Additional Table 6.
Differentially expressed genes in the APP/PS1 mouse cortices at 1,3,6,9 months in contrast to the same age of control mice
| Gene name | Mean TPM (APP/PS1) | Mean TPM (WT) | log2 fold change | P-value | Q-value | Result |
|---|---|---|---|---|---|---|
| 1-month-old | ||||||
| Lamr1-ps1 | 8.331597 | 0.0001 | 16.34631 | 5.35E-15 | 1.88E-11 | Up |
| Prnp | 1468.837 | 507.0883 | 1.534365 | 2.11E-95 | 6.69E-91 | Up |
| Pianp | 63.76651 | 149.0635 | -1.22506 | 3.88E-45 | 4.09E-41 | Down |
| Bloc1s6 | 7.290459 | 21.08952 | -1.53244 | 1.30E-06 | 0.001642 | Down |
| Rn7s1 | 53.21294 | 17.1677 | 1.63208 | 5.37E-05 | 0.045954 | Up |
| Gm15501 | 0.623963 | 7.492632 | -3.58594 | 1.07E-11 | 3.07E-08 | Down |
| Slc35e2 | 4.542831 | 10.98109 | -1.27336 | 7.13E-08 | 0.000113 | Down |
| AC147560.1 | 26.13961 | 0.315753 | 6.371299 | 1.62E-05 | 0.014659 | Up |
| Tanc2 | 8.460478 | 36.47014 | -2.1079 | 2.22E-32 | 1.01E-28 | Down |
| Erbb4 | 7.498425 | 1.720321 | 2.12391 | 2.57E-10 | 5.82E-07 | Up |
| AY036118 | 468.1067 | 205.2829 | 1.189224 | 1.08E-05 | 0.010017 | Up |
| Dagla | 40.63331 | 11.55615 | 1.814002 | 8.98E-36 | 5.68E-32 | Up |
| Armc10 | 6.946772 | 16.88577 | -1.28139 | 1.66E-22 | 6.57E-19 | Down |
| AC157822.1 | 21.46617 | 0.921064 | 4.542619 | 1.53E-06 | 0.001794 | Up |
| 3-month-old | ||||||
| Lamr1-ps1 | 7.63259 | 0.0001 | 16.21989 | 2.60E-14 | 5.40E-11 | Up |
| Nedd4 | 109.3076 | 42.50165 | 1.362803 | 1.79E-06 | 0.001427 | Up |
| Prnp | 1620.196 | 499.8317 | 1.696654 | 3.20E-89 | 6.64E-85 | Up |
| Xiap | 7.290938 | 24.78462 | -1.76527 | 6.42E-12 | 1.11E-08 | Down |
| Fcho2 | 16.98941 | 8.289213 | 1.035329 | 6.17E-12 | 1.11E-08 | Up |
| Zmym5 | 6.216562 | 14.43682 | -1.21556 | 1.07E-18 | 2.48E-15 | Down |
| Fkbp1a | 517.338 | 181.6905 | 1.509624 | 3.31E-64 | 3.43E-60 | Up |
| Commd8 | 23.31535 | 11.25659 | 1.050511 | 3.98E-05 | 0.021741 | Up |
| Ahcyl2 | 15.73925 | 48.70363 | -1.62966 | 1.05E-38 | 5.45E-35 | Down |
| Gm27505 | 0.248576 | 31.26797 | -6.97485 | 2.16E-11 | 2.80E-08 | Down |
| Mpv17l | 14.64497 | 39.01993 | -1.41381 | 7.24E-08 | 7.15E-05 | Down |
| Grb2 | 38.69309 | 81.70496 | -1.07835 | 1.62E-28 | 5.59E-25 | Down |
| Ndn | 86.16586 | 42.15611 | 1.031375 | 7.52E-12 | 1.20E-08 | Up |
| Macrod2 | 7.089322 | 17.83625 | -1.33109 | 4.46E-07 | 0.000375 | Down |
| 6-month-old | ||||||
| Gm3375 | 4.885447 | 47.44031 | -3.27955 | 2.03E-21 | 3.93E-18 | Down |
| Gm22133 | 836.8698 | 0.001819 | 18.8115 | 1.63E-13 | 1.97E-10 | Up |
| Lamr1-ps1 | 13.91555 | 0.0001 | 17.08634 | 1.20E-17 | 1.55E-14 | Up |
