Affymetrix U133A Array | Ziplex Automated Workstation | Platform Comparison | |||||||||||
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Selection Criteria1 | Gene Probe | NOSE mean SI (n = 11) | TOV mean SI (n = 12) | ratio (N/T)2 | ratio (T/N)2 | p-value3 | NOSE mean SI (n = 11) | TOV mean SI (n = 12) | ratio (N/T)2 | ratio (T/N)2 | p-value3 | significance based on p-value3 | concordance based on ratio fold-change direction |
A | RGS4 | 291 | 2 | 181.2 | 0.01 | <0.0001 | 863 | 41 | 21.1 | 0.05 | <0.0001 | agree | concordance |
C | SERPINE1 | 1912 | 12 | 162.4 | 0.01 | <0.0001 | 1426 | 17 | 82.2 | 0.01 | <0.0001 | agree | concordance |
A | PDPN | 57 | 2 | 23.9 | 0.04 | 0.0008 | 100 | 35 | 2.9 | 0.35 | 0.0023 | disagree | concordance |
A | ALDH1A3 | 661 | 29 | 22.6 | 0.04 | 0.0020 | 1887 | 76 | 24.8 | 0.04 | 0.0051 | agree | concordance |
A | IL8 | 1353 | 69 | 19.7 | 0.05 | 0.0151 | 4465 | 231 | 19.3 | 0.05 | 0.0015 | agree | concordance |
A | PTGIS | 1470 | 80 | 18.4 | 0.05 | <0.0001 | 3474 | 184 | 18.9 | 0.05 | <0.0001 | agree | concordance |
A | HEG1 | 923 | 66 | 14.1 | 0.07 | <0.0001 | 3184 | 252 | 12.6 | 0.08 | <0.0001 | agree | concordance |
A | TMEM158 | 461 | 33 | 13.9 | 0.07 | <0.0001 | 869 | 46 | 18.8 | 0.05 | <0.0001 | agree | concordance |
C | CDKN1A | 598 | 53 | 11.4 | 0.09 | <0.0001 | 385 | 63 | 6.1 | 0.16 | <0.0001 | agree | concordance |
A | CCL2 | 570 | 54 | 10.6 | 0.09 | 0.0010 | 1923 | 207 | 9.3 | 0.11 | 0.0001 | agree | concordance |
A | LXN | 731 | 73 | 10.1 | 0.10 | <0.0001 | 926 | 124 | 7.5 | 0.13 | 0.0002 | agree | concordance |
C | SPARC | 1037 | 108 | 9.6 | 0.10 | <0.0001 | 2841 | 341 | 8.3 | 0.12 | <0.0001 | agree | concordance |
C | IL1B | 666 | 70 | 9.6 | 0.10 | 0.0247 | 1559 | 46 | 34.0 | 0.03 | 0.0035 | agree | concordance |
A | BDKRB1 | 152 | 18 | 8.7 | 0.11 | 0.0004 | 464 | 22 | 21.0 | 0.05 | <0.0001 | agree | concordance |
B | SLC16A3 | 425 | 63 | 6.8 | 0.15 | <0.0001 | 197 | 37 | 5.3 | 0.19 | <0.0001 | agree | concordance |
A | FSTL1 | 1837 | 277 | 6.6 | 0.15 | <0.0001 | 5293 | 732 | 7.2 | 0.14 | <0.0001 | agree | concordance |
C | THBS2 | 846 | 135 | 6.3 | 0.16 | <0.0001 | 668 | 105 | 6.4 | 0.16 | 0.0009 | agree | concordance |
A | IGFBP4 | 1484 | 238 | 6.2 | 0.16 | <0.0001 | 692 | 122 | 5.7 | 0.18 | 0.0001 | agree | concordance |
A | PTRF | 976 | 168 | 5.8 | 0.17 | <0.0001 | 217 | 77 | 2.8 | 0.35 | <0.0001 | agree | concordance |
