ESC+ CIS vs Oo,Gon,NT Significant up in ESC+CIS Input parameters Study Design: Two Class Unpaired Imputation Engine: K-Nearest Neighbors Number of K-Nearest Neighbors: 10 Delta: 1.232 Upper Cutoff: 3.462057 Lower Cutoff: -4.2173448 All permutations unique? false Number of Permutations: 100 Fold Change Criterion Used: No HCL: no linkage Time: 14901 ms Computed Quantiles Computed Exchangeability Factor s0: 0.18402982 s0 Percentile: 1.0 Pi0Hat: 0.82013094 Num. False Sig. Genes (Median): 1.64026 Num. False Sig. Genes (90th %ile): 20.50327 False Discovery Rate (Median): 0.92670 % False Discovery Rate (90th %ile): 11.58377 % Results Positive Significant# of PositiveGenes Significant Genes: 162 % of Positive Significant Genes: 0% Negative Significant# Genes of Negative Significant Genes: 15 % of Negative Significant Genes: 0% All Significant GenesTotal # of Significant Genes: 177 % of Genes that are Significant: 0% Non-Significant GenesTotal # of Non-Significant Genes: 43199 % of Genes that are Not Significant: 100% Expected score Observed Numerator Denominator ProbeID Acc No HUGO Name Fold change q-value (%) (dExp) score (d) (r) (s+s0) A_32_P81674 AK091593 LOC157627 0.8224995 -5.522918 -6.855621 1.241304 0.014933664 0.7009666 A_23_P145724 NM_006658 C7orf16 -0.84460914 -4.971844 -5.4247065 1.0910853 0.04294284 0.56560755 A_32_P149288 ENST00000354271 ENST00000354271 -0.3369156 -4.8684034 -2.1406336 0.4396993 0.23353566 0.56560755 A_23_P250122 NM_020223 FAM20C 0.614345 -4.705595 -1.4391937 0.30584735 0.3723636 0.9881096 A_32_P32406 X15675 X15675 -0.24166806 -4.6141524 -6.5238457 1.4138774 0.002122805 0.9881096 A_23_P124619 NM_020672 S100A14 1.002037 -4.552065 -3.48658 0.7659337 0.08215146 0.9881096 A_24_P351283 NM_018000 MREG 0.373876 -4.432416 -2.6824012 0.6051781 0.12981768 0.9881096 A_24_P252310 NM_014690 FAM131B 0.8797154 -4.3596897 -4.691379 1.0760809 0.09375565 0.9881096 A_23_P90273 NM_022467 CHST8 0.6046405 -4.354433 -2.531434 0.5813464 0.170064 0.9881096 A_23_P135595 NM_032329 ING5 -1.3220888 -4.336276 -3.1131902 0.7179409 0.10597495 0.9881096 A_23_P17673 NM_013369 DNMT3L 1.4538249 -4.327721 -4.479163 1.0349935 0.044912152 0.9881096 A_23_P119778 NM_020342 SLC39A10 -0.7632112 -4.2425666 -3.418871 0.8058497 0.084524214 0.95364064 A_23_P103269 AF242772 LOC51336 -0.35310197 -4.2316866 -3.7269282 0.88071936 0.0535082 0.95364064 A_23_P134484 NM_001742 CALCR 0.20234203 -4.2243314 -5.074961 1.2013644 0.049506035 0.95364064 A_23_P204246 NM_004426 PHC1 -0.104349 -4.2173448 -2.4296188 0.57610154 0.18633255 0.95364064 CIS+Oo vs ESC,Gon,NT Significant up in CIS + Oo Input parameters Study Design: Two Class Unpaired Imputation Engine: K-Nearest Neighbors Number of K-Nearest Neighbors: 10 Delta: 1.193 Upper Cutoff: 3.9326658 Lower Cutoff: -4.0489993 All permutations unique? false Number of Permutations: 100 Fold Change Criterion Used: No HCL: no linkage Time: 24083 ms Computed Quantiles Computed Exchangeability Factor s0: 0.1809463 s0 Percentile: 1.0 Pi0Hat: 0.6370343 Num. False Sig. Genes (Median): 0.63703 Num. False Sig. Genes (90th %ile): 14.65179 False Discovery Rate (Median): 0.92324 % False Discovery Rate (90th %ile): 21.23448 % Results Positive Significant #Genes of Positive Significant Genes: 42 % of Positive Significant Genes: 0% Negative Significant# Genes of Negative Significant Genes: 27 % of Negative Significant Genes: 0% All Significant GenesTotal # of Significant Genes: 69 % of Genes that are Significant: 0% Non-Significant GenesTotal # of Non-Significant Genes: 43307 % of Genes that are Not Significant: 100% Expected score Observed Numerator Denominator ProbeID Acc No HUGO Name Fold change q-value (%) (dExp) score (d) (r) (s+s0) A_23_P76799 NM_013448 BAZ1A 0.46986562 3.9326658 2.308405 0.58698225 4.327397 0.93681514 A_23_P76799 NM_013448 BAZ1A 0.09361901 3.9758356 2.1509 0.54099315 4.0580716 1.0443186 A_23_P76799 NM_013448 BAZ1A -0.8589524 3.979695 2.2844458 0.57402533 4.2801247 1.0443186 A_24_P278172 NM_006007 ZFAND5 0.58774894 3.9851449 2.1909375 0.54977614 4.16514 1.0443186 A_23_P12643 NM_020682 AS3MT 0.673183 3.994299 3.1313505 0.783955 7.6182137 1.0443186 A_23_P57268 NM_001338 CXADR 0.31080467 4.00446 4.6864944 1.1703187 16.739403 1.0443186 A_24_P53051 NM_171846 LACTB 0.38155034 4.0306673 4.0658584 1.0087308 6.8292794 1.1375612 A_24_P70993 NM_002414 CD99 -0.93209964 4.0330005 4.1292267 1.0238597 20.236265 1.1375612 A_24_P345123 NM_003953 MPZL1 0.09538944 4.0588956 3.717463 0.91588044 9.837251 1.1796931 A_23_P140821 NM_016948 PARD6A -1.125216 4.0678334 3.0458312 0.74876004 9.568967 1.1796931 A_32_P230138 CA431053 CA431053 -0.29207706 4.117919 2.5994096 0.6312435 5.5683007 1.225066 A_24_P350576 AB011123 TNIK -0.063313715 4.13281 4.511723 1.0916841 13.763751 1.2490869 A_24_P184803 NM_004086 COCH 0.944961 4.146195 3.8934016 0.93903005 19.15364 1.2740686 A_24_P185709 NM_012156 EPB41L1 1.1146014 4.166986 2.7647743 0.663495 5.1433406 1.3848572 A_32_P233727 CK570365 SLMO2 -0.10615703 4.1697197 3.3043451 0.79246217 6.0204782 1.3848572 A_23_P369948 NM_024955 FOXRED2 0.6002224 4.20234 3.937982 0.93709266 13.645968 0 A_23_P364024 NM_006851 GLIPR1 1.5337305 4.212257 3.645565 0.865466 13.528672 0 A_23_P138308 NM_001779 CD58 0.24719526 4.232161 4.16426 0.9839559 8.590657 0 A_32_P205139 CA943539 PTEN 0.3610789 4.2392774 3.9079561 0.9218449 6.4094152 0 A_24_P846755 A_24_P846755 A_24_P846755 -0.17360649 4.2752304 5.1019964 1.1933851 19.499683 0 A_32_P202977 THC2383225 THC2383225 -0.31859857 4.286073 3.6653152 0.8551686 8.618072 0 A_24_P388033 NM_033055 HIAT1 -0.44128892 4.371553 4.8173065 1.1019669 31.216665 0 A_23_P133438 NM_019018 FAM105A 0.6740633 4.477504 3.8056273 0.849944 7.5414762 0 A_23_P137381 NM_002167 ID3 0.12693632 4.491157 4.779557 1.0642151 18.842564 0 A_32_P225355 NM_182485 CPEB2 -0.18965065 4.5685916 3.7825208 0.8279402 21.46156 0 A_24_P297680 BC063633 PDXDC2 -0.7803692 4.6100025 2.947515 0.63937384 9.399402 0 A_23_P11372 NM_000194 HPRT1 1.176598 4.637163 1.9753094 0.42597365 4.1474614 0 A_24_P81691 NM_014758 SNX19 0.51488096 4.677278 3.6612558 0.7827749 14.103683 0 A_23_P11372 NM_000194 HPRT1 0.6278126 4.8065267 1.964181 0.40864873 4.0886083 0 A_23_P11372 NM_000194 HPRT1 -0.6977348 4.816077 2.0018444 0.4156587 4.205325 0 A_23_P11372 NM_000194 HPRT1 -0.33900505 4.8235087 1.8776293 0.38926628 3.8249865 0 A_23_P11372 NM_000194 HPRT1 0.9855167 4.8401003 1.9373827 0.40027738 4.0033126 