.08 | NM_001039091.1 | Homo sapiens phosphoribosyl pyrophosphate synthetase 2 (PRPS2), transcript variant 1, mRNA. |
| DERA | 1.70E- 04 |
1.99E-02 | 4.88E- 05 |
1.26 | 1.80E-04 | 1.24 | 5.36E-01 (NS) |
−1.02 | NM_015954.2 | Homo sapiens 2-deoxyribose-5- phosphate aldolase homolog (DERA), mRNA. |
| TKT | 5.22E- 04 |
3.17E-02 | 6.69E- 04 |
−1.67 | 1.35E-04 | −1.81 | 4.02E-01 (NS) |
−1.08 | NM_001064.1 | Homo sapiens transketolase (Wernicke-Korsakoff syndrome) (TKT), mRNA. |
| PGLS | 1.13E- 05 |
9.66E-03 | 2.87E- 06 |
−1.68 | 1.97E-05 | −1.58 | 3.65E-01 (NS) |
1.06 | NM_012088.2 | Homo sapiens 6- phosphogluconolactonase (PGLS), mRNA. |