A | GBE1 | 775 | 136 | 5.7 | 0.18 | <0.0001 | 988 | 173 | 5.7 | 0.17 | <0.0001 | agree | concordance |
A | PLOD2 | 654 | 123 | 5.3 | 0.19 | <0.0001 | 926 | 132 | 7.0 | 0.14 | <0.0001 | agree | concordance |
A | VAT1 | 874 | 175 | 5.0 | 0.20 | <0.0001 | 255 | 78 | 3.3 | 0.31 | <0.0001 | agree | concordance |
A | COL1A1 | 2940 | 614 | 4.8 | 0.21 | 0.0001 | 1502 | 289 | 5.2 | 0.19 | 0.0003 | agree | concordance |
C | CCND2 | 324 | 70 | 4.7 | 0.21 | 0.0127 | 481 | 117 | 4.1 | 0.24 | 0.0337 | agree | concordance |
A | SELT | 558 | 148 | 3.8 | 0.27 | 0.0010 | 166 | 137 | 1.2 | 0.8 | >0.05 | disagree | concordance |
B | C1QTNF1 | 169 | 48 | 3.6 | 0.28 | <0.0001 | 30 | 3 | 11.7 | 0.09 | <0.0001 | agree | concordance |
A | VGLL3 | 35 | 10 | 3.5 | 0.29 | <0.0001 | 75 | 12 | 6.1 | 0.16 | 0.0015 | disagree | concordance |
C | PGAM1 | 1482 | 473 | 3.1 | 0.32 | <0.0001 | 1603 | 504 | 3.2 | 0.31 | <0.0001 | agree | concordance |
C | TP53 | 55 | 18 | 3.0 | 0.33 | 0.0178 | 197 | 226 | 0.9 | 1.1 | >0.05 | agree | discordance |
B | MSN | 746 | 250 | 3.0 | 0.33 | <0.0001 | 818 | 354 | 2.3 | 0.43 | <0.0001 | agree | concordance |
B | PSMD3 | 196 | 66 | 3.0 | 0.34 | <0.0001 | 735 | 384 | 1.9 | 0.5 | <0.0001 | agree | concordance |
B | WSB1 | 300 | 103 | 2.9 | 0.34 | 0.0003 | 313 | 155 | 2.0 | 0.50 | 0.0006 | agree | concordance |
B | MRC2 | 313 | 109 | 2.9 | 0.35 | <0.0001 | 528 | 138 | 3.8 | 0.26 | <0.0001 | agree | concordance |
A | MYH10 | 1113 | 420 | 2.6 | 0.38 | 0.0006 | 1096 | 464 | 2.4 | 0.42 | 0.0106 | disagree | concordance |
B | NSF | 180 | 72 | 2.5 | 0.40 | <0.0001 | 304 | 170 | 1.8 | 0.6 | 0.0023 | disagree | concordance |
A | P4HB | 2276 | 917 | 2.5 | 0.40 | <0.0001 | 4567 | 1553 | 2.9 | 0.34 | <0.0001 | agree | concordance |
C | SERPIND1 | 7 | 3 | 2.2 | 0.45 | >0.05 | 79 | 117 | 0.7 | 1.5 | 0.0363 | agree | discordance |
B | RAB5C | 309 | 142 | 2.2 | 0.46 | 0.0106 | 132 | 61 | 2.2 | 0.46 | <0.0001 | disagree | concordance |
B | PFN2 | 800 | 392 | 2.0 | 0.49 | <0.0001 | 699 | 444 | 1.6 | 0.6 | 0.0005 | agree | concordance |
B | TRAF4 | 47 | 23 | 2.0 | 0.50 | 0.0363 | 30 | 27 | 1.1 | 0.9 | >0.05 | agree | concordance |
B | LSM12 | 59 | 31 | 1.9 | 0.5 | 0.0023 | 53 | 36 | 1.5 | 0.7 | 0.0106 | agree | concordance |
B | PLP2 | 294 | 157 | 1.9 | 0.5 | 0.0051 | 270 | 190 | 1.4 | 0.7 | 0.0151 | agree | concordance |
B | PAFAH1B1 | 181 | 98 | 1.9 | 0.5 | 0.0006 | 556 | 387 | 1.4 | 0.7 | 0.0089 | disagree | concordance |
