Supplementary Table 1. Salivary miRNAs associated with ASD phenotypes* miRNAs identified in previous ASD studies

miRNAs identified in the present study

GI disturbance R t-stat p-value FDR ADHD R t-stat p-value FDR*hsa-miR-4700-3p 0.36789 677900 2.39E-07 6.33E-05 *hsa-miR-628-5p -0.2207 1309100 0.002469 0.46576hsa-miR-4485-3p -0.26598 1357700 0.000243 0.042879 *hsa-miR-16-2-3p -0.21626 1304400 0.00303 0.46576*hsa-miR-548a-3p -0.25237 1343100 0.000511 0.067552 *hsa-miR-4788 0.20716 850280 0.004553 0.46576*hsa-miR-548aa -0.24377 1333900 0.0008 0.080418 *hsa-miR-30a-5p -0.20648 1293900 0.004691 0.46576hsa-miR-4698 0.2398 815270 0.000979 0.080418 *hsa-miR-548ae-3p -0.20226 1289400 0.005632 0.46576hsa-miR-6787-5p 0.23813 817060 0.001064 0.080418 hsa-miR-125b-5p -0.19808 1284900 0.006724 0.46576hsa-let-7g-5p -0.2343 1323700 0.001287 0.081009 hsa-miR-5706 0.19698 861200 0.007044 0.46576hsa-miR-3607-5p -0.23096 1320100 0.001516 0.081009 hsa-miR-24-2-5p -0.19255 1278900 0.008463 0.49744hsa-miR-3909 -0.22929 1318400 0.001643 0.081009 hsa-miR-17-3p -0.188 1274100 0.010181 0.53856hsa-miR-4459 0.22878 827090 0.001685 0.081009 *hsa-miR-186-5p -0.17917 1264600 0.014411 0.62603hsa-miR-340-5p 0.22536 830760 0.001984 0.084373 hsa-miR-941 -0.17844 1263800 0.014816 0.62603hsa-miR-3150b-3p 0.22443 831760 0.002073 0.084373 *hsa-miR-548an 0.17746 882130 0.015384 0.62603hsa-miR-151a-5p -0.22242 1311000 0.002279 0.086117 hsa-miR-339-3p -0.16705 1251600 0.022675 0.76936hsa-miR-4510 -0.21392 1301900 0.00337 0.11459 hsa-miR-126-3p -0.16621 1250700 0.023375 0.76936hsa-miR-98-5p -0.2133 1301200 0.003466 0.11459 hsa-miR-589-5p -0.16285 1247100 0.026358 0.76936^hsa-miR-125b-2-3p -0.20963 1297300 0.004083 0.12033 *hsa-miR-28-5p -0.16167 1245800 0.027488 0.76936hsa-miR-133a-5p 0.20957 847700 0.004095 0.12033 *hsa-miR-1249-5p -0.16161 1245800 0.02754 0.76936hsa-miR-4760-5p -0.20009 1287000 0.006178 0.16789 *hsa-miR-29b-1-5p -0.16002 1244100 0.029124 0.76936hsa-miR-4709-5p -0.19945 1286300 0.006348 0.16789 *hsa-miR-34b-3p 0.15929 901610 0.029877 0.76936^hsa-miR-193a-5p -0.19689 1283600 0.007071 0.17341 *hsa-miR-424-5p -0.15854 1242500 0.030669 0.76936^hsa-miR-7706 -0.19638 1283000 0.007223 0.17341 *hsa-miR-484 -0.1564 1240200 0.033028 0.76936hsa-miR-1299 0.19535 862950 0.00754 0.17341 *hsa-miR-450b-5p -0.15603 1239800 0.033451 0.76936hsa-let-7f-5p -0.19116 1277400 0.00896 0.19749 hsa-miR-423-3p -0.15308 1236600 0.036976 0.7883*hsa-miR-766-3p 0.18382 875310 0.012022 0.25312 *hsa-miR-205-3p -0.15267 1236200 0.037492 0.7883hsa-miR-941 -0.18295 1268600 0.012441 0.25312 hsa-miR-6834-5p 0.15004 911540 0.040947 0.7883hsa-miR-4738-3p 0.17985 879570 0.014037 0.26066 *hsa-miR-4728-5p 0.14957 912040 0.041595 0.7883hsa-miR-421 -0.17935 1264800 0.01431 0.26066 *hsa-miR-424-3p -0.14884 1232100 0.042604 0.7883hsa-let-7b-5p -0.17884 1264200 0.014593 0.26066 *hsa-miR-652-5p -0.14841 1231600 0.043215 0.7883hsa-miR-6763-3p 0.17831 881220 0.014893 0.26066 *hsa-miR-940 -0.14695 1230000 0.045344 0.79574

Significant FDR values (<0.05) are highlighted in pinkmiRNAs correlated with both ADOS social and ADOStotal scores are highlighted in green

Table S1. Salivary miRNAs Associated with ASD Phenotypes

Supplementary Table 1 Continued. Salivary miRNAs associated with ASD phenotypes* miRNAs identified in previous ASD studies

miRNAs identified in the present study

VABS Communication R t-stat p-value FDR VABS Socialization R t-stat p-value FDR*hsa-miR-4700-3p -0.2465 -3.1048 0.00228 0.25176 hsa-miR-152-3p 0.29867 3.8201 0.000195 0.022984^hsa-miR-125b-2-3p 0.24554 3.0918 0.002375 0.25176 *hsa-miR-379-5p -0.29665 -3.7917 0.000217 0.022984*hsa-miR-3935 0.23787 2.9894 0.003271 0.28892 hsa-miR-4781-3p -0.28321 -3.6045 0.000426 0.037606^hsa-let-7a-5p 0.22783 2.8562 0.0049 0.32934 hsa-miR-26a-5p -0.27837 -3.5378 0.000538 0.039336hsa-miR-3621 -0.22747 -2.8514 0.004971 0.32934 *hsa-miR-221-3p 0.27633 3.5096 0.000594 0.039336*hsa-miR-185-3p -0.21948 -2.7461 0.006774 0.36163 *hsa-miR-629-5p 0.26657 3.3761 0.000938 0.055226*hsa-miR-199b-5p -0.21862 -2.7347 0.007001 0.36163 hsa-miR-6739-5p -0.26334 -3.3321 0.001087 0.057493*hsa-miR-18b-5p 0.2163 2.7044 0.00764 0.36163 hsa-miR-1180-3p 0.26128 3.3041 0.001193 0.057493hsa-miR-1273a -0.21033 -2.6261 0.009539 0.36163 hsa-miR-331-3p 0.25609 3.2338 0.001504 0.060433*hsa-miR-3687 -0.20957 -2.6163 0.009805 0.36163 hsa-miR-99a-3p 0.25493 3.2181 0.001584 0.060433hsa-miR-6724-5p 0.20485 2.5548 0.011629 0.36163 hsa-miR-548h-5p 0.25474 3.2156 0.001596 0.060433*hsa-miR-181a-2-3p 0.20388 2.5421 0.01204 0.36163 *hsa-miR-205-5p 0.24838 3.13 0.002104 0.074342hsa-miR-221-5p 0.20378 2.5407 0.012085 0.36163 hsa-miR-339-3p 0.24386 3.0694 0.002549 0.082209*hsa-miR-483-5p -0.20345 -2.5365 0.012226 0.36163 hsa-miR-210-3p 0.24306 3.0586 0.002637 0.082209hsa-miR-151a-5p 0.20209 2.5187 0.012833 0.36163 *hsa-miR-494-3p -0.23351 -2.9314 0.003907 0.10452*hsa-miR-335-3p 0.19809 2.4669 0.014763 0.36163 *hsa-miR-27a-3p 0.23255 2.9186 0.004062 0.10452hsa-miR-362-5p 0.19803 2.4661 0.014795 0.36163 *hsa-miR-212-5p -0.23207 -2.9123 0.00414 0.10452hsa-miR-6787-5p -0.19684 -2.4507 0.015414 0.36163 hsa-miR-4429 0.23206 2.9122 0.004141 0.10452hsa-miR-1236-5p -0.19652 -2.4466 0.015586 0.36163 *hsa-miR-148a-3p -0.22863 -2.8667 0.004748 0.11026hsa-miR-98-5p 0.19632 2.444 0.015693 0.36163 *hsa-miR-181a-5p-1 -0.22635 -2.8366 0.005195 0.11026hsa-miR-625-3p 0.19349 2.4073 0.017293 0.37439 hsa-miR-4668-5p -0.22607 -2.8329 0.005252 0.11026*hsa-miR-223-3p -0.19266 -2.3966 0.017787 0.37439 hsa-miR-19b-3p -0.22574 -2.8286 0.00532 0.11026hsa-miR-378a-5p 0.19171 2.3844 0.018366 0.37439 *hsa-miR-219b-5p -0.22346 -2.7984 0.005815 0.11026hsa-miR-222-3p 0.18989 2.3609 0.019527 0.3833 *hsa-miR-92b-3p 0.22261 2.7873 0.006008 0.11026hsa-miR-3150b-3p -0.18576 -2.3076 0.022395 0.42391 *hsa-miR-342-3p -0.22233 -2.7836 0.006074 0.11026hsa-miR-19b-3p -0.18386 -2.2832 0.023832 0.43221 hsa-miR-224-5p 0.22213 2.7809 0.006121 0.11026*hsa-miR-142-5p -0.18305 -2.2729 0.024465 0.43221 hsa-miR-3133 -0.22101 -2.7661 0.006391 0.11026hsa-miR-99a-5p 0.18155 2.2535 0.025688 0.43918 ^hsa-miR-7706 0.21988 2.7514 0.006672 0.11026hsa-miR-193a-3p 0.17931 2.2248 0.027597 0.44738 hsa-miR-378i 0.21958 2.7474 0.006749 0.11026

Table S1 Continued. Salivary miRNAs Associated with ASD Phenotypes

Supplementary Table 1 Continued. Salivary miRNAs associated with ASD phenotypes* miRNAs identified in previous ASD studies

