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Table S2. Genes Differentially Expressed Between Human and Chimpanzee Brain We Calculated Differential Expression Using a Mask A

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Table S2. Genes Differentially Expressed Between Human and Chimpanzee Brain We Calculated Differential Expression Using a Mask A Table S2. Genes differentially expressed between human and chimpanzee brain We calculated differential expression using a mask accounting only for sequence differences between species (species mask only) or the combination of this species mask and a second mask removing probes with multiple hits in either genome (species and unique mask). This table compares the results from these two different analyses. All genes differentially expressed between human and chimpanzee brain with either mask are listed. To be called differentially expressed, a gene had to be significant with p<0.05 in t-test after Benjamini-Hochberg correction for multiple testing (p), have a fold change (FC) of >1.2, and a difference in unlogged units of expression (UD) of >20. The last columns indicate to which TF family a TF belongs (TF family), if a gene associated with any TF (TA), and if a TF in the brain wTO network (N). nd=not detected, and includes genes with detection p-value >0.05 as well as probesets that included too few probes (<4) after masking for accurate detection. Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N 76P 0.002101 1.276145 220.3311 Yes 0.000264 1.346755 372.3989 Yes no TF Yes No AASS 0.050991 1.2218027.451443 No 0.0334021.35444 54.41867Yes no TF Yes No ABCA8 0.019492 2.26484 541.6135 Yes 0.010835 2.355025 561.8352 Yes no TF Yes No ABCB10 0.006016 1.963964 100.8908 Yes 0.015467 1.874999 123.7652 Yes no TF Yes No ABCF2 0.000319 2.051627 373.7187 Yes 0.001279 1.547559 204.7208 Yes no TF Yes No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N ABHD6 0.011121 1.409179 276.5826 Yes 0.014998 1.344751 210.2857 Yes no TF Yes No ABI3BP 0.00081 2.245241193.6929 Yes nd nd nd No no TF No No ACAD11 0.048372 1.246835 83.37943 Yes 0.046995 1.242362 85.30523 Yes no TF Yes No ACAD8 0.000503 2.440463 126.973 Yes 0.000796 2.130244 141.8243 Yes no TF Yes No ACADM 0.001751 4.6452 782.0687 Yes 0.000435 1.820035 418.5473 Yes no TF Yes No ACN9 nd nd nd No 0.0026581.589313 60.63251Yes no TF Yes No ACOT6 0.001308 1.994079 67.9982 Yes 0.001219 2.007423 68.1632 Yes no TF No No ACOX1 0.063043 1.48674 131.2432 No 0.040309 1.504971 153.9699 Yes no TF Yes No ACOX3 0.065208 1.263293 87.54937 No 0.011075 1.852469 155.3061 Yes no TF No No ACP6 nd nd nd No 0.0007841.599693 195.6229Yes no TF Yes No ACTR6 0.00597 1.280672 90.78578 Yes 0.009122 1.239558 80.01446 Yes no TF Yes No ACVR1C 0.042562 1.437522 173.0288 Yes 0.065808 1.399339 137.1889 No no TF No No ACY1 0.031354 1.2142 97.37801 Yes 0.013163 1.206433 94.08058 Yes no TF Yes No ACYP2 0.001014 1.51936 1160.892 Yes 0.00116 1.563708 1294.391 Yes no TF Yes No ADAMTS13 nd nd nd No 0.0055081.353308 116.0457Yes no TF Yes No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N ADARB1 0.014177 1.287386 99.67365 Yes 0.013163 1.289545 103.6576 Yes no TF Yes No ADARB2 0.033092 1.701972 150.8255 Yes 0.039596 1.683925 118.1544 Yes no TF No No