| Sik1 | 3.044825 | 6.180057 | -1.02126 | 3.00E-05 | 0.010762 | Down |
| Prnp | 2598.264 | 670.9482 | 1.953274 | 1.02E-34 | 2.81E-31 | Up |
| Lpin1 | 6.730367 | 1.05942 | 2.667411 | 1.47E-28 | 3.17E-25 | Up |
| Rasa3 | 18.69434 | 6.679233 | 1.484848 | 4.18E-05 | 0.014469 | Up |
| Arhgef9 | 26.89973 | 137.7715 | -2.35661 | 1.08E-89 | 1.05E-85 | Down |
| Egr2 | 1.947307 | 6.371476 | -1.71015 | 1.39E-06 | 0.000655 | Down |
| Gm15501 | 1.511224 | 10.68873 | -2.8223 | 5.14E-08 | 3.56E-05 | Down |
| Tjap1 | 11.55973 | 1.682152 | 2.780728 | 1.86E-43 | 6.02E-40 | Up |
| Ptprt | 17.44061 | 4.689551 | 1.894929 | 2.58E-05 | 0.009801 | Up |
| Fkbp1a | 662.6176 | 179.4312 | 1.884746 | 4.94E-51 | 2.40E-47 | Up |
| Cyr61 | 3.232472 | 6.781883 | -1.06905 | 4.41E-05 | 0.014492 | Down |
| Zfx | 0.192459 | 6.660784 | -5.11307 | 9.42E-90 | 1.05E-85 | Down |
| Gp1bb | 19.49666 | 47.08275 | -1.27197 | 4.29E-10 | 3.96E-07 | Down |
| Bcas3 | 43.73818 | 20.4742 | 1.095086 | 0.000116 | 0.034095 | Up |
| AC147560.1 | 0.218599 | 21.13628 | -6.59529 | 4.18E-05 | 0.014469 | Down |
| Stxbp1 | 346.1299 | 107.8913 | 1.681736 | 4.33E-07 | 0.000262 | Up |
| 2700081O15Rik | 4.00902 | 12.23863 | -1.61012 | 7.30E-29 | 1.77E-25 | Down |
| Brd4 | 26.71231 | 6.680526 | 1.999471 | 1.65E-45 | 6.40E-42 | Up |
| Sel1l | 9.919385 | 3.658156 | 1.439134 | 4.09E-08 | 3.05E-05 | Up |
| Icmt | 13.76329 | 5.797461 | 1.247332 | 0.000106 | 0.031634 | Up |
| 2-Sep | 4.048975 | 14.4711 | -1.83755 | 1.52E-09 | 1.28E-06 | Down |
| 12.22894 | 25.97062 | -1.08658 | 1.06E-18 | 1.47E-15 | Down | |
| Xpo7 | 3.723344 | 9.880672 | -1.40801 | 2.74E-21 | 4.83E-18 | Down |
| Arc | 66.9146 | 170.5302 | -1.34963 | 2.88E-05 | 0.010526 | Down |
| Fos | 11.17202 | 27.47285 | -1.29812 | 7.75E-09 | 6.01E-06 | Down |
| Il33 | 40.51075 | 19.46344 | 1.057538 | 4.48E-08 | 3.22E-05 | Up |
| Klf2 | 7.280256 | 15.40376 | -1.08122 | 2.19E-10 | 2.24E-07 | Down |
| Nr4a1 | 40.94647 | 82.88205 | -1.01732 | 6.23E-11 | 7.11E-08 | Down |
| Tnpo1 | 0.423412 | 14.81462 | -5.12882 | 1.05E-73 | 6.80E-70 | Down |
| Taf13 | 9.450447 | 22.09557 | -1.2253 | 1.28E-19 | 1.91E-16 | Down |
| Brsk2 | 38.12381 | 87.1189 | -1.19229 | 1.03E-20 | 1.66E-17 | Down |
| 9-month-old | ||||||
| Cst7 | 56.13222 | 0.410771 | 7.094351 | 4.02E-102 | 7.04E-98 | Up |
| Hnrnpc | 48.85224 | 110.192 | -1.17352 | 1.95E-38 | 6.82E-35 | Down |
| Mgat1 | 16.04041 | 7.332844 | 1.129266 | 5.09E-10 | 1.48E-07 | Up |
| Lamr1-ps1 | 8.060656 | 0.026737 | 8.235934 | 6.63E-13 | 3.14E-10 | Up |
| Nedd4 | 30.13857 | 106.1997 | -1.8171 | 8.02E-05 | 0.006562 | Down |