miRNAs identified in the present study

VABS ADLs R t-stat p-value FDR ADOS Social R t-stat p-value FDR*hsa-miR-629-5p 0.28332 3.6061 0.000423 0.054193 *hsa-miR-223-3p 0.33478 4.1585 5.62E-05 0.008178hsa-miR-3909 0.27944 3.5525 0.000511 0.054193 *hsa-miR-142-3p 0.33305 4.1343 6.17E-05 0.008178^hsa-miR-584-5p 0.26382 3.3386 0.001064 0.084278 *hsa-miR-182-5p -0.31562 -3.8933 0.000154 0.01603^hsa-let-7d-3p 0.25851 3.2666 0.001351 0.084278 *hsa-miR-142-5p 0.31236 3.8486 0.000181 0.01603hsa-miR-361-3p 0.25732 3.2505 0.001425 0.084278 ^hsa-miR-125b-2-3p -0.29306 -3.5877 0.000463 0.035076hsa-miR-3925-5p -0.25369 -3.2014 0.001672 0.084278 *hsa-miR-181c-5p 0.28767 3.5157 0.000595 0.035854*hsa-miR-433-3p -0.25341 -3.1976 0.001693 0.084278 *hsa-miR-148b-3p -0.28717 -3.5091 0.000609 0.035854hsa-miR-4781-3p -0.25265 -3.1875 0.001749 0.084278 hsa-miR-143-3p 0.28016 3.4159 0.000837 0.044351^hsa-miR-193a-5p 0.24816 3.127 0.002124 0.093814 ^*hsa-miR-151a-3p -0.27308 -3.3227 0.001144 0.055097hsa-miR-221-5p 0.24339 3.0631 0.0026 0.106 hsa-miR-98-5p -0.26769 -3.2519 0.001443 0.055693hsa-miR-151a-5p 0.23973 3.0142 0.003029 0.11412 hsa-miR-378i -0.26736 -3.2475 0.001464 0.055693hsa-miR-1180-3p 0.23747 2.984 0.003326 0.11412 hsa-miR-6724-5p -0.26724 -3.246 0.001471 0.055693hsa-miR-4794 -0.23516 -2.9533 0.003655 0.11412 *hsa-miR-130a-3p 0.2577 3.1217 0.002194 0.077507*hsa-miR-219b-5p -0.23512 -2.9528 0.00366 0.11412 ^hsa-let-7a-5p -0.25324 -3.0639 0.002631 0.087155hsa-miR-27b-5p 0.23267 2.9202 0.004042 0.119 hsa-miR-766-5p 0.24614 2.9725 0.003491 0.10569hsa-miR-6739-5p -0.22837 -2.8632 0.004799 0.12604 hsa-miR-1285-3p 0.24543 2.9633 0.00359 0.10569*hsa-miR-424-3p 0.22759 2.8529 0.004949 0.12604 hsa-miR-4642 0.24304 2.9326 0.003941 0.10645hsa-miR-423-3p 0.22627 2.8355 0.005212 0.12604 *hsa-miR-1249-5p -0.24054 -2.9006 0.004341 0.10645*hsa-miR-363-3p 0.22405 2.8062 0.005683 0.12604 *hsa-miR-199b-5p 0.24011 2.8951 0.004413 0.10645hsa-miR-331-3p 0.2233 2.7964 0.005849 0.12604 hsa-miR-4485-3p -0.24007 -2.8946 0.004419 0.10645hsa-miR-3914 -0.22184 -2.7771 0.006191 0.12604 hsa-miR-338-3p 0.23657 2.8498 0.00505 0.11638*hsa-miR-101-3p -0.22104 -2.7665 0.006383 0.12604 hsa-miR-151a-5p -0.23306 -2.8052 0.005761 0.11968hsa-miR-1236-5p -0.22065 -2.7615 0.006479 0.12604 hsa-miR-582-5p 0.23279 2.8017 0.005821 0.11968hsa-miR-6876-3p -0.22043 -2.7585 0.006535 0.12604 *hsa-miR-219b-5p -0.23133 -2.7831 0.006145 0.11968hsa-miR-3128 -0.21993 -2.752 0.006659 0.12604 hsa-let-7c-5p -0.231 -2.7789 0.00622 0.11968*hsa-miR-128-3p 0.21828 2.7303 0.00709 0.12682 ^hsa-miR-944 -0.23056 -2.7733 0.006323 0.11968*hsa-miR-4700-3p -0.21796 -2.726 0.007179 0.12682 hsa-miR-660-5p -0.22768 -2.7369 0.007026 0.12727hsa-miR-6787-5p -0.21698 -2.7132 0.007448 0.12733 hsa-miR-210-3p -0.22658 -2.7228 0.007315 0.12727hsa-let-7c-5p 0.21317 2.6632 0.008591 0.13845 *hsa-miR-103a-3p -0.2261 -2.7167 0.007444 0.12727

Table S1 Continued. Salivary miRNAs Associated with ASD Phenotypes

Supplementary Table 1 Continued. Salivary miRNAs associated with ASD phenotypes* miRNAs identified in previous ASD studies

miRNAs identified in the present study

ADOS RRB R t-stat p-value FDR ADOS Total R t-stat p-value FDR*hsa-miR-136-3p 0.5182 7.0919 6.42E-11 1.70E-08 *hsa-miR-223-3p 0.34452 4.2955 3.28E-05 0.004348hsa-miR-8485 0.42122 5.436 2.42E-07 3.21E-05 *hsa-miR-142-3p 0.34047 4.2383 4.11E-05 0.00436*hsa-miR-106a-5p 0.37678 4.761 4.84E-06 0.000513 *hsa-miR-142-5p 0.31327 3.8611 0.000173 0.015079hsa-miR-3679-5p 0.36147 4.5377 1.23E-05 0.001088 *hsa-miR-182-5p -0.3105 -3.8233 0.000199 0.015079hsa-miR-573 0.33215 4.1217 6.48E-05 0.004905 *hsa-miR-148b-3p -0.30131 -3.6986 0.000313 0.020723hsa-miR-6733-5p 0.30028 3.6847 0.000329 0.021781 ^*hsa-miR-151a-3p -0.27984 -3.4117 0.000849 0.049986hsa-miR-8061 0.29448 3.6067 0.000433 0.025525 *hsa-miR-181c-5p 0.27638 3.3661 0.00099 0.05095*hsa-miR-130a-3p 0.28242 3.4459 0.000756 0.04007 hsa-miR-378i -0.27487 -3.3462 0.001058 0.05095hsa-miR-766-5p 0.27595 3.3604 0.001009 0.044993 hsa-miR-6724-5p -0.27213 -3.3101 0.001192 0.052659*hsa-miR-431-5p 0.27572 3.3574 0.001019 0.044993 hsa-miR-98-5p -0.2686 -3.2639 0.001388 0.054471hsa-miR-4642 0.2512 3.0376 0.002856 0.11255 hsa-miR-143-3p 0.26776 3.2528 0.001439 0.054471hsa-miR-3621 0.24868 3.0051 0.003158 0.11255 ^hsa-miR-125b-2-3p -0.25605 -3.1003 0.002347 0.074964hsa-miR-135b-5p -0.24846 -3.0023 0.003185 0.11255 hsa-miR-766-5p 0.25521 3.0895 0.002428 0.074964*hsa-miR-574-5p 0.24131 2.9104 0.004214 0.13171 *hsa-miR-130a-3p 0.2537 3.0699 0.002583 0.074964hsa-miR-3132 0.24124 2.9096 0.004225 0.13171 hsa-miR-4642 0.25178 3.0451 0.00279 0.074964^hsa-miR-125a-5p -0.23192 -2.7907 0.006011 0.17699 *hsa-miR-181d-3p -0.25052 -3.0289 0.002935 0.074964^*hsa-miR-500a-3p 0.22189 2.6636 0.008658 0.23439 *hsa-miR-199b-5p 0.25033 3.0264 0.002957 0.074964*hsa-miR-23a-3p 0.22129 2.656 0.008845 0.23439 ^hsa-let-7a-5p -0.25022 -3.025 0.00297 0.074964hsa-miR-31-5p -0.21852 -2.6211 0.009756 0.24102 *hsa-miR-1249-5p -0.24322 -2.935 0.003912 0.094254hsa-miR-1273a 0.2178 2.612 0.010005 0.24102 hsa-miR-375 -0.23863 -2.8762 0.00467 0.10761*hsa-miR-3613-3p 0.21126 2.5298 0.012544 0.27701 hsa-let-7c-5p -0.23322 -2.8071 0.005728 0.12649hsa-miR-152-3p -0.20917 -2.5037 0.013465 0.28546 hsa-miR-582-5p 0.23002 2.7665 0.006448 0.1367hsa-miR-125b-5p -0.19739 -2.3568 0.019851 0.40465 hsa-miR-6763-3p 0.22836 2.7454 0.006854 0.13972hsa-miR-17-5p 0.19131 2.2813 0.024073 0.47254 *hsa-miR-191-5p 0.22434 2.6945 0.007932 0.1557*hsa-miR-484 -0.18637 -2.2203 0.028041 0.53078 hsa-miR-31-5p -0.2233 -2.6814 0.008232 0.15582*hsa-miR-548ay-5p -0.18334 -2.183 0.03074 0.56181 *hsa-miR-708-5p -0.21952 -2.6337 0.009417 0.17111*hsa-miR-577 -0.18217 -2.1686 0.031841 0.56253 ^hsa-miR-148a-5p -0.21555 -2.5836 0.010824 0.17111*hsa-miR-550b-3p -0.17798 -2.117 0.036067 0.5995 hsa-miR-151a-5p -0.21549 -2.583 0.010843 0.17111*hsa-miR-335-3p -0.17741 -2.11 0.036674 0.5995 hsa-miR-210-3p -0.21534 -2.5811 0.0109 0.17111

Table S1 Continued. Salivary miRNAs Associated with ASD Phenotypes

Supplementary Table 2. Salivary miRNAs associated with clinical/demographic characteristics* miRNAs identified in previous ASD studies^ miRNAs identified in the present study

Age (months) R t-stat p-value FDR Female Sex R t-stat p-value FDRhsa-miR-1304-3p 0.21667 4.3094 2.09E-05 0.002844 *hsa-miR-651-5p 0.19457 7307900 0.000138 0.036694hsa-miR-197-3p 0.21643 4.3043 2.14E-05 0.002844 ^hsa-miR-130b-3p 0.1519 7695000 0.00303 0.24345hsa-miR-98-5p 0.22022 4.3835 1.52E-05 0.002844 hsa-miR-29c-5p -0.15397 10470000 0.002651 0.24345^hsa-let-7e-5p 0.21027 4.1761 3.69E-05 0.003923 hsa-miR-329-5p -0.14893 10425000 0.003661 0.24345hsa-miR-152-3p -0.2043 -4.0522 6.16E-05 0.004685 hsa-miR-5588-5p -0.15327 10464000 0.002774 0.24345hsa-miR-766-5p -0.20529 -4.0727 5.67E-05 0.004685 *hsa-miR-181d-3p 0.15017 7710700 0.003384 0.24345hsa-miR-4429 -0.201 -3.9841 8.13E-05 0.005407 ^hsa-miR-125a-5p 0.14703 7739300 0.004125 0.24383*hsa-miR-548ab -0.1982 -3.9262 0.000103 0.005724 hsa-miR-31-5p 0.14371 7769300 0.005061 0.26319*hsa-miR-93-5p 0.19762 3.9143 0.000108 0.005724 hsa-miR-6803-5p -0.14252 10366000 0.005442 0.26319*hsa-miR-21-3p -0.18953 -3.748 0.000206 0.009973 hsa-miR-10b-5p -0.13102 10262000 0.010673 0.47317hsa-let-7i-5p -0.18444 -3.6436 0.000307 0.012543 *hsa-miR-181b-3p -0.12827 10237000 0.012448 0.50942*hsa-miR-182-5p -0.18484 -3.6519 0.000297 0.012543 ^hsa-let-7e-5p 0.12417 7946700 0.015579 0.52655hsa-miR-338-3p 0.18183 3.5903 0.000374 0.013267 hsa-miR-361-5p 0.12273 7959700 0.016826 0.52655^hsa-miR-374a-5p 0.18097 3.5728 0.000399 0.013267 hsa-miR-744-5p 0.1228 7959000 0.016762 0.52655*hsa-miR-7-1-3p 0.18148 3.5831 0.000384 0.013267 *hsa-miR-548b-3p 0.12542 7935300 0.014557 0.52655^hsa-miR-374b-5p 0.17916 3.5358 0.000457 0.014158 hsa-miR-5694 -0.12094 10171000 0.018511 0.54711*hsa-miR-106b-5p 0.17853 3.523 0.000479 0.014158 hsa-miR-22-5p -0.11766 10141000 0.021969 0.57797hsa-miR-8053 -0.17518 -3.4548 0.000613 0.017175 hsa-miR-6510-3p 0.11542 8026100 0.024639 0.57797hsa-let-7g-5p 0.17381 3.4269 0.000678 0.017682 hsa-miR-8061 -0.11516 10118000 0.024956 0.57797hsa-miR-16-5p 0.17318 3.4141 0.000709 0.017682 hsa-miR-96-5p 0.1153 8027100 0.02478 0.57797hsa-miR-6745 -0.17276 -3.4056 0.000731 0.017682 *hsa-miR-194-3p -0.11514 10118000 0.024988 0.57797*hsa-miR-628-5p 0.17142 3.3783 0.000805 0.018628 ^hsa-let-7a-5p 0.10833 8090400 0.03502 0.62462*hsa-miR-4700-3p -0.16917 -3.3328 0.000945 0.020946 hsa-miR-151a-5p 0.1119 8058000 0.029403 0.62462hsa-miR-22-5p -0.1677 -3.3029 0.001049 0.021852 hsa-miR-3065-3p 0.10753 8097600 0.036397 0.62462hsa-miR-664a-3p 0.16726 3.2941 0.001081 0.021852 ^hsa-miR-374c-5p -0.11208 10090000 0.029142 0.62462*hsa-miR-326 0.1669 3.2866 0.001109 0.021852 *hsa-miR-182-5p 0.10773 8095800 0.036045 0.62462*hsa-miR-186-5p 0.16614 3.2713 0.001169 0.022213 *hsa-miR-212-5p 0.1107 8068900 0.031196 0.62462*hsa-miR-181c-3p 0.16558 3.2601 0.001215 0.022293 *hsa-miR-29b-1-5p 0.10913 8083100 0.033685 0.62462*hsa-miR-7-2-3p 0.16458 3.2398 0.001303 0.023098 *hsa-miR-4700-3p -0.1097 10069000 0.032756 0.62462hsa-miR-505-3p 0.15893 3.1255 0.001913 0.032482 hsa-miR-1180-3p 0.099751 8168200 0.052333 0.63111*hsa-miR-548k 0.1577 3.1007 0.002076 0.033462 hsa-miR-361-3p 0.10414 8128300 0.042739 0.63111hsa-miR-361-3p 0.15676 3.0819 0.002208 0.034548 hsa-miR-365a-3p 0.097416 8189400 0.058129 0.63111*hsa-miR-212-3p 0.15334 3.013 0.002762 0.041974 hsa-miR-365b-3p 0.097416 8189400 0.058129 0.63111*hsa-miR-181c-5p 0.15266 2.9993 0.002886 0.042641 hsa-miR-3909 0.10436 8126400 0.0423 0.63111*hsa-miR-148b-3p -0.14954 -2.9365 0.003523 0.050658 hsa-miR-3913-3p -0.09835 9965600 0.055746 0.63111