B | TIMM22 | 42 | 23 | 1.8 | 0.5 | 0.0392 | 126 | 82 | 1.5 | 0.6 | 0.0001 | disagree | concordance |
B | AMOTL2 | 308 | 173 | 1.8 | 0.6 | 0.0015 | 776 | 484 | 1.6 | 0.6 | 0.0113 | agree | concordance |
B | ATP1B3 | 668 | 386 | 1.7 | 0.6 | <0.0001 | 832 | 449 | 1.9 | 0.5 | 0.0015 | disagree | concordance |
C | DAPK1 | 181 | 117 | 1.5 | 0.6 | >0.05 | 186 | 146 | 1.3 | 0.8 | >0.05 | agree | concordance |
B | TFRC | 894 | 606 | 1.5 | 0.7 | 0.0089 | 386 | 216 | 1.8 | 0.6 | 0.0062 | agree | concordance |
B | ATG3 | 200 | 139 | 1.4 | 0.7 | 0.0106 | 342 | 319 | 1.1 | 0.9 | >0.05 | agree | concordance |
B | RNF7 | 177 | 125 | 1.4 | 0.7 | 0.0178 | 54 | 63 | 0.9 | 1.2 | >0.05 | agree | concordance |
A | IL18 | 21 | 16 | 1.4 | 0.7 | 0.0148 | 125 | 104 | 1.2 | 0.8 | 0.0210 | agree | concordance |
C | CRKL | 38 | 28 | 1.4 | 0.7 | >0.05 | 18 | 23 | 0.8 | 1.3 | >0.05 | agree | concordance |
B | XIST | 103 | 76 | 1.4 | 0.7 | >0.05 | 256 | 378 | 0.7 | 1.5 | >0.05 | agree | discordance |
C | PI4KA | 59 | 44 | 1.4 | 0.7 | 0.0127 | 110 | 113 | 1.0 | 1.0 | >0.05 | agree | concordance |
D | MSH6 | 62 | 47 | 1.3 | 0.8 | >0.05 | 227 | 519 | 0.4 | 2.3 | 0.0010 | disagree | discordance |
C | LZTR1 | 82 | 69 | 1.2 | 0.8 | >0.05 | 81 | 74 | 1.1 | 0.9 | >0.05 | agree | concordance |
D | MLH1 | 171 | 150 | 1.1 | 0.9 | >0.05 | 143 | 150 | 1.0 | 1.0 | >0.05 | agree | concordance |
C | MYC | 151 | 142 | 1.1 | 0.9 | >0.05 | 119 | 212 | 0.6 | 1.8 | >0.05 | agree | discordance |
B | PCOLCE2 | 22 | 21 | 1.0 | 1.0 | >0.05 | 39 | 39 | 1.0 | 1.0 | >0.05 | agree | concordance |
C | CCND3 | 136 | 139 | 1.0 | 1.0 | >0.05 | 101 | 134 | 0.7 | 1.3 | 0.0127 | agree | concordance |
D | KRAS | 157 | 162 | 1.0 | 1.0 | >0.05 | 150 | 200 | 0.8 | 1.3 | >0.05 | agree | concordance |
A | SEPT9 | 880 | 918 | 1.0 | 1.0 | >0.05 | 543 | 394 | 1.4 | 0.7 | >0.05 | agree | concordance |
D | RB1 | 67 | 73 | 0.9 | 1.1 | >0.05 | 166 | 225 | 0.7 | 1.4 | >0.05 | agree | concordance |
D | BRCA2 | 10 | 12 | 0.8 | 1.2 | >0.05 | 15 | 23 | 0.6 | 1.6 | 0.0210 | agree | concordance |
B | SNX4 | 43 | 52 | 0.8 | 1.2 | >0.05 | 199 | 339 | 0.6 | 1.7 | 0.0042 | agree | concordance |
A | BTN3A2 | 40 | 48 | 0.8 | 1.2 | >0.05 | 89 | 173 | 0.5 | 1.9 | 0.0005 | disagree | concordance |
C | TFF1 | 12 | 16 | 0.7 | 1.4 | >0.05 | 226 | 61 | 3.7 | 0.3 | <0.0001 | disagree | discordance |
B | NUP85 | 71 | 101 | 0.7 | 1.4 | >0.05 | 85 | 134 | 0.6 | 1.6 | 0.0028 | agree | concordance |
C | JUND | 759 | 1181 | 0.6 | 1.6 | >0.05 | 1725 | 2479 | 0.7 | 1.4 | >0.05 | agree | concordance |