| Gpnmb | 6.932263 | 1.463214 | 2.244185 | 3.39E-11 | 1.16E-08 | Up |
| Itgax | 5.909267 | 0.159953 | 5.207256 | 9.49E-37 | 2.77E-33 | Up |
| Ctsz | 73.35858 | 33.67782 | 1.123167 | 8.06E-16 | 4.86E-13 | Up |
| Prnp | 1874.794 | 523.9732 | 1.839167 | 1.09E-34 | 2.74E-31 | Up |
| Capg | 5.834883 | 1.694853 | 1.783543 | 3.67E-09 | 9.30E-07 | Up |
| Slc11a1 | 7.507433 | 3.393156 | 1.145692 | 2.11E-12 | 9.03E-10 | Up |
| Lcn2 | 12.74023 | 0.238077 | 5.741817 | 0.000423 | 0.02372 | Up |
| Mpeg1 | 31.47217 | 13.46518 | 1.224843 | 7.80E-19 | 6.20E-16 | Up |
| Ly86 | 54.01884 | 23.03132 | 1.229865 | 3.19E-08 | 7.06E-06 | Up |
| Olfml3 | 10.90158 | 1.88724 | 2.530188 | 0.001177 | 0.047787 | Up |
| Rasa3 | 26.90664 | 12.72583 | 1.080203 | 4.20E-22 | 5.25E-19 | Up |
| Ndst4 | 2.53883 | 5.793142 | -1.19018 | 1.28E-09 | 3.43E-07 | Down |
| Hbb-bs | 87.68476 | 317.0072 | -1.85412 | 0.000721 | 0.03419 | Down |
| Csf3r | 10.2598 | 5.069636 | 1.017049 | 8.16E-08 | 1.68E-05 | Up |
| Fyb | 8.614782 | 3.643961 | 1.241307 | 0.000542 | 0.028191 | Up |
| Ifitm3 | 58.16765 | 25.94524 | 1.164747 | 9.37E-06 | 0.001086 | Up |
| Hba-a2 | 65.71364 | 256.5913 | -1.96521 | 0.000257 | 0.016528 | Down |
| Hba-a1 | 61.25622 | 233.2518 | -1.92896 | 0.000625 | 0.030723 | Down |
| Lag3 | 13.25408 | 5.91718 | 1.163455 | 5.91E-14 | 3.34E-11 | Up |
| Ifit3 | 15.28814 | 6.210571 | 1.299616 | 2.84E-12 | 1.16E-09 | Up |
| Rab26os | 20.04657 | 8.868279 | 1.176629 | 0.000132 | 0.009603 | Up |
| C1qa | 176.116 | 85.48203 | 1.042833 | 4.56E-22 | 5.31E-19 | Up |
| Atp8a1 | 16.20754 | 40.22233 | -1.31133 | 2.43E-05 | 0.002486 | Down |
| Gm15501 | 11.03089 | 0.729388 | 3.91872 | 2.92E-06 | 0.000399 | Up |
| mt-Ts2 | 0.534649 | 77.19743 | -7.17382 | 1.68E-06 | 0.000251 | Down |
| Cd300c2 | 8.388576 | 4.042001 | 1.053356 | 3.54E-06 | 0.00047 | Up |
| Pde1a | 16.58869 | 56.96195 | -1.7798 | 1.21E-11 | 4.71E-09 | Down |
| S100a8 | 11.53033 | 0.0001 | 16.81507 | 2.90E-05 | 0.002872 | Up |
| Cd9 | 93.21046 | 45.89574 | 1.022132 | 5.23E-12 | 2.08E-09 | Up |
| C4b | 45.46685 | 8.71795 | 2.382754 | 2.96E-26 | 4.71E-23 | Up |
| Clec7a | 11.98666 | 0.400086 | 4.904976 | 6.92E-59 | 6.05E-55 | Up |
| AU020206 | 5.639614 | 2.392004 | 1.237377 | 1.18E-12 | 5.30E-10 | Up |
| Bst2 | 11.60964 | 3.56583 | 1.703014 | 1.26E-11 | 4.71E-09 | Up |
| Serpina3n | 41.74544 | 10.41401 | 2.003093 | 1.65E-10 | 5.26E-08 | Up |
| Mef2c | 52.97231 | 113.2346 | -1.09601 | 2.42E-08 | 5.44E-06 | Down |
| Gfap | 356.9862 | 83.29594 | 2.09955 | 2.02E-16 | 1.26E-13 | Up |