Significant FDR values (<0.05) are highlighted in pink

Table S2. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Supplementary Table 2. Salivary miRNAs associated with clinical/demographic characteristics* miRNAs identified in previous ASD studies

miRNAs identified in the present study

Ethnicity R t-stat p-value FDR BMI (kg/m2) R t-stat p-value FDRhsa-miR-941 -0.22078 5772700 0.000101 0.026688 *hsa-miR-15a-5p 0.20501 4.0018 7.61E-05 1.98E-02*hsa-miR-921 0.17977 3878600 0.001619 0.25949 hsa-miR-5697 0.20022 3.9043 1.13E-04 1.98E-02^hsa-let-7d-3p -0.17438 5553300 0.00224 0.25949 *hsa-miR-381-5p 0.17551 3.4061 7.32E-04 9.67E-02hsa-miR-335-5p -0.17 5532600 0.002897 0.25949 hsa-miR-452-5p 0.16081 3.1128 2.00E-03 2.11E-01*hsa-miR-450b-5p -0.16411 5504700 0.004056 0.25949 *hsa-miR-142-5p -0.14478 -2.7955 5.46E-03 4.12E-01hsa-miR-4644 0.1633 3956500 0.004244 0.25949 hsa-miR-17-3p 0.14229 2.7464 6.32E-03 4.12E-01*hsa-miR-320b -0.1631 5500000 0.004292 0.25949 *hsa-miR-142-3p -0.14215 -2.7437 6.37E-03 4.12E-01*hsa-miR-148b-3p 0.16256 3960000 0.004423 0.25949 hsa-let-7a-3p 0.13976 2.6966 7.33E-03 4.12E-01*hsa-miR-221-3p -0.15902 5480700 0.005378 0.26437 *hsa-miR-548a-3p 0.13868 2.6753 7.80E-03 4.12E-01*hsa-miR-146a-3p 0.15858 3978800 0.005508 0.26437 *hsa-miR-186-3p 0.13303 2.5643 1.07E-02 5.15E-01hsa-miR-625-3p -0.15555 5464300 0.00649 0.28555 hsa-miR-340-5p -0.12738 -2.4537 1.46E-02 6.43E-01hsa-miR-183-5p 0.15237 4008200 0.007683 0.29599 *hsa-miR-221-3p 0.12518 2.4105 1.64E-02 6.67E-01hsa-miR-491-3p 0.15195 4010200 0.007855 0.29599 *hsa-miR-223-3p -0.1198 -2.3054 2.17E-02 7.32E-01hsa-miR-4698 0.15065 4016300 0.008409 0.29599 hsa-miR-22-3p 0.11884 2.2866 2.28E-02 7.32E-01hsa-miR-423-3p -0.14379 5408600 0.011941 0.37399 *^hsa-miR-598-5p 0.11821 2.2743 2.35E-02 7.32E-01*hsa-miR-30a-5p -0.14325 5406100 0.012263 0.37399 *hsa-miR-4270 -0.11631 -2.2372 2.59E-02 7.32E-01*hsa-miR-548c-5p -0.14247 5402400 0.01275 0.37399 *hsa-miR-654-5p -0.1151 -2.2136 2.75E-02 7.32E-01hsa-let-7f-1-3p -0.13764 5379600 0.016157 0.42814 ^hsa-miR-675-3p 0.11372 2.1868 2.94E-02 7.32E-01hsa-miR-1285-5p 0.13755 4078300 0.016229 0.42814 hsa-miR-361-5p 0.11371 2.1866 2.94E-02 7.32E-01hsa-miR-744-5p -0.13655 5374400 0.017028 0.42814 hsa-miR-143-3p -0.11249 -2.1628 3.12E-02 7.32E-01hsa-miR-6826-5p -0.13453 5364900 0.01875 0.45 ^hsa-miR-193a-5p 0.11228 2.1588 3.15E-02 7.32E-01*hsa-miR-128-3p -0.1334 5359500 0.019772 0.4539 hsa-miR-99a-5p 0.11194 2.1521 3.20E-02 7.32E-01hsa-miR-22-3p -0.13095 5347900 0.022172 0.48456 *hsa-miR-191-5p -0.11116 -2.1369 3.33E-02 7.32E-01^hsa-miR-193a-5p -0.13021 5344400 0.022943 0.48456 hsa-miR-145-5p -0.10951 -2.1049 3.60E-02 7.55E-01*hsa-miR-320a -0.1277 5332600 0.025741 0.51113 hsa-miR-576-5p 0.10644 2.0451 4.16E-02 7.55E-01hsa-miR-421 -0.12736 5331000 0.026137 0.51113 hsa-miR-3615 -0.10475 -2.0122 4.49E-02 7.55E-01hsa-miR-24-3p -0.12573 5323300 0.028131 0.51549 hsa-miR-4776-5p 0.10461 2.0096 4.52E-02 7.55E-01hsa-miR-3909 -0.12558 5322600 0.028313 0.51549 *hsa-miR-136-3p -0.10423 -2.0023 4.60E-02 7.55E-01hsa-miR-5588-5p 0.1248 4138600 0.029321 0.51604 *hsa-miR-181c-5p -0.10418 -2.0013 4.61E-02 7.55E-01

Table S2 Continued. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Supplementary Table 2 Continued. Salivary miRNAs associated with clinical/demographic characteristics* miRNAs identified in previous ASD studies

miRNAs identified in the present study

Asthma R t-stat p-value FDR Allergic Rhinitis R t-stat p-value FDRhsa-miR-6763-3p -0.15377 10468000 0.002686 0.38581 ^hsa-miR-125a-5p -0.14944 10429000 0.003544 0.32062hsa-miR-6834-5p -0.15258 10458000 0.002901 0.38581 ^hsa-miR-193a-5p -0.14166 10359000 0.005733 0.32062hsa-miR-133a-5p -0.13399 10289000 0.009011 0.43569 hsa-miR-26b-3p -0.15442 10474000 0.002574 0.32062hsa-miR-3914 -0.13756 10321000 0.00732 0.43569 hsa-miR-3942-5p 0.14222 7782900 0.005542 0.32062hsa-miR-5694 0.13952 7807400 0.006518 0.43569 hsa-miR-4457 0.14908 7720700 0.003627 0.32062hsa-miR-625-3p -0.13426 10291000 0.008873 0.43569 hsa-miR-4485-3p 0.15161 7697700 0.003088 0.32062hsa-miR-6793-5p -0.13917 10336000 0.006654 0.43569 hsa-miR-4760-5p 0.13924 7809900 0.006629 0.32062*hsa-miR-1249-5p 0.13459 7852100 0.008702 0.43569 hsa-miR-5694 0.14012 7801900 0.006288 0.32062*hsa-miR-450b-5p -0.14094 10352000 0.005987 0.43569 *hsa-miR-132-3p -0.14308 10371000 0.005261 0.32062*hsa-miR-642a-3p 0.13247 7871300 0.009828 0.43569 ^hsa-miR-620 0.1346 7852000 0.0087 0.38572hsa-miR-30b-5p 0.12713 7919800 0.013253 0.50655 hsa-miR-1273g-3p 0.1179 8003500 0.021688 0.55423hsa-miR-30c-5p -0.12247 10184000 0.01706 0.50655 ^hsa-miR-1277-5p 0.12109 7974500 0.018357 0.55423^hsa-miR-374b-5p 0.12534 7936000 0.014615 0.50655 hsa-miR-183-5p 0.12572 7932600 0.014323 0.55423hsa-miR-378d 0.12308 7956500 0.016512 0.50655 ^hsa-miR-1972 0.10901 8084200 0.033883 0.55423hsa-miR-4644 -0.12269 10186000 0.016861 0.50655 hsa-miR-3607-5p 0.1119 8057900 0.029394 0.55423*hsa-miR-548aq-3p 0.12239 7962800 0.017139 0.50655 ^hsa-miR-374c-5p 0.12363 7951500 0.016031 0.55423hsa-miR-515-5p -0.11897 10153000 0.020524 0.51573 hsa-miR-423-5p -0.11952 10158000 0.019939 0.55423*hsa-miR-3613-3p -0.12058 10167000 0.01886 0.51573 hsa-miR-548i -0.11294 10098000 0.027918 0.55423*hsa-miR-449b-5p 0.11869 7996400 0.020828 0.51573 hsa-miR-744-5p -0.11593 10125000 0.024003 0.55423*hsa-miR-656-5p 0.11823 8000500 0.021327 0.51573 *hsa-miR-130a-3p -0.1092 10064000 0.033562 0.55423hsa-miR-3065-5p 0.1091 8083400 0.033738 0.55921 *hsa-miR-146a-5p -0.11366 10105000 0.026921 0.55423hsa-miR-338-3p -0.10802 10053000 0.035542 0.55921 *hsa-miR-155-5p -0.12496 10207000 0.01492 0.55423hsa-miR-3668 -0.11201 10090000 0.029232 0.55921 *hsa-miR-194-5p -0.11072 10078000 0.03116 0.55423hsa-miR-3671 -0.10833 10056000 0.035019 0.55921 *hsa-miR-2277-5p -0.12068 10168000 0.018762 0.55423hsa-miR-4436b-3p -0.10979 10069000 0.032618 0.55921 *hsa-miR-25-5p -0.113 10099000 0.027833 0.55423hsa-miR-766-5p -0.10625 10037000 0.038684 0.55921 *hsa-miR-346 -0.11025 10074000 0.031886 0.55423^hsa-miR-944 0.10724 8100200 0.0369 0.55921 *hsa-miR-451a -0.11184 10088000 0.02948 0.55423*hsa-let-7g-3p 0.10787 8094600 0.035806 0.55921 *hsa-miR-486-3p -0.11501 10117000 0.025156 0.55423*hsa-miR-1-3p -0.10533 10029000 0.040413 0.55921 *hsa-miR-548am-5p -0.11108 10081000 0.03062 0.55423