0 A_23_P11372 NM_000194 HPRT1 -0.34054983 4.8763022 1.8405819 0.37745443 3.671119 0 A_23_P11372 NM_000194 HPRT1 -0.82863426 4.929704 1.9700308 0.39962456 4.074263 0 A_23_P11372 NM_000194 HPRT1 2.145265 4.9763246 1.9509687 0.39205015 4.0284076 0 A_23_P11372 NM_000194 HPRT1 0.9160912 4.977657 2.0412054 0.41007355 4.309906 0 A_23_P11372 NM_000194 HPRT1 -1.1129072 5.009658 2.0302725 0.40527168 4.245344 0 A_24_P216968 ENST00000367142 ENST00000367142 0.5217399 5.1173162 4.8014116 0.9382675 43.281456 0 A_24_P130952 NM_032435 KIAA1804 -0.29949218 5.125391 5.0454373 0.98440045 56.106506 0 A_24_P349117 NM_020752 GPR158 -1.7036519 5.2812567 4.6603026 0.88242304 28.546621 0 A_23_P139434 NM_006248 PRB2 -0.58351964 5.3396435 5.423881 1.0157759 92.38469 0 A_32_P133072 NM_006108 SPON1 0.3362832 5.468335 3.2894049 0.6015368 9.235191 0 CIS + Gon vs ESC,Oo,NT Significant up in CIS + Gon Input parameters Study Design: Two Class Unpaired Imputation Engine: K-Nearest Neighbors Number of K-Nearest Neighbors: 10 Delta: 1.1 Upper Cutoff: 2.6732464 Lower Cutoff: -2.457588 All permutations unique? false Number of Permutations: 100 Fold Change Criterion Used: No HCL: no linkage Time: 11422 ms Computed Quantiles Computed Exchangeability Factor s0: 0.32644853 s0 Percentile: 9.0 Pi0Hat: 0.5430192 Num. False Sig. Genes (Median): 17.91963 Num. False Sig. Genes (90th %ile): 89.05515 False Discovery Rate (Median): 0.93918 % False Discovery Rate (90th %ile): 4.66746 % Results Positive Significant# ofGenes Positive Significant Genes: 632 % of Positive Significant Genes: 1% Negative Significant# Genes of Negative Significant Genes: 1276 % of Negative Significant Genes: 3% All Significant GenesTotal # of Significant Genes: 1908 % of Genes that are Significant: 4% Non-Significant GenesTotal # of Non-Significant Genes: 41468 % of Genes that are Not Significant: 96% Expected score Observed Numerator Denominator ProbeID Acc No HUGO Name Fold change q-value (%) (dExp) score (d) (r) (s+s0) A_23_P423331 NM_032536 NTNG2 -0.003585179 -4.6608396 -4.859108 1.0425392 0.03549816 0.15971152 A_24_P634768 AK026416 FLJ22763 0.9634413 -4.506478 -4.881654 1.0832525 0.028646223 0.15971152 A_24_P883577 THC2442727 THC2442727 0.23539987 -4.4966207 -4.706494 1.0466735 0.048275832 0.15971152 A_24_P784203 AI885390 AI885390 -1.1508468 -4.4069467 -2.5972404 0.5893515 0.16187035 0.15971152 A_23_P250444 NM_000166 GJB1 -0.12834935 -4.11679 -3.6554203 0.8879298 0.078782864 0.49166727 A_23_P149441 AF172850 LOC51152 0.23428312 -4.096271 -5.5022974 1.3432454 0.046524018 0.49166727 A_23_P64611 NM_176798 P2RY6 0.16516803 -4.0752826 -2.9416566 0.7218289 0.13749719 0.49166727 A_23_P421032 NM_174977 SEC14L4 -0.04271415 -3.982618 -4.898387 1.2299414 0.092557006 0.49166727 A_32_P170454 AK094730 LOC283454 -1.4287357 -3.9782026 -4.345393 1.0923007 0.091263354 0.49166727 A_24_P25544 NM_000514 GDNF -0.17861782 -3.9261417 -6.025608 1.5347403 0.00460199 0.49166727 A_24_P929202 AA814903 AA814903 -0.3886899 -3.9222445 -4.532756 1.1556536 0.08932942 0.49166727 A_32_P121674 A_32_P121674 A_32_P121674 -0.33721867 -3.903812 -3.7885904 0.97048485 0.067726225 0.49166727 A_32_P5086 BU632168 STOM 0.18238331 -3.9001167 -4.041771 1.0363206