B | OSBPL11 | 46 | 74 | 0.6 | 1.6 | 0.0151 | 56 | 148 | 0.4 | 2.6 | <0.0001 | disagree | concordance |
D | BRCA1 | 15 | 24 | 0.6 | 1.6 | >0.05 | 27 | 40 | 0.7 | 1.5 | >0.05 | agree | concordance |
B | SR140 | 144 | 243 | 0.6 | 1.7 | 0.0089 | 13 | 64 | 0.2 | 5.0 | <0.0001 | disagree | concordance |
D | BRAF | 27 | 46 | 0.6 | 1.7 | 0.0089 | 22 | 47 | 0.5 | 2.1 | <0.0001 | disagree | concordance |
C | ZNF74 | 12 | 21 | 0.6 | 1.8 | 0.0042 | 16 | 44 | 0.4 | 2.8 | 0.0002 | disagree | concordance |
B | TOMM70A | 212 | 383 | 0.6 | 1.8 | 0.0004 | 115 | 306 | 0.4 | 2.7 | <0.0001 | agree | concordance |
B | RPL24 | 1895 | 3503 | 0.5 | 1.8 | 0.0002 | 1834 | 4179 | 0.4 | 2.3 | 0.0003 | agree | concordance |
C | HSPD1 | 899 | 1682 | 0.5 | 1.9 | 0.0002 | 461 | 1189 | 0.4 | 2.6 | 0.0004 | agree | concordance |
D | MSH2 | 27 | 53 | 0.5 | 2.0 | 0.0023 | 112 | 495 | 0.2 | 4.4 | <0.0001 | disagree | concordance |
B | MYNN | 27 | 55 | 0.5 | 2.1 | 0.0001 | 16 | 40 | 0.4 | 2.5 | 0.0005 | agree | concordance |
D | ERBB2 | 99 | 230 | 0.4 | 2.3 | 0.0003 | 50 | 142 | 0.4 | 2.8 | 0.0002 | agree | concordance |
B | ICAM2 | 14 | 34 | 0.4 | 2.5 | 0.0011 | 13 | 25 | 0.5 | 1.9 | 0.0089 | agree | concordance |
B | CEP70 | 23 | 59 | 0.4 | 2.6 | <0.0001 | 56 | 182 | 0.3 | 3.3 | <0.0001 | agree | concordance |
B | TMEM97 | 70 | 195 | 0.4 | 2.8 | 0.0015 | 51 | 140 | 0.4 | 2.8 | 0.0004 | disagree | concordance |
B | CD300A | 11 | 36 | 0.3 | 3.3 | <0.0001 | 4 | 36 | 0.1 | 9.2 | 0.0006 | agree | concordance |
A | STAT1 | 30 | 109 | 0.3 | 3.6 | 0.0127 | 48 | 110 | 0.4 | 2.3 | 0.0210 | agree | concordance |
A | EVI1 | 11 | 197 | 0.06 | 17.5 | <0.0001 | 36 | 636 | 0.06 | 17.5 | <0.0001 | agree | concordance |
C | APOE | 7 | 126 | 0.06 | 17.9 | <0.0001 | 39 | 326 | 0.12 | 8.4 | <0.0001 | agree | concordance |
A | CP | 7 | 295 | 0.02 | 43.5 | <0.0001 | 33 | 972 | 0.03 | 29.3 | <0.0001 | agree | concordance |
A | RGS1 | 2 | 112 | 0.02 | 47.0 | <0.0001 | 3 | 169 | 0.02 | 56.5 | <0.0001 | agree | concordance |
A | SPON1 | 5 | 271 | 0.02 | 57.8 | <0.0001 | 6 | 257 | 0.02 | 44.9 | <0.0001 | agree | concordance |
A | CD24 | 6 | 481 | 0.01 | 77.2 | <0.0001 | 63 | 3697 | 0.02 | 58.5 | <0.0001 | agree | concordance |
A | IGKC | 7 | 991 | 0.01 | 151.6 | <0.0001 | 27 | 873 | 0.03 | 32.6 | 0.0008 | agree | concordance |
A | IGHG1 | 3 | 1262 | 0.003 | 374.3 | <0.0001 | 19 | 203 | 0.10 | 10.5 | <0.0001 | agree | concordance |