Table S2 Continued. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Supplementary Table 2 Continued. Salivary miRNAs associated with clinical/demographic characteristics* miRNAs identified in previous ASD studies

miRNAs identified in the present study

Time of saliva collection R t-stat p-value FDR Time Since Last Meal (hrs) R t-stat p-value FDRhsa-miR-210-3p -0.34563 -6.6094 1.60E-10 4.23E-08 *hsa-miR-23b-3p 0.25066 4.151 4.51E-05 0.011897hsa-miR-200a-3p -0.31371 -5.9285 7.87E-09 1.32E-06 *hsa-miR-574-3p 0.19517 3.1902 0.001599 0.28134*hsa-miR-223-3p 0.31159 5.8843 1.00E-08 1.32E-06 hsa-miR-3135b 0.1817 2.9623 0.00334 0.3854hsa-miR-660-5p -0.30577 -5.7629 1.93E-08 2.04E-06 hsa-miR-365a-3p 0.17652 2.8749 0.00438 0.3854*hsa-miR-218-5p -0.30262 -5.6974 2.75E-08 2.42E-06 hsa-miR-365b-3p 0.17652 2.8749 0.00438 0.3854*hsa-miR-23b-3p -0.29671 -5.5754 5.23E-08 3.93E-06 *hsa-miR-193b-3p 0.17111 2.7842 0.005764 0.4297*hsa-miR-191-5p 0.29551 5.5507 5.95E-08 3.93E-06 hsa-miR-203a-5p 0.16867 2.7433 0.006511 0.4297hsa-miR-338-3p 0.29364 5.5122 7.28E-08 4.27E-06 hsa-miR-197-3p 0.16264 2.6425 0.008735 0.47775*hsa-miR-338-5p 0.28769 5.3903 1.36E-07 7.19E-06 hsa-miR-378h -0.1619 -2.6302 0.009048 0.47775hsa-miR-143-3p 0.28426 5.3204 1.94E-07 8.76E-06 *hsa-miR-7-2-3p 0.15806 2.5661 0.010853 0.52096*hsa-miR-107 -0.28403 -5.3156 1.99E-07 8.76E-06 hsa-miR-361-5p 0.15348 2.4899 0.01341 0.59004*hsa-miR-199b-5p 0.27645 5.1619 4.29E-07 1.64E-05 ^hsa-miR-374a-5p 0.14632 2.3713 0.018466 0.75*hsa-miR-140-3p 0.27629 5.1586 4.36E-07 1.64E-05 *hsa-miR-139-5p 0.1437 2.3279 0.020697 0.76879hsa-miR-3135b -0.27447 -5.1218 5.22E-07 1.84E-05 hsa-miR-374a-3p 0.14157 2.2926 0.022679 0.76879hsa-miR-425-5p 0.27045 5.0408 7.75E-07 2.56E-05 hsa-miR-378i -0.13938 -2.2565 0.024882 0.76879hsa-miR-99a-5p -0.2677 -4.9857 1.01E-06 3.14E-05 hsa-let-7g-5p 0.1379 2.2321 0.026471 0.76879hsa-miR-532-5p -0.26577 -4.947 1.22E-06 3.57E-05 *hsa-miR-30a-5p 0.13685 2.2147 0.027658 0.76879*hsa-miR-181c-5p 0.26502 4.9319 1.31E-06 3.63E-05 hsa-miR-320c -0.13684 -2.2146 0.027665 0.76879hsa-miR-203a-3p -0.25845 -4.8009 2.42E-06 6.4E-05 hsa-miR-423-5p -0.13003 -2.1023 0.036497 0.91871*hsa-miR-193b-3p -0.2542 -4.7163 3.58E-06 9.01E-05 *hsa-miR-887-3p 0.13 2.1019 0.03654 0.91871*hsa-miR-30e-3p 0.25309 4.6944 3.96E-06 9.51E-05 *hsa-miR-127-3p -0.12661 -2.0461 0.041763 0.92792*hsa-miR-103a-3p -0.24591 -4.5525 7.53E-06 0.000173 hsa-miR-200b-3p 0.12537 2.0258 0.043816 0.92792*hsa-miR-142-3p 0.242 4.4755 1.06E-05 0.000233 ^hsa-miR-374b-5p 0.12484 2.0172 0.044719 0.92792hsa-miR-200a-5p -0.23769 -4.391 1.53E-05 0.000324 *hsa-miR-95-5p 0.12232 1.9758 0.049246 0.92792*hsa-miR-181b-5p 0.23218 4.2834 2.43E-05 0.000494 hsa-miR-6510-3p 0.12046 1.9453 0.052832 0.92792*hsa-miR-574-3p -0.23004 -4.2416 2.90E-05 0.000568 *hsa-miR-29b-2-5p 0.11871 1.9166 0.056394 0.92792hsa-miR-141-3p -0.22906 -4.2225 3.15E-05 0.000578 *hsa-miR-548k 0.1187 1.9164 0.05642 0.92792hsa-miR-664a-3p -0.22871 -4.2158 3.24E-05 0.000578 hsa-miR-331-3p 0.11749 1.8967 0.058986 0.92792hsa-miR-331-3p -0.22854 -4.2125 3.28E-05 0.000578 hsa-miR-210-5p 0.11702 1.8889 0.06003 0.92792

Table S2 Continued. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Supplementary Table 2 Continued. Salivary miRNAs associated with clinical/demographic characteristicsTime of saliva collection R t-stat p-value FDR Time Since Last Meal (hrs) R t-stat p-value FDRhsa-miR-192-5p 0.22806 4.2031 3.41E-05 0.000582 *hsa-miR-18b-5p 0.11636 1.8782 0.061489 0.92792*^hsa-miR-598-5p 0.22457 4.1355 4.52E-05 0.000747 hsa-miR-135a-5p 0.1157 1.8674 0.062988 0.92792*hsa-miR-34a-5p -0.22348 -4.1143 4.94E-05 0.00079 *hsa-miR-548ah-5p 0.11514 1.8582 0.064287 0.92792hsa-let-7i-5p -0.22266 -4.0984 5.27E-05 0.000819 hsa-miR-1180-3p 0.11464 1.85 0.065466 0.92792hsa-miR-27a-5p -0.2197 -4.0412 6.66E-05 0.001004 hsa-miR-576-5p 0.11452 1.848 0.065744 0.92792hsa-miR-429 -0.21935 -4.0343 6.84E-05 0.001004 hsa-miR-324-5p 0.11426 1.8437 0.066372 0.92792hsa-miR-215-5p 0.2173 3.9948 8.03E-05 0.001146 hsa-miR-4429 -0.11387 -1.8374 0.067308 0.92792^hsa-miR-944 -0.21673 -3.9838 8.39E-05 0.001166 hsa-miR-3128 0.11293 1.822 0.069616 0.92792hsa-miR-200b-3p -0.21467 -3.944 9.84E-05 0.001332 *hsa-miR-106b-3p -0.11104 -1.7912 0.074438 0.92792hsa-miR-374a-3p -0.21399 -3.931 0.000104 0.001368 hsa-miR-3150b-3p -0.11094 -1.7896 0.074697 0.92792hsa-miR-6876-3p 0.21315 3.9149 0.00011 0.001422 *hsa-miR-23a-3p 0.11024 1.7781 0.076562 0.92792*hsa-miR-142-5p 0.21131 3.8795 0.000127 0.001596 *hsa-miR-326 0.11015 1.7767 0.076802 0.92792*hsa-miR-708-5p -0.20882 -3.8316 0.000153 0.00188 *hsa-miR-431-3p -0.10998 -1.7738 0.077281 0.92792hsa-miR-4436b-3p 0.20032 3.6689 0.000285 0.00342 hsa-miR-6748-3p -0.10989 -1.7725 0.077503 0.92792*hsa-miR-181a-5p-1 0.19974 3.6579 0.000297 0.003484 *hsa-miR-708-5p 0.10932 1.763 0.079084 0.92792hsa-miR-3202 0.19913 3.6463 0.00031 0.00356 hsa-miR-4760-5p 0.10825 1.7457 0.082065 0.94196hsa-miR-96-5p -0.19717 -3.6089 0.000356 0.004004 *hsa-miR-328-3p 0.10688 1.7233 0.086031 0.9471hsa-miR-941 0.19505 3.5686 0.000414 0.004549 hsa-miR-98-5p 0.10637 1.715 0.087551 0.9471*hsa-miR-21-5p -0.19297 -3.5291 0.000478 0.005122 ^hsa-miR-374c-5p -0.10528 -1.6972 0.090874 0.9471hsa-miR-505-3p 0.19275 3.5249 0.000485 0.005122 hsa-miR-99a-3p 0.10496 1.692 0.091864 0.9471hsa-miR-708-3p -0.19246 -3.5194 0.000495 0.005124 hsa-miR-152-3p -0.10442 -1.6832 0.093555 0.9471hsa-miR-222-3p -0.19031 -3.4786 0.000573 0.005749 *hsa-miR-30a-3p -0.10373 -1.6719 0.095756 0.9471hsa-miR-125b-5p -0.19022 -3.4768 0.000577 0.005749 *hsa-miR-449b-5p 0.10342 1.6669 0.096762 0.9471*hsa-miR-128-3p 0.18934 3.4602 0.000613 0.00599 hsa-miR-215-5p -0.10299 -1.6599 0.098161 0.9471hsa-miR-1296-5p -0.18593 -3.3956 0.000771 0.007398 hsa-miR-200c-3p 0.10284 1.6574 0.098656 0.9471hsa-miR-340-5p 0.18558 3.389 0.000789 0.007436 *hsa-miR-494-3p -0.10127 -1.6318 0.10394 0.97786hsa-miR-345-5p 0.18525 3.3828 0.000806 0.007467 *hsa-miR-221-3p 0.099521 1.6034 0.11007 0.97786hsa-miR-24-3p -0.18368 -3.3531 0.000894 0.008142 *hsa-miR-550a-5p 0.099511 1.6032 0.11011 0.97786hsa-miR-365a-3p -0.18311 -3.3424 0.000929 0.008171 hsa-miR-6724-5p 0.097547 1.5713 0.11734 0.97786hsa-miR-365b-3p -0.18311 -3.3424 0.000929 0.008171 hsa-miR-192-5p -0.09642 -1.553 0.12165 0.97786*hsa-miR-221-3p -0.18213 -3.3238 0.00099 0.008573 *hsa-miR-195-5p -0.09537 -1.5359 0.1258 0.97786hsa-miR-99a-3p -0.18164 -3.3146 0.001022 0.008707 hsa-miR-519d-5p -0.09418 -1.5166 0.13059 0.97786hsa-miR-4709-5p 0.18105 3.3034 0.001063 0.008908 hsa-miR-378g -0.09378 -1.5101 0.13224 0.97786hsa-miR-4454 -0.17877 -3.2604 0.001232 0.010136 hsa-miR-125b-5p 0.092657 1.4918 0.13697 0.97786