| Tyrobp | 179.4221 | 50.84766 | 1.819104 | 1.15E-46 | 5.02E-43 | Up |
| Fcer1g | 74.58019 | 35.05207 | 1.089293 | 2.39E-13 | 1.31E-10 | Up |
| Ccl3 | 13.76641 | 0.103299 | 7.058177 | 1.63E-23 | 2.38E-20 | Up |
| Ifitm2 | 44.15068 | 20.8988 | 1.079016 | 0.000706 | 0.033667 | Up |
| Pcp2 | 9.978739 | 0.812252 | 3.618858 | 0.00093 | 0.040775 | Up |
| Ccl6 | 15.43149 | 3.330178 | 2.212206 | 4.57E-13 | 2.35E-10 | Up |
| Lsp1 | 8.248022 | 3.885915 | 1.085794 | 0.000368 | 0.021535 | Up |
| Tmem181b-ps | 103.2725 | 50.46891 | 1.03299 | 9.55E-17 | 6.43E-14 | Up |
| Pomc | 13.90785 | 0.843073 | 4.044098 | 3.24E-10 | 9.77E-08 | Up |
| S100a9 | 17.61923 | 0.248051 | 6.150368 | 8.08E-05 | 0.006578 | Up |
| Hbb-bt | 20.79302 | 84.56809 | -2.02401 | 1.40E-07 | 2.72E-05 | Down |
| Lyz2 | 53.46002 | 15.71911 | 1.765941 | 3.57E-31 | 7.80E-28 | Up |
| Oprk1 | 2.66741 | 7.020116 | -1.39606 | 4.56E-05 | 0.004206 | Down |
| Mid1-ps1 | 1.777277 | 7.015588 | -1.9809 | 7.81E-07 | 0.000133 | Down |
| Bcl2a1b | 5.293898 | 1.208159 | 2.13152 | 1.24E-08 | 2.89E-06 | Up |
| Spp1 | 37.59672 | 13.60768 | 1.466186 | 1.07E-06 | 0.000174 | Up |
| Lgals3bp | 35.8531 | 17.20962 | 1.058883 | 1.92E-11 | 6.85E-09 | Up |
| Erbb4 | 0.498413 | 8.41588 | -4.0777 | 0.00012 | 0.008989 | Down |
| Ifit3b | 8.604208 | 4.127797 | 1.05967 | 2.95E-10 | 9.06E-08 | Up |
| Gm694 | 12.25915 | 3.51378 | 1.802764 | 0.000173 | 0.011942 | Up |
| Trem2 | 42.76004 | 15.90794 | 1.426516 | 4.16E-19 | 3.47E-16 | Up |
| Oasl2 | 6.292386 | 2.665781 | 1.239049 | 2.85E-07 | 5.25E-05 | Up |
| Eps8l1 | 3.553843 | 8.104072 | -1.18927 | 6.40E-06 | 0.000789 | Down |
| Hist2h3c1 | 6.397843 | 2.655042 | 1.268851 | 5.74E-05 | 0.005027 | Up |
| Cd52 | 27.41597 | 6.647257 | 2.044186 | 6.68E-21 | 6.87E-18 | Up |
| Abi3 | 9.706694 | 4.683315 | 1.05145 | 1.31E-05 | 0.001458 | Up |
| Ifi27l2a | 8.036828 | 1.690128 | 2.249494 | 1.80E-07 | 3.43E-05 | Up |
| Cd14 | 7.541097 | 2.928268 | 1.364727 | 7.29E-07 | 0.000126 | Up |
| Cd68 | 55.73383 | 18.69902 | 1.575591 | 1.59E-30 | 3.09E-27 | Up |
| Ttbk2 | 1.047009 | 13.96846 | -3.73783 | 0.000204 | 0.013596 | Down |
| Snx10 | 31.4692 | 85.79997 | -1.44704 | 3.78E-50 | 2.21E-46 | Down |
| Camk2d | 25.34241 | 63.82576 | -1.33259 | 9.63E-18 | 7.03E-15 | Down |
| Hist2h2aa1 | 0.0001 | 22.909 | -17.8056 | 2.38E-18 | 1.81E-15 | Down |
| Fcgr2b | 12.93337 | 3.258524 | 1.988808 | 2.01E-19 | 1.85E-16 | Up |
| Grp | 21.454 | 9.28983 | 1.207523 | 0.000561 | 0.028589 | Up |
APP: Amyloid-beta peptide precursor protein; PS1: presenilin 1; TPM: transcripts per million; WT: wild type.