ADAT1 0.002213 1.594694 143.0566 Yes 0.002032 1.592908 145.5218 Yes no TF Yes No ADCY5 0.006562 1.338739 212.779 Yes 0.006501 1.33322 209.3532 Yes no TF Yes No ADCY9 0.022026 1.258689 163.1216 Yes 0.024781 1.297741 213.1414 Yes no TF Yes No ADSSL1 0.006562 2.08415 219.7116 Yes 0.006958 2.025943 211.5599 Yes no TF Yes No AGGF1 0.009323 1.239582 82.25923 Yes 0.04399 1.155299 55.67235 No no TF No No AGTPBP1 0.024446 1.292796 176.2424 Yes 0.024333 1.288847 170.4615 Yes no TF Yes No AGTRL1 0.021636 1.297244 66.35472 Yes 0.02216 1.292676 64.86617 Yes no TF No No AHCY 0.036105 1.383558 204.4338 Yes 0.029619 1.338778 317.6586 Yes no TF Yes No AHDC1 nd nd nd No 0.0375351.289134 55.92248Yes no TF No No AHR 0.027738 1.368265 25.48613 Yes 0.02673 1.3651 25.95165 Yes bHLH Yes Yes AIG1 0.018962 1.282828 45.78286 Yes 0.018332 1.280015 44.97098 Yes no TF Yes No AIP 0.005009 1.276919 147.7823 Yes 0.00174 1.277941 210.1154 Yes no TF Yes No AKAP1 0.010825 1.469467 317.8906 Yes 0.039731 1.229086 158.4778 Yes no TF Yes No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N AKAP12 0.003161 1.600293 279.3965 Yes 0.002693 1.815279 366.2747 Yes no TF Yes No AKAP13 0.005903 1.211375 38.68919 Yes 0.015702 1.157842 35.65921 No no TF No No AKAP2 /// PALM2 0.001178 2.040926 467.5931 Yes 0.014357 1.473919 256.6468 Yes no TF Yes No /// AKAP2 AKAP7 0.048564 1.09881322.37779 No 0.0213741.20076 37.77528Yes no TF Yes No AKR1C2 0.001794 1.369747 25.37059 Yes 0.010986 1.480714 23.87766 Yes no TF Yes No ALDH1B1 0.002356 1.471902 92.88785 Yes 0.000389 1.852536 266.7046 Yes no TF Yes No ALDH4A1 0.051087 2.058441 390.8274 No 0.04867 2.045467 344.5559 Yes no TF No No ALKBH6 0.020543 1.375679 265.9807 Yes 0.049461 1.303788 109.6423 Yes no TF Yes No ALKBH7 0.03827 1.329279 172.7658 Yes 0.025259 1.354803 184.4019 Yes no TF Yes No ALKBH8 0.025055 1.394347 49.5901 Yes 0.023376 1.401132 49.68115 Yes no TF Yes No AMD1 0.004908 1.669955 816.0521 Yes 0.000717 1.597406 775.324 Yes no TF Yes No AMOTL1 0.005291 1.294998 121.3228 Yes 0.004976 1.297056 121.2908 Yes no TF Yes No AMOTL2 0.005837 1.783513 672.4175 Yes 0.003451 1.510262 610.6037 Yes no TF Yes No AMY1A /// 0.046693 1.86855 255.3497Yes nd nd nd No no TF No No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N AMY1B /// AMY1C /// AMY2A /// AMY2B /// LOC647537 /// LOC648759 ANAPC1 0.017764 1.72883553.79848 Yes nd nd nd No no TF No No ANAPC11 /// 0.037763 1.231691713.1763 Yes nd nd nd No no TF No No LOC653419 /// LOC653531 ANAPC13 0.020647 1.234042 636.8533 Yes 0.011085 1.183266 615.4968 No no TF No No ANK2 0.018327 1.28971 133.3404 Yes 0.019568 1.280752 129.8948 Yes no TF Yes No ANKH 0.016163 1.238565 144.7499 Yes 0.028116 1.269343 151.2025 Yes no TF Yes No ANKRD15 0.010451 1.293133 153.1121 Yes 0.739046 1.020918 9.642736 No no TF No No ANKRD20A1 /// 0.013469 1.77481 1335.339Yes nd nd nd No no TF No No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N C21orf81 /// LOC392331 /// ANKRD20A3 /// ANKRD20A2 ANKRD32 0.033605 1.456035 61.77272 Yes 0.029181 1.441938 57.55023 Yes no TF Yes No ANKRD35 0.004895 1.586946 120.8225 Yes 0.004826 1.576776 121.4046 Yes no TF Yes No ANKRD42 0.000772 2.194898 60.25109 Yes 0.000898 2.189725 60.09822 Yes no TF Yes No ANKRD50 0.023379 1.52049 132.133 Yes 0.023732 1.395421 