Table S2 Continued. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Supplementary Table 2 Continued. Salivary miRNAs associated with clinical/demographic characteristicsTime of saliva collection R t-stat p-value FDR Time Since Last Meal (hrs) R t-stat p-value FDRhsa-miR-4485-3p 0.17836 3.2527 0.001265 0.010136 ^hsa-miR-148a-5p -0.09103 -1.4653 0.14405 0.97786*hsa-miR-7-5p-1 0.17833 3.2521 0.001267 0.010136 *hsa-miR-4669 -0.09006 -1.4497 0.14835 0.97786*^hsa-miR-151a-3p -0.17685 -3.2242 0.001393 0.010975 *hsa-miR-107 0.089772 1.445 0.14968 0.97786hsa-miR-31-5p -0.17654 -3.2184 0.00142 0.011027 *hsa-miR-4700-3p -0.0892 -1.4357 0.1523 0.97786hsa-miR-1180-3p -0.17626 -3.2132 0.001446 0.011062 hsa-miR-515-5p -0.08898 -1.4322 0.1533 0.97786hsa-miR-151a-5p -0.17506 -3.1905 0.00156 0.011766 hsa-miR-361-3p 0.0889 1.4308 0.15369 0.97786hsa-miR-3671 0.17377 3.1663 0.001692 0.012581 *hsa-miR-5739 -0.08889 -1.4306 0.15375 0.97786hsa-miR-3614-5p 0.17323 3.1562 0.001749 0.012828 *hsa-miR-500a-5p 0.088433 1.4233 0.15587 0.97786*hsa-miR-93-5p 0.17101 3.1146 0.002008 0.014477 *hsa-miR-130b-5p 0.087742 1.4121 0.15914 0.97786hsa-miR-145-5p 0.17084 3.1114 0.002029 0.014477 hsa-miR-1285-3p 0.087299 1.4049 0.16126 0.97786hsa-miR-26b-3p 0.17003 3.0961 0.002133 0.015015 hsa-miR-3675-5p 0.087148 1.4024 0.162 0.97786hsa-miR-4461 0.16766 3.0517 0.002465 0.017124 *hsa-miR-548ab -0.08566 -1.3782 0.16933 0.97786*hsa-miR-21-3p -0.16609 -3.0224 0.002709 0.018576 *hsa-miR-95-3p 0.085513 1.3759 0.17004 0.97786hsa-miR-141-5p -0.16501 -3.0022 0.00289 0.019334 hsa-miR-30b-5p 0.085214 1.3711 0.17155 0.97786*hsa-let-7g-3p -0.16499 -3.0017 0.002894 0.019334 *hsa-miR-182-3p -0.08488 -1.3657 0.17323 0.97786hsa-miR-324-3p -0.16479 -2.998 0.002929 0.019334 hsa-miR-27b-5p 0.083993 1.3513 0.17779 0.97786hsa-miR-6510-3p -0.16433 -2.9895 0.00301 0.019531 *hsa-miR-652-3p 0.083216 1.3387 0.18185 0.97786*hsa-miR-629-5p -0.1642 -2.987 0.003033 0.019531 hsa-miR-362-5p 0.083179 1.3381 0.18204 0.97786*hsa-miR-27a-3p -0.16199 -2.9456 0.003458 0.021997 *hsa-miR-431-5p 0.082762 1.3313 0.18426 0.97786hsa-miR-224-5p -0.16112 -2.9294 0.003638 0.022869 *hsa-miR-548b-3p 0.082575 1.3283 0.18525 0.97786^hsa-miR-149-5p -0.16051 -2.9181 0.00377 0.023417 hsa-miR-941 -0.08231 -1.324 0.18667 0.97786hsa-miR-221-5p -0.15987 -2.9061 0.003913 0.024022 hsa-miR-324-3p 0.081995 1.3189 0.18837 0.97786hsa-miR-27b-3p -0.1563 -2.8396 0.004804 0.029154 *hsa-miR-654-5p 0.081283 1.3074 0.19225 0.97786*hsa-miR-30a-3p -0.15478 -2.8113 0.005236 0.031417 *hsa-miR-136-3p 0.08117 1.3056 0.19287 0.97786hsa-miR-135b-5p -0.15434 -2.8031 0.005369 0.031851 *hsa-miR-663b 0.081138 1.305 0.19304 0.97786hsa-miR-27b-5p -0.15341 -2.7858 0.005656 0.033181 hsa-miR-452-5p 0.080687 1.2977 0.19554 0.97786hsa-miR-4457 0.15235 2.766 0.006002 0.034824 *hsa-miR-3529-3p -0.08046 -1.2941 0.19681 0.97786hsa-miR-378i -0.15059 -2.7335 0.006613 0.037954 hsa-miR-6733-5p 0.080309 1.2916 0.19765 0.97786hsa-miR-4760-5p 0.15035 2.7289 0.006704 0.03806 hsa-miR-3671 0.080119 1.2886 0.19871 0.97786^hsa-miR-374c-5p -0.14828 -2.6906 0.007506 0.041772 *hsa-miR-3960 0.079966 1.2861 0.19958 0.97786hsa-miR-210-5p -0.14826 -2.6901 0.007516 0.041772 hsa-miR-4698 -0.07975 -1.2826 0.20078 0.97786hsa-miR-99b-5p -0.14486 -2.6272 0.009022 0.04946 *hsa-miR-148a-3p 0.078944 1.2695 0.2054 0.97786*hsa-miR-548ah-5p 0.14461 2.6226 0.009142 0.04946 hsa-miR-429 0.078361 1.2601 0.20877 0.97786hsa-miR-30c-5p 0.14454 2.6211 0.00918 0.04946 ^hsa-miR-125a-5p 0.078056 1.2552 0.21056 0.97786*hsa-miR-136-5p 0.14372 2.606 0.009587 0.051132 hsa-miR-378a-3p 0.077624 1.2482 0.21311 0.97786

Table S2 Continued. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Supplementary Table 2 Continued. Salivary miRNAs associated with clinical/demographic characteristics* miRNAs identified in previous ASD studies

miRNAs identified in the present study

Dietary restrictions R t-stat p-value FDR*hsa-miR-548a-5p -0.15697 10498000 0.002178 0.57928hsa-miR-362-5p 0.14314 7774500 0.005241 0.75041hsa-miR-4698 -0.13688 10315000 0.007617 0.75041hsa-miR-532-5p 0.13645 7835200 0.007813 0.75041*hsa-miR-539-5p -0.13507 10299000 0.008463 0.75041*hsa-miR-328-3p 0.13201 7875500 0.010087 0.76662hsa-miR-3621 -0.12774 10232000 0.012818 0.83105hsa-miR-324-5p 0.12318 7955600 0.016424 0.83105*hsa-miR-130a-3p -0.12234 10183000 0.017186 0.83105*hsa-miR-921 -0.12127 10174000 0.018186 0.83105*hsa-miR-328-5p -0.11797 10144000 0.021615 0.83105*hsa-miR-146b-5p 0.11605 8020300 0.023858 0.83105*hsa-miR-190b 0.11487 8031000 0.025327 0.83105*hsa-miR-155-5p 0.11428 8036300 0.026095 0.83105hsa-miR-505-3p 0.11185 8058400 0.029472 0.83105*^hsa-miR-190a-5p -0.11088 10079000 0.030924 0.83105*hsa-miR-34c-3p 0.10934 8081200 0.033336 0.83105Allergies 0.10836 8090000 0.034955 0.83105*hsa-miR-486-5p-1 0.10803 8093100 0.035533 0.83105*hsa-miR-1-3p -0.10785 10052000 0.035833 0.83105hsa-miR-4785 -0.10646 10039000 0.038303 0.83105hsa-miR-223-5p 0.10542 8116800 0.040244 0.83105*hsa-miR-15a-5p 0.10502 8120400 0.041017 0.83105hsa-miR-423-5p -0.10464 10023000 0.041755 0.83105*hsa-miR-133b -0.1031 10009000 0.044872 0.83105hsa-miR-4429 -0.10205 9999200 0.047112 0.83105*hsa-miR-219b-5p -0.1017 9996000 0.047879 0.83105hsa-miR-22-5p -0.10114 9990900 0.049118 0.83105*hsa-miR-502-3p 0.09923 8172900 0.053584 0.83105

Table S2 Continued. Salivary miRNAs Associated with Clinical/Demographic Characteristics

Table S3. Individual mRNA targets of the salivary miRNAs of interestList A includes individual mRNAs targeted by the 14 miRNAs identified on KW testing (Figure 1)List B includes individual mRNAs targeted by the 8 miRNAs associated with ADOS-II social/total scores (Table S1; miR-182-5p, miR-223-3p, miR-142-5p, miR-151a-3p, miR-142-3p, miR-142-5p, miR148b-5p, miR-125b-2-3p, miR-181c-5p, miR-143-3p)

A miRNA mRNA target Ensemble ID micro-T-cds target score

Experimentally validated B miRNA mRNA target Ensemble ID micro-T-cds

target scoreExperimentally

validatedmiR-1277-5p RORA ENSG00000069667 1 Yes miR-223-3p FBXW7 ENSG00000109670 1 YesmiR-1277-5p ARHGAP21 ENSG00000107863 1 Yes miR-223-3p SP3 ENSG00000172845 1 YesmiR-1277-5p PHIP ENSG00000146247 1 Yes miR-142-3p FAM208B ENSG00000108021 1 YesmiR-1277-5p VEGFA ENSG00000112715 1 Yes miR-142-3p MLXIP ENSG00000175727 1 YesmiR-125a-5p KIAA1522 ENSG00000162522 1 Yes miR-182-5p RGS17 ENSG00000091844 1 YesmiR-125a-5p PCTP ENSG00000141179 1 Yes miR-182-5p FRS2 ENSG00000166225 1 YesmiR-125a-5p SMEK1 ENSG00000100796 1 Yes miR-182-5p BCL11A ENSG00000119866 1 YesmiR-125a-5p MFHAS1 ENSG00000147324 1 Yes miR-182-5p EVI5 ENSG00000067208 1 YesmiR-125a-5p ZNF543 ENSG00000178229 1 Yes miR-182-5p MITF ENSG00000187098 1 YesmiR-125a-5p ZSWIM6 ENSG00000130449 1 Yes miR-182-5p CTTN ENSG00000085733 1 YesmiR-125a-5p LFNG ENSG00000106003 1 Yes miR-182-5p KTN1 ENSG00000126777 1 YesmiR-125a-5p STARD13 ENSG00000133121 1 Yes miR-182-5p FOXN3 ENSG00000053254 1 YesmiR-125a-5p TNRC6A ENSG00000090905 1 Yes miR-182-5p BCL2L12 ENSG00000126453 1 YesmiR-125a-5p SUV39H1 ENSG00000101945 1 Yes miR-182-5p ZCCHC14 ENSG00000140948 1 Yeslet-7a-5p POU2F1 ENSG00000143190 1 Yes miR-182-5p FOXO3 ENSG00000118689 1 Yeslet-7a-5p ACTB ENSG00000075624 1 Yes miR-182-5p ARF4 ENSG00000168374 1 Yeslet-7a-5p YOD1 ENSG00000180667 1 Yes miR-182-5p PCMT1 ENSG00000120265 1 Yeslet-7a-5p NR6A1 ENSG00000148200 1 Yes miR-125b-2-3p PPP2CA ENSG00000113575 1 Yeslet-7a-5p BACH1 ENSG00000156273 1 Yes miR-181c-5p ZNF570 ENSG00000171827 1 Yeslet-7a-5p GAN ENSG00000261609 1 Yes miR-143-3p IGFBP5 ENSG00000115461 1 Yeslet-7a-5p MAP4K3 ENSG00000011566 1 Yes miR-143-3p UBE2E3 ENSG00000170035 1 Yeslet-7a-5p ARID3B ENSG00000179361 1 Yes miR-143-3p ABL2 ENSG00000143322 1 Yeslet-7a-5p LIN28B ENSG00000187772 1 Yes miR-143-3p SECISBP2L ENSG00000138593 1 Yeslet-7a-5p IGDCC3 ENSG00000174498 1 Yes miR-223-3p RHOB ENSG00000143878 0.999 Yeslet-7a-5p IGF2BP1 ENSG00000159217 1 Yes miR-142-3p TWF1 ENSG00000151239 0.999 Yeslet-7a-5p FAM222B ENSG00000173065 1 Yes miR-142-3p ZEB2 ENSG00000169554 0.999 Yeslet-7a-5p LRIG2 ENSG00000198799 1 Yes miR-142-3p WASL ENSG00000106299 0.999 Yeslet-7a-5p PRTG ENSG00000166450 1 Yes miR-142-3p ROCK2 ENSG00000134318 0.999 Yeslet-7a-5p NFAT5 ENSG00000102908 1 Yes miR-142-3p RICTOR ENSG00000164327 0.999 Yeslet-7a-5p SLC35D2 ENSG00000130958 1 Yes miR-142-3p ARNTL ENSG00000133794 0.999 Yeslet-7a-5p SKIL ENSG00000136603 1 Yes miR-142-3p UTRN ENSG00000152818 0.999 Yeslet-7a-5p PRKAR2A ENSG00000114302 1 Yes miR-182-5p MFAP3 ENSG00000037749 0.999 Yeslet-7a-5p RNFT1 ENSG00000189050 1 Yes miR-182-5p LPHN2 ENSG00000117114 0.999 Yeslet-7a-5p FIGN ENSG00000182263 1 Yes miR-182-5p USP6NL ENSG00000148429 0.999 Yeslet-7a-5p COL1A2 ENSG00000164692 1 Yes miR-182-5p SNX30 ENSG00000148158 0.999 Yeslet-7a-5p TRIM71 ENSG00000206557 1 Yes miR-182-5p LPP ENSG00000145012 0.999 Yeslet-7a-5p CAPRIN2 ENSG00000110888 1 Yes miR-182-5p TP53INP1 ENSG00000164938 0.999 Yeslet-7a-5p ARHGAP28 ENSG00000088756 1 Yes miR-182-5p MTSS1 ENSG00000170873 0.999 Yeslet-7a-5p COIL ENSG00000121058 1 Yes miR-182-5p WIPI2 ENSG00000157954 0.999 Yeslet-7a-5p SYNCRIP ENSG00000135316 1 Yes miR-182-5p FOXF2 ENSG00000137273 0.999 YesmiR-125b-2-3p PPP2CA ENSG00000113575 1 Yes miR-182-5p VAMP3 ENSG00000049245 0.999 Yes

Table S3. Individual mRNA Targets of the Salivary miRNAs of Interest

*Brain-related pathways List A includes KEGG pathways targeted by the 14 miRNAs identified on KW testing (Figure 1)List B includes KEGG pathways targeted by the 9 miRNAs associated with ADOS-II social/total scores (Table S1; miR-182-5p, miR-223-3p, miR-142-5p, miR-151a-3p, miR-142-3p, miR-142-5p, miR148b-5p, miR-125b-2-3p, miR-181c-5p, miR-143-3p)

A KEGG pathway FDR #genes #miRNAs B KEGG pathway FDR #genes #miRNAsTGF-beta signaling pathway 3.72E-10 47 12 Prion diseases* 2.06E-13 9 6Hippo signaling pathway 2.52E-09 77 10 Thyroid hormone signaling pathway 2.42E-06 42 8Signaling pathways regulating pluripotency of stem cells 8.19E-09 77 13 Estrogen signaling pathway 2.64E-05 35 8FoxO signaling pathway 2.05E-07 73 12 Proteoglycans in cancer 0.000115 58 8Prion diseases* 1.79E-06 10 5 Phosphatidylinositol signaling system 0.000304 28 7Pathways in cancer 2.03E-06 178 13 Signaling pathways regulating pluripotency of stem cells0.001251 46 8Morphine addiction* 2.19E-06 41 11 Long-term depression* 0.001675 23 7Renal cell carcinoma 2.42E-06 40 11 Morphine addiction* 0.001675 26 7Proteoglycans in cancer 5.48E-06 99 13 Ras signaling pathway 0.001675 63 8Chronic myeloid leukemia 8.02E-06 41 10 PI3K-Akt signaling pathway* 0.001685 93 8ErbB signaling pathway 8.02E-06 47 13 Platelet activation 0.004161 40 8PI3K-Akt signaling pathway* 3.75E-05 154 13 Glioma* 0.007206 21 8Lysine degradation* 8.77E-05 23 11 Inositol phosphate metabolism 0.008534 21 7N-Glycan biosynthesis 0.000221 21 9 ECM-receptor interaction 0.008534 21 7Axon guidance* 0.00041 63 11 Retrograde endocannabinoid signaling* 0.008534 34 7Melanoma 0.000449 39 10 Pathways in cancer 0.008534 110 8Rap1 signaling pathway 0.000449 97 13 Sphingolipid signaling pathway 0.009021 36 8Colorectal cancer 0.000513 34 11 Nicotine addiction* 0.011562 13 5Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate 0.001972 9 5 Pancreatic cancer 0.011795 20 8Endometrial cancer 0.002108 28 12 Vasopressin-regulated water reabsorption 0.01335 15 5Wnt signaling pathway* 0.002865 64 12 Hippo signaling pathway 0.01335 43 7Ras signaling pathway 0.003711 98 13 cGMP-PKG signaling pathway 0.01335 49 8GABAergic synapse* 0.004337 35 10 cAMP signaling pathway 0.01335 57 8Transcriptional misregulation in cancer 0.004337 81 12 Melanoma 0.01335 26 8MAPK signaling pathway 0.0049 110 13 Neurotrophin signaling pathway* 0.013382 38 8Glioma* 0.007 31 10 Non-small cell lung cancer 0.013382 18 8Non-small cell lung cancer 0.009888 28 12 Endometrial cancer 0.01517 20 8Endocytosis 0.013499 87 13 Glutamatergic synapse* 0.018048 36 7p53 signaling pathway 0.015377 34 11 Endocrine and other factor-regulated calcium reabsorption0.018048 16 7Estrogen signaling pathway 0.017001 42 12 Bacterial invasion of epithelial cells 0.01805 26 8Retrograde endocannabinoid signaling* 0.019685 45 12 Transcriptional misregulation in cancer 0.018386 49 7Viral carcinogenesis 0.02812 74 12 Oxytocin signaling pathway* 0.020687 43 7Gap junction 0.028969 38 11 Colorectal cancer 0.020687 21 7Prostate cancer 0.028969 42 11 FoxO signaling pathway* 0.020687 37 8Circadian entrainment* 0.028969 42 12 Cholinergic synapse* 0.020687 37 8T cell receptor signaling pathway 0.028969 48 13 Chronic myeloid leukemia 0.020687 23 8Arrhythmogenic right ventricular cardiomyopathy (ARVC) 0.032915 32 11 Prolactin signaling pathway* 0.021221 21 8ECM-receptor interaction 0.033842 33 11 Adrenergic signaling in cardiomyocytes 0.02286 40 8Hepatitis B 0.033842 61 13 Acute myeloid leukemia 0.023394 19 8Glycosaminoglycan biosynthesis - heparan sulfate / heparin 0.04454 12 5 GABAergic synapse* 0.023841 23 7Platelet activation 0.04454 55 11 TGF-beta signaling pathway 0.026461 26 7

Viral carcinogenesis 0.026461 43 7Axon guidance* 0.026679 34 7Rap1 signaling pathway 0.028323 57 8Prostate cancer 0.028919 29 8Choline metabolism in cancer 0.032679 33 8Renal cell carcinoma 0.045996 23 7

Table S4. KEGG Pathway Targets of the Salivary miRNAs of Interest

Table S5. Quantile Normalized Expression Values for the 4 miRNAs of interest across all participants