82.56258 Yes no TF Yes No ANTXR2 0.031629 1.411592 30.85628 Yes 0.022472 1.33592 46.9253 Yes no TF Yes No ANXA11 0.036313 1.279827 288.8962 Yes 0.025686 1.277403 250.7413 Yes no TF Yes No ANXA7 0.031364 1.362032 902.4822 Yes 0.021409 1.41824 730.4276 Yes no TF Yes No AP1M1 0.045333 1.234961 304.7819 Yes 0.058145 1.240652 294.3856 No no TF No No AP1S1 0.023817 1.577823 400.4627 Yes 0.031709 1.435423 193.7643 Yes no TF Yes No AP3S2 0.003099 1.31145 247.1272 Yes 0.003084 1.305691 243.303 Yes no TF Yes No APCS 0.008883 1.204574 52.31179 Yes 0.008709 1.2097 54.32158 Yes no TF Yes No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N APITD1 0.004078 1.841947 97.87374 Yes 0.005508 1.637385 83.79424 Yes no TF Yes No APLP1 0.006196 1.493092 2237.52 Yes 0.007525 1.424696 3595.735 Yes no TF No No APOD 0.004526 1.764687 2818.839 Yes 0.003998 1.768991 2799.754 Yes no TF Yes No APPBP2 0.034098 1.23735 147.4711 Yes 0.036697 1.192816 126.9796 No no TF No No APRT 0.014797 1.383857 222.4486 Yes 0.087568 1.152862 74.90937 No no TF No No AQP1 0.027132 3.100591 664.7193 Yes 0.028293 2.169786 361.2957 Yes no TF Yes No ARF3 0.021892 1.215237 359.9621 Yes 0.054313 1.185262 603.3409 No no TF No No ARHGAP12 0.045773 1.301442 93.99867 Yes 0.100217 1.258422 116.8369 No no TF No No ARHGEF10 0.040534 1.206634 50.55077 Yes 0.221771 1.187891 133.8804 No no TF No No ARL2 0.005963 1.347512 564.3724 Yes 0.005557 1.344626 554.3345 Yes no TF Yes No ARL5A 0.000864 2.095443 415.06 Yes 0.001833 1.715958 312.3087 Yes no TF Yes No ARL6 0.029428 1.458876 106.8218 Yes 0.036544 1.429491 104.1956 Yes no TF Yes No ARL6IP5 0.042562 1.356999 1390.934 Yes 0.038176 1.43259 1107.343 Yes no TF Yes No ARMC9 0.0118 1.403603 119.8374 Yes 0.007222 1.502012 140.5792 Yes no TF No No ARMCX2 0.049976 1.262264 471.8362 Yes 0.11134 1.193735 431.7144 No no TF No No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N ARMET 0.048056 1.288284 310.6634 Yes 0.034978 1.268564 283.0993 Yes no TF Yes No ARS2 0.046272 1.224089 28.99726 Yes 0.972102 1.004144 3.72925 No no TF No No ART3 nd nd nd No 0.0157311.43257 245.1729Yes no TF No No AS3MT 0.035847 1.305624 58.79103 Yes 0.036545 1.300938 57.07597 Yes no TF Yes No ASB13 0.038068 1.345092455.4278 Yes nd nd nd No no TF No No ASB2 0.002354 1.574176 65.57596 Yes 0.002017 1.595786 65.67069 Yes no TF No No ASB3 0.001132 1.556376 562.4019 Yes 0.001095 1.551505 552.1146 Yes no TF Yes No ASCC3L1 0.005366 1.257487 153.489 Yes 0.001462 1.30849 182.0356 Yes no TF Yes No ASCIZ 0.110706 1.226058 261.402 No 0.002184 1.692359 379.2927 Yes no TF Yes No ASPHD1 0.012707 1.254682 358.2324 Yes 0.014647 1.384016 948.1688 Yes no TF No No ASRGL1 0.011785 1.546096 607.908 Yes 0.018609 1.427511 543.273 Yes no TF No No ASS1 0.078115 1.390554 415.2339 No 0.008578 2.010964 619.1624 Yes no TF Yes No ATE1 0.015042 1.114187 19.82747 No 0.01115 1.27694 45.84607 Yes no TF Yes No ATF7IP2 0.027681 1.308615 111.8213 Yes 0.006617 1.328992 138.5746 Yes no TF Yes No ATG12 0.01721 1.533106661.1271 Yes 0.1328831.192347 128.6803No no TF No No Species mask only Species and unique mask Gene p FC UD C p FC UD C TF family TA N ATP13A3 0.224545 1.071806 18.5667 No 0.028098 1.200935 50.17118 Yes no TF Yes No ATP1B3
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