Sample ID hsa-miR-125b-2-3p hsa-miR-151a-3p hsa-miR-28-3p hsa-miR-148a-5p

125 -0.66972 -0.31442 -0.88131 -0.21945

126 -0.19858 -0.10776 -0.22298 0.232126

127 -0.70289 -0.73068 -1.48696 -1.06995

128 -0.84575 -0.73068 -0.22298 -1.01953

129 -0.25363 -0.10776 0.160273 -0.18661

130 -0.63515 0.132105 -0.75219 -0.36979

131 0.254965 -0.50042 0.119524 0.587111

132 -0.28257 0.743742 -0.64015 -0.18661

133 0.042235 0.653493 -0.14246 0.156398

135 0.430481 0.132105 0.711203 -0.15662

137 -0.33372 0.419001 0.836286 0.769475

139 -0.33372 -0.38088 -0.04039 0.007095

140 -0.30898 -0.50042 -0.57177 -0.47986

141 -1.32578 -1.40987 -1.21028 -1.44489

143 -1.47171 -1.67285 -1.62672 -1.51462

144 -0.48627 -0.88654 -0.57177 0.29357

145 -0.95461 -1.28813 -1.03687 -1.10017

146 0.430481 -0.50042 -0.40609 -0.21945

147 -0.98861 -0.67834 -0.88131 -0.50444

149 -0.14223 0.056071 -0.51085 -0.64981

225 -1.31885 -1.501 1.076537 0.847133

226 -0.53742 -0.02677 -0.40609 0.271139

228 -0.59602 -0.56355 -0.14246 -0.60763

229 -0.60646 -0.98022 -0.92722 -0.63076

231 0.009586 -0.40864 -0.57177 0.587111

232 -0.30898 -0.50042 -0.44394 -0.63076

235 -0.65199 -0.56355 -0.47849 -0.53012

236 -0.30898 -0.61546 -0.57177 0.156398

237 -0.38029 -0.02677 -0.33407 -0.36979

238 -0.85317 -0.61546 -1.33096 -1.12479

239 -0.53742 -0.79117 -0.98323 -0.99977

240 -0.78712 -0.31442 -0.69516 -0.69632

241 -0.16945 0.056071 -0.40609 -0.60763

243 -0.49792 -0.17799 -0.06174 0.741205

244 0.525902 0.132105 0.020855 -0.09216

245 0.009586 0.97775 -0.14246 -0.42672

246 -0.02081 0.132105 -0.01903 0.082374

247 0.009586 -0.38088 -0.36765 0.5425

248 2.658697 3.204401 3.578364 5.178903

249 0.14815 -0.17799 -0.60438 -0.45665

1000 -0.16945 -0.31442 -0.77733 1.189203

1001 -0.16945 -0.02677 -0.06174 0.156398

1003 -0.43256 0.056071 0.923747 -0.39816

1004 -1.75931 -2.20196 -2.2684 -2.35842

1006 -0.71156 -0.88654 -0.72566 -0.80805

1007 1.957864 1.574559 1.546939 0.099675

1008 -0.38029 -0.24874 -0.10151 -0.3397

1011 -1.53299 -0.93612 0.284476 2.012829

1012 -0.88218 -0.99968 -0.57177 -1.79717

1013 0.042235 0.844489 -0.14246 -0.15662

1015 -0.79416 -0.24874 0.551855 0.251633

1016 -0.45452 -0.4364 -0.36765 -0.60763

1018 -0.96663 -0.73068 -0.01903 -0.83071

1019 -1.01311 -1.10589 0.488866 -0.42672

1020 -0.84575 -0.38088 0.119524 -0.69632

1021 -0.81537 0.228521 0.747174 1.310522

1022 0.072726 1.574559 0.551855 1.068452

1023 -0.43256 -0.24874 0.284476 0.195146

1024 0.478631 0.228521 0.259259 -0.31244

1025 -0.45452 -0.02677 -0.51085 -0.66142

1026 -0.77949 -0.67834 -0.854 -0.21945

1027 0.293518 1.324575 0.259259 0.195146

1028 2.178708 2.119732 0.836286 0.741205

1030 -0.16945 -0.17799 0.119524 -0.27066

1032 -0.15584 -0.38088 0.119524 -1.26327

1033 -0.22425 -0.83662 1.354855 1.010542

1035 0.946997 3.04524 0.364682 1.968067

1036 -0.30898 1.192856 -0.14246 0.042193

1038 2.418887 0.653493 0.613695 0.156398

1040 -0.59602 0.529599 -0.08163 -0.53012

1041 -1.40918 -1.501 -1.14095 -0.90544

1042 0.383956 1.192856 0.020855 -0.05943

1043 -1.10004 -0.24874 -0.93881 -0.77907

1044 -0.87615 -0.10776 -0.44394 -0.05943

1045 0.072726 -0.4364 -0.22298 -0.256

1047 0.214734 1.990595 -0.22298 2.150241

1048 0.946997 -0.17799 -0.88131 -0.31244

1049 -0.38029 0.419001 -0.10151 0.175772

1051 -0.30898 0.132105 -0.18361 0.271139

1052 -1.20671 -1.44194 -0.72566 -0.69632

1053 -1.26049 -0.93612 -0.9504 -0.64028

1054 -1.22765 -0.88654 -0.51085 -0.56918

1055 -1.11999 -1.28813 -0.60438 -0.74388

1056 -1.07521 -0.73068 0.000911 -0.61919

1057 -1.42597 -1.56935 -1.57137 -1.34124

1058 0.525902 0.228521 0.206628 -0.64028

1059 0.072726 0.228521 -0.12199 -0.18661

1060 0.478631 1.446439 0.309693 0.5425

1061 -0.5678 -1.01914 -1.10398 -0.58158

1062 -1.08494 -1.32156 -1.38339 -1.51462

1063 -0.38029 0.529599 -0.54118 0.232126

1065 -0.05211 -0.56355 -1.02667 -0.29888

1069 0.627935 -0.93612 -1.03687 -0.28533

1070 0.824282 0.056071 0.428003 1.642446

1071 -0.33372 -0.02677 -0.36765 0.116976

1072 -0.63515 0.056071 -0.9504 -0.88747

1073 -0.33372 -0.38088 -0.54118 -0.31244

1074 -0.77187 -0.38088 -0.44394 -0.68468

1077 -0.75288 -1.35384 -1.25295 -1.0776

1078 0.335553 1.192856 -0.01903 0.685518

1079 -1.40918 -1.97025 0.613695 0.116976

1080 -0.98861 0.132105 -0.20329 -0.21945

1081 1.85381 2.732918 4.283045 3.331374

1082 0.627935 0.132105 -0.01903 -0.09216

1083 -0.14223 -0.50042 -0.76476 0.007095

1084 0.762911 0.056071 -0.47849 -0.3397

1085 -0.22425 -0.56355 -0.80367 -0.92585

1086 -0.02081 -0.67834 -0.77733 -0.50444

1087 -0.02081 -0.61546 -1.10398 0.082374

1092 1.957864 0.056071 -0.01903 0.007095

1096 -0.34531 -0.67834 -0.52601 -0.49215

1097 0.430481 -0.61546 -0.29596 -0.44169

2000 0.009586 0.97775 2.283246 -0.02533

2001 -0.06784 -0.02677 2.215643 1.098713

2002 -0.05211 0.325917 0.094174 -0.64981

2003 -0.40521 -0.31442 1.004032 2.697257

2004 0.478631 0.056071 1.004032 1.247697

2005 0.109394 1.70248 2.350849 0.797745

2006 -0.5182 -0.83662 0.428003 -0.18661

2007 0.478631 1.446439 1.872545 0.497501

2008 0.525902 1.852978 2.350849 2.057591

2009 0.824282 0.97775 0.923747 0.95558

2010 4.178184 4.945391 5.657167 5.883713

2011 1.396573 1.70248 1.662008 0.5425

2012 0.109394 0.325917 0.206628 0.449534

2013 0.254965 -0.10776 0.068824 0.271139

2014 2.178708 0.056071 -0.51085 -0.47986

2015 0.293518 -0.17799 -0.06174 2.697257

2016 -0.16945 -0.17799 0.96389 -0.58158

2017 0.383956 -0.24874 0.613695 0.354655

2018 0.14815 -0.24874 -0.33407 -0.84865

2019 -0.14223 0.325917 -0.35086 0.5425

2020 0.179299 0.056071 0.747174 0.316

2021 0.627935 0.419001 1.076537 1.189203

2022 1.327249 2.249354 1.164567 2.057591

2024 1.016692 1.324575 1.458619 1.574263

2025 -0.59602 0.653493 -0.31501 -0.13994

2026 -0.81537 0.743742 -0.06174 0.082374

2027 0.009586 1.324575 0.836286 1.189203

2028 -0.40521 -0.24874 -0.40609 -0.72018

2029 -0.16945 -0.02677 0.675232 1.339857

2030 1.327249 1.446439 -0.01903 0.713362

2031 0.009586 1.70248 0.551855 0.685518

2032 -0.16945 0.132105 -0.80367 -0.18661

2033 -0.19858 -0.17799 -1.09401 -0.79841

2034 1.957864 1.70248 -0.01903 0.251633

2035 0.335553 0.132105 -0.22298 1.514325

2036 1.016692 1.852978 0.923747 0.847133

2037 0.824282 1.990595 -0.08163 1.21845

2038 1.85381 1.446439 0.836286 1.608354

2039 1.092456 -0.4364 0.119524 0.007095

2040 -0.45452 -0.67834 0.613695 -0.91564

2041 -0.03646 1.083946 -0.12199 0.797745

2042 -0.49792 -0.10776 0.068824 0.116976

2044 -0.08357 -0.02677 0.309693 -0.256

2045 -0.19858 2.732918 0.836286 1.247697

2046 -0.25363 1.70248 -0.01903 0.156398

2047 1.488187 3.04524 1.255741 2.921996

2048 2.527089 2.119732 1.255741 2.437536

2049 0.478631 0.653493 0.836286 0.587111

2050 2.527089 1.574559 2.095385 0.136687

2051 -0.82319 0.529599 -0.22298 -0.63076

2052 1.239289 0.653493 0.675232 1.159089

2053 1.171775 0.056071 -0.22298 0.929388

2054 1.396573 1.192856 1.004032 2.150241

2055 0.824282 0.97775 0.309693 2.057591

2056 0.478631 -1.35384 2.095385 -0.07579

2057 -0.8606 0.653493 0.020855 -0.31244

2058 -0.45452 -0.50042 -0.90517 -1.12479

2059 0.696054 -0.24874 0.206628 -0.02533

2060 0.197017 -0.10776 0.747174 0.116976

2061 -0.66972 0.419001 0.206628 0.449534

2062 -0.33372 -0.38088 -0.40609 -0.64981

2063 -0.30898 0.132105 0.836286 0.271139

2064 0.478631 0.228521 1.354855 0.007095

2065 -0.11366 0.97775 0.675232 0.497501

2066 6.188369 4.683364 4.921307 5.421558

2067 -0.22425 -0.02677 -0.29596 -0.60763

2068 -0.02081 -0.10776 0.284476 -0.63076

2069 0.214734 -0.02677 0.160273 -0.18661

3000 0.430481 0.132105 0.364682 0.903196

3001 0.335553 0.97775 1.076537 0.316

3002 -1.04371 0.529599 0.259259 0.232126

3003 0.293518 0.97775 0.551855 0.316

3004 0.478631 1.324575 1.662008 0.741205

3005 0.335553 0.419001 0.068824 0.5425

3006 0.627935 0.419001 0.613695 0.156398

3007 0.627935 0.844489 0.119524 0.634707

3008 0.109394 1.083946 0.836286 1.189203

3009 1.327249 0.056071 -0.06174 0.634707

3010 1.327249 1.192856 0.613695 1.43975

3011 1.016692 0.529599 -0.36765 2.241201

3012 2.792141 3.204401 1.164567 2.331716

3013 1.750456 1.324575 0.259259 1.189203

3014 1.016692 -0.67834 0.337188 -0.05943

3015 0.042235 0.529599 0.428003 1.43975

3016 2.178708 0.228521 -0.01903 0.903196

3017 -0.33372 -0.31442 1.989247 -0.09216

3018 -0.63515 -0.24874 0.488866 0.29357

3019 -0.08357 -0.31442 -0.33407 0.042193

3020 0.879706 0.529599 0.259259 0.5425

3021 -0.19858 0.97775 0.364682 0.396915

3022 1.092456 1.083946 1.255741 1.247697

3023 -0.68673 -0.50042 -1.3453 -0.64028

3024 2.658697 0.529599 -0.90517 0.903196

3025 -0.11366 0.844489 0.488866 0.660112

3026 0.407219 1.083946 1.076537 0.847133

3027 1.488187 0.132105 0.747174 0.497501

3028 0.335553 0.743742 0.068824 0.929388

3029 -0.47461 -0.4364 -1.15117 -0.79841

3031 -1.1584 -0.79117 -0.36765 -1.36535

3032 -1.11999 -1.42591 -0.9938 -0.60763

3033 -1.28243 -0.88654 -1.20011 -1.14098

3036 0.946997 -0.24874 0.309693 -0.79841

3038 0.214734 0.743742 0.551855 1.189203

3039 -0.05211 -0.50042 -1.565 -0.51728

3040 -0.19858 -0.4364 -0.77733 -0.47986

AF002 -0.05211 0.743742 1.546939 0.769475

AF003 -0.55755 0.228521 0.428003 0.007095

AF004 1.016692 0.325917 0.364682 0.797745

AF005 0.572942 1.70248 1.354855 0.271139

AF006 0.478631 0.419001 1.164567 1.719861

AF007 0.762911 0.844489 0.551855 0.520001

AF008 0.335553 0.228521 0.923747 1.310522

AF009 0.072726 0.653493 1.458619 1.128975

AF010 0.478631 1.324575 0.309693 0.587111

AF011 -0.33372 0.228521 0.613695 -0.10771

AF012 0.696054 0.419001 0.119524 0.271139

AF013 -0.08357 -0.17799 -0.29596 -0.35474

AF014 0.430481 -0.24874 -0.18361 -0.18661

AF016 -0.45452 -0.4364 0.337188 -0.44169

AF017 -0.70289 -0.73068 -0.47849 -0.97281

AF018 -1.21911 -0.61546 0.551855 -0.36979

AF019 0.824282 -0.17799 0.675232 0.520001

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AF022 -1.50269 -1.40987 -0.44394 -0.49215

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AF037 -0.63515 -0.31442 -0.36765 -0.67304

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AF040 -0.94784 -0.38088 -0.62227 0.875164

AF043 0.525902 -0.31442 1.354855 1.128975

AF044 0.627935 -0.02677 0.551855 0.497501

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AF058 0.214734 0.743742 1.255741 0.713362

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AF066 -0.05211 -0.31442 1.354855 0.903196

AF067 0.14815 -0.02677 1.076537 1.310522

AF068 1.658529 0.228521 0.613695 0.354655

AF069 2.052602 0.844489 0.160273 0.271139

AF070 1.957864 0.743742 0.259259 0.497501

AF074 3.046418 0.97775 -0.33407 1.514325

AF075 -1.23593 -1.47462 0.613695 0.634707

AF102 1.488187 0.228521 0.364682 1.247697

AF103 1.327249 1.446439 0.364682 1.642446

AF104 -0.05211 -0.38088 0.836286 0.396915

AF106 1.658529 0.844489 0.206628 0.685518

AF107 2.658697 0.529599 -0.92722 0.741205

AF108 0.072726 -0.56355 0.160273 -0.02533

AF109 0.293518 0.529599 0.020855 0.042193

AF110 -0.3569 0.653493 -0.24166 0.116976

AF111 1.239289 -0.17799 -0.35086 0.232126

AF112 -0.33372 -0.02677 -0.57177 -0.47986

AF113 0.430481 -0.02677 -0.18361 0.232126

AF114 0.824282 0.132105 -0.51085 0.449534

AF115 0.762911 -0.38088 -0.33407 -0.36979

AF116 0.072726 0.529599 -0.47849 0.797745

AUT-001 2.658697 0.743742 -0.06174 0.082374

AUT-002 -0.8606 -1.06194 -0.06174 -1.06995

AUT-003 -0.25363 -0.38088 -0.26034 -0.81938

AUT-005 -0.33372 0.743742 -0.06174 0.136687

AUT-006 -0.90099 -1.52357 -0.54118 -0.88747

AUT-007 -0.05211 -0.24874 -0.64015 -0.256

AUT-009 -0.75288 -0.24874 -0.44394 -0.58158

AUT-010 -0.09861 0.529599 -0.10151 0.232126

AUT-011 -1.12944 -0.93612 -0.47849 -1.06995

AUT-012 -0.61691 -0.73068 -0.18361 -0.60763

AUT-013 -0.59602 -0.56355 -0.64015 0.042193

AUT-014 0.214734 -0.67834 -0.36765 -0.45665

AUT-015 -1.10938 -1.77126 -0.69516 -1.13301

AUT-016 -0.53742 -0.50042 -0.26034 -0.42672

AUT-017 -0.05211 -0.4364 -0.60438 -0.09216

AUT-021 -0.59602 0.325917 -0.01903 -0.28533

AUT-022 -1.72429 -2.15346 -0.93881 -1.36535

AUT-023 -0.68673 -0.31442 -0.29596 -1.23841

AUT-024 -1.04371 -0.83662 -0.47849 -0.50444

AUT-025 -0.02081 0.653493 -0.26034 -0.02533

AUT-026 -1.46714 -1.91142 0.160273 0.042193

AUT-027 -0.65199 -1.18134 -0.01903 -1.10017

AUT-028 1.488187 2.869816 1.989247 2.195721

AUT-029 -0.61691 -0.67834 -0.10151 -0.63076

AUT-030 -0.66972 -0.67834 -0.60438 -0.60763

AUT-031 -0.40521 -0.79117 -1.79086 -1.58449

AUT-032 0.214734 0.228521 -0.54118 -0.42672

AUT-033 -0.47461 0.132105 -0.14246 -0.12327

AUT-034 -1.01311 -1.32156 -0.92722 -1.29567

AUT-035 0.383956 0.132105 -0.10151 -0.45665

AUT-036 -0.43256 -0.56355 -0.80367 -0.36979

AUT-037 -0.14223 -0.88654 -0.54118 -0.78877

AUT-038 0.383956 1.083946 -0.40609 -0.50444

AUT-039 -0.47461 -0.24874 -1.10398 -0.76938

AUT-040 0.762911 0.653493 -0.51085 0.007095

AUT-041 0.383956 -0.17799 -0.14246 0.007095

AUT-042 -0.30898 -0.24874 0.068824 0.316

AUT-043 -0.12794 -1.28813 1.752698 -0.93494

AUT-044 0.572942 0.743742 0.551855 0.741205

AUT-045 -0.55755 -0.4364 -0.60438 -0.39816

AUT-046 0.525902 -0.56355 -0.18361 -1.24647

AUT-047 -1.342 -1.28813 -0.88131 -1.11658

AUT-049 0.293518 -0.10776 0.520361 -0.256

AUT-050 -0.02081 -0.67834 -0.92722 -0.50444

AUT-051 -0.49792 -0.88654 -1.20011 -1.57536

AUT-052 -0.88821 -0.61546 0.160273 -1.02888

AUT-053 0.383956 -0.02677 -1.12241 -0.47986

AUT-054 1.750456 -0.24874 0.551855 -0.77907

AUT-055 -0.63515 -0.24874 -0.29596 -0.256

AUT-057 -0.33372 -1.38043 1.164567 -0.29888

AUT-058 -0.47461 -0.4364 -0.36765 -0.36979

AUT-059 0.214734 -0.10776 -0.01903 -1.13301

AUT-060 -0.25363 -0.10776 0.160273 -0.31244

AUT-061 1.396573 0.844489 -0.54118 0.195146

AUT-062 0.072726 0.653493 -0.40609 -0.42672

AUT-063 -1.01311 -0.73068 1.004032 -0.04238

AUT-064 0.109394 1.083946 -0.36765 -0.12327

AUT-065A -0.43256 0.228521 -0.77733 -0.55677

AUT-066A 1.658529 0.653493 -1.1614 -0.61919

AUT-067A -0.61691 -0.24874 -0.60438 -0.00912

AUT-068A -0.3569 -0.56355 -0.66888 -0.73203

AUT-069A -0.45452 -0.31442 -0.06174 -0.64981

AUT-070A -0.83101 0.325917 -0.26034 -0.31244

AUT-071A -0.61691 0.056071 -0.29596 0.232126

AUT-072A -0.28257 0.794116 -0.18361 -0.83071

AUT-073A 1.016692 0.325917 -0.69516 -0.09216

AUT-074A -1.11999 -1.87112 -0.06174 -0.45665

AUT-081 -0.81537 -0.61546 -0.88131 -0.92585

AUT-082 1.750456 0.529599 -0.54118 -0.28533

AUT-083 -0.02081 0.844489 0.551855 0.520001

AUT-084 0.793596 -0.10776 -0.16303 0.741205

HO 1014 1.957864 2.572416 1.752698 -0.44169

HO 1037 -1.23593 -0.06727 -2.2778 -0.83071

HO 1068 -1.42883 -1.18134 -1.565 -1.52012

HO 1076 -1.29989 -1.7556 -2.16971 -0.44169

HO 1088 -0.53742 -0.79117 -1.35177 -0.42672

HO 1089 -0.66972 -0.24874 -0.66888 -0.98217

HO 1090 -1.31543 -1.38043 -1.22045 -1.66226

HO 1093 -0.91433 -1.28813 -1.5518 -1.72055

HO 1094 -0.83101 -0.02677 -0.96153 -0.75663

HO 1099 -1.46228 -1.10589 -0.68202 -1.11658

HO 1100 -0.64357 -0.02677 -0.36765 -0.18661

HO 1102 -0.87615 -0.98022 -0.72566 -0.88747

HO 1103 -1.12944 -1.18134 -1.01647 -1.72055

HO 1104 -1.05877 -0.50042 -0.29596 -1.03823

HO 1105 -0.59602 -0.4364 -0.69516 -1.11658

HO 1106 -0.85317 -0.93612 -0.9504 -0.64028

HO 1107 0.072726 -0.98022 -1.01647 -0.53012

HO 1108 0.383956 -0.73068 -0.854 -1.10017

HO 1109 -1.05877 -0.38088 -2.0615 -0.32607

HO 1110 -1.21058 -1.21373 -0.83047 -0.87781

HO 1111 -0.84575 -0.61546 -0.51085 -0.54345

HO 1112 -1.16868 -1.28813 -1.44625 -1.46322

HO 1113 -1.50045 -1.12252 -0.9938 -1.08525

HO AF015 2.052602 0.056071 1.989247 1.477037

HO AF031 -1.09503 -1.58051 0.160273 -0.64981

HO AUT-085 -0.90766 -1.18134 -0.9938 -1.31508

HO AUT-087 -0.72022 -0.24874 -0.33407 -0.95374

HO AUT-088 -0.93463 -0.61546 -0.66888 -0.39816

HO AUT-089 -1.21911 -0.83662 -0.66888 -1.49744

HO AUT-091 0.009586 -1.01914 -0.54118 -1.03823

HO AUT-092 -0.57804 -0.91133 1.004032 -0.81938

HO AUT-093 -0.40521 -0.34765 -0.83047 -0.61919

HO AUT-094 -1.17839 -1.10589 -1.10398 -0.95374

HO AUT-095 -0.05211 -0.56355 -0.69516 -0.42672

HO AUT-099 -1.44419 -0.83662 -0.33407 -1.39068

HO AUT-104 -0.87615 -0.4364 0.364682 -1.03823

HO AUT-105 -1.33586 -1.65355 0.020855 -1.11658

HO AUT-109 -0.16945 -0.56355 -0.10151 -0.39816

HO AUT-106 -0.43256 1.324575 0.551855 0.497501

HO 3041 -1.05877 -0.50042 -0.60438 -0.92585

HO 3045 -0.33372 0.653493 -0.33407 -0.44169

HO 3046 -0.95461 -0.28158 -0.97265 -0.05943

HO AF001 -1.28243 -1.36714 -0.97265 -0.66142

HO AF061 0.851994 -0.02677 0.428003 -0.3397

HO AUT-086 -1.20671 -0.79117 -1.25295 -1.19621

HO AUT-090 -0.16945 0.844489 -0.36765 -0.60763

HO AUT-096 -0.57804 -0.4364 -0.22298 -0.94403

HO AUT-097 -1.21058 -0.56355 -1.05919 -1.17316

HO AUT-098 -1.01311 -0.93612 -0.46122 -0.88747

HO AUT-100 0.042235 0.844489 -0.18361 -0.69632

HO AUT-101 -1.08494 -0.79117 0.613695 -0.99977

HO AUT-102 -0.95461 -0.79117 -0.72566 -1.21123

HO AUT-103 -0.65199 -0.67834 0.183451 -0.63076

HO AUT-107 -0.08357 1.192856 0.923747 0.741205

HO AUT-108 -0.8606 -0.98022 -0.29596 -0.28533

HO 2023 1.171775 0.97775 2.775878 1.010542

HO 2043 -1.10938 -1.56935 1.040285 -0.15662

HO 2071 -1.10004 -1.13914 -0.80367 -1.21123

HO 2073 -1.0007 -1.68984 -1.12241 -1.65361

HO 2074 -0.93463 -0.67834 -0.854 -1.40995

HO 2075 -1.05376 -0.24874 -0.84223 -1.40314

HO 2076 -1.24031 -1.52357 2.215643 -0.55677

K01 2.658697 1.324575 -0.55647 0.903196

SC-001 0.946997 -0.02677 -0.44394 0.5425

SC-003 -0.90766 -1.40987 -1.26167 -1.19621

SC-004 0.696054 -0.17799 -0.40609 0.497501

SC-005 -0.15584 0.228521 -0.44394 0.5425

SC-006 -0.16945 0.97775 0.309693 0.95558

SC-007 -0.85317 -0.67834 -0.57177 -0.41244

SC-C001 -0.05211 0.132105 0.428003 0.423224

SC-DD001 1.327249 0.325917 0.428003 1.21845

Figure S1. Functional Relationships of Salivary miRNAs Altered in Children with Autism Spectrum Disorder

The 14 miRNAs of interest are hierarchically clustered (left column) based on the function of their mRNA targets (identified in DIANA miRPath with the microT-cds algorithm). The 14 miRNAs targeted mRNAs from 41 KEGG pathways with greater frequency than that expected by chance (including 9 brain-related pathways). The total number of mRNA targets for each miRNA are shown, as well as the number of mRNAs targeted in the 9 brain-related pathways. Note that three pairs of miRNAs which cluster here based on functional targets (miR-193a-5p/miR-125a-5p; miR-148a-5p/miR-944; and miR-620/miR-4705) were also clustered based on salivary concentration patterns among ASD, TD, and DD groups (Figure 1).

Figure S2. Bio-analyzer Output Demonstrating Robust Small RNA Presence Irrespective of RIN Value

This bio-analyzer output from sample #2012 demonstrates robust peaks of small RNAs (including miRNA) at 25 nucleotides. In the present study small yields are specifically facilitate by the use of RNA stabilizing solution with saliva collection, an RNA extraction technique that enriches for small RNA, and the biophysical properties of miRNA in extracellular-fluid, which confer resistance to salivary endonucleases. Not that the yield and quality of miRNA are not always accurately reflected by a low RNA integrity number (RIN).

mature miRNA, piRNA

precursor miRNA, 5S RNA 18S RNA 28S RNA