Background
Methods
Source of RNA
Ziplex array and probe design
Selection Criteria Categories | Affymetrix U133A Probe Set | GeneID* | Gene Name | Reference |
---|---|---|---|---|
A: Differentially expressed genes based on Affymetrix U133A analysis
| 208782_at | 11167 |
FSTL1
| 25 |
213069_at | 57493 |
HEG1
| 25 | |
218729_at | 56925 |
LXN
| 25 | |
202620_s_at | 5352 |
PLOD2
| 25 | |
217811_at | 51714 |
SELT
| 25 | |
213338_at | 25907 |
TMEM158
| 25 | |
203282_at | 2632 |
GBE1
| 25 | |
204846_at | 1356 |
CP
| 25 | |
221884_at | 2122 |
EVI1
| 25 | |
202310_s_at | 1277 |
COL1A1
| 26 | |
201508_at | 3487 |
IGFBP4
| 26 | |
200654_at | 5034 |
P4HB
| 26 | |
212372_at | 4628 |
MYH10
| 26 | |
216598_s_at | 6347 |
CCL2
| 26 | |
208626_s_at | 10493 |
VAT1
| 26 | |
41220_at | 10801 |
SEPT9
| 26 | |
208789_at | 284119 |
PTRF
| 26 | |
206295_at | 3606 |
IL18
| 22 | |
202859_x_at | 3576 |
IL8
| 22 | |
209969_s_at | 6772 |
STAT1
| 22 | |
209846_s_at | 11118 |
BTN3A2
| 22 | |
220327_at | 389136 |
VGLL3
| 11 | |
203180_at | 220 |
ALDH1A3
| 26 | |
204338_s_at | 5999 |
RGS4
| 26 | |
204879_at | 10630 |
PDPN
| 26 | |
207510_at | 623 |
BDKRB1
| 26 | |
208131_s_at | 5740 |
PTGIS
| 26 | |
211430_s_at | 3500 |
IGHG1
| 26 | |
216834_at | 5996 |
RGS1
| 26 | |
266_s_at | 100133941 |
CD24
| 26 | |
213994_s_at | 10418 |
SPON1
| 26 | |
221671_x_at | 3514 |
IGKC
| 26 | |
B: Genes exhibiting a range of expression values based on Affymetrix U133A analysis
| 218304_s_at | 114885 |
OSBPL11
| 25 |
219295_s_at | 26577 |
PCOLCE2
| 25 | |
205329_s_at | 8723 |
SNX4
| 25 | |
219036_at | 80321 |
CEP70
| 25 | |
218926_at | 55892 |
MYNN
| 25 | |
208836_at | 483 |
ATP1B3
| 25 | |
204992_s_at | 5217 |
PFN2
| 25 | |
214143_x_at | 6152 |
RPL24
| 25 | |
208691_at | 7037 |
TFRC
| 25 | |
203002_at | 51421 |
AMOTL2
| 25 | |
221492_s_at | 64422 |
ATG3
| 25 | |
218286_s_at | 9616 |
RNF7
| 25 | |
212058_at | 23350 |
SR140
| 25 | |
201519_at | 9868 |
TOMM70A
| 25 | |
209933_s_at | 11314 |
CD300A
| 26 | |
219184_x_at | 29928 |
TIMM22
| 26 | |
204683_at | 3384 |
ICAM2
| 26 | |
212529_at | 124801 |
LSM12
| 26 | |
211899_s_at | 9618 |
TRAF4
| 26 | |
218014_at | 79902 |
NUP85
| 26 | |
200816_s_at | 5048 |
PAFAH1B1
| 26 | |
202395_at | 4905 |
NSF
| 26 | |
201388_at | 5709 |
PSMD3
| 26 | |
220975_s_at | 114897 |
C1QTNF1
| 26 | |
210561_s_at | 26118 |
WSB1
| 26 | |
202856_s_at | 9123 |
SLC16A3
| 26 | |
212279_at | 27346 |
TMEM97
| 26 | |
37408_at | 9902 |
MRC2
| 26 | |
201140_s_at | 5878 |
RAB5C
| 26 | |
214218_s_at | 7503 |
XIST
| 24 | |
200600_at | 4478 |
MSN
| 24 | |
201136_at | 5355 |
PLP2
| 24 | |
C: Genes exhibiting differential expression profiles based on older generation Affymetrix GeneChips (Hs 6000 (6), Hu 6800 (22))
| 202431_s_at | 4609 |
MYC
| 6 |
203752_s_at | 3727 |
JUND
| 6 | |
205009_at | 7031 |
TFF1
| 6 | |
205067_at | 3553 |
IL1B
| 6 | |
200807_s_at | 3329 |
HSPD1
| 6 | |
203139_at | 1612 |
DAPK1
| 6 | |
200886_s_at | 5223 |
PGAM1
| 6 | |
203083_at | 7058 |
THBS2
| 6 | |
202284_s_at | 1026 |
CDKN1A
| 6 | |
212667_at | 6678 |
SPARC
| 6 | |
202627_s_at | 5054 |
SERPINE1
| 6 | |
203382_s_at | 348 |
APOE
| 6 | |
211300_s_at | 7157 |
TP53
| 6 | |
200953_s_at | 894 |
CCND2
| 6 | |
201700_at | 896 |
CCND3
| 6 | |
205881_at | 7625 |
ZNF74
| 23 | |
207081_s_at | 5297 |
PI4KA
| 23 | |
205576_at | 3053 |
SERPIND1
| 23 | |
203412_at | 8216 |
LZTR1
| 23 | |
206184_at | 1399 |
CRKL
| 23 | |
D: Known oncogenes and tumour U133A analysis suppressor genes relevant to ovarian cancer biology
| 203132_at | 5925 |
RB1
| |
204531_s_at | 672 |
BRCA1
| ||
214727_at | 675 |
BRCA2
| ||
202520_s_at | 4292 |
MLH1
| ||
216836_s_at | 2064 |
ERBB2
| ||
204009_s_at | 3845 |
KRAS
| ||
206044_s_at | 673 |
BRAF
| ||
209421_at | 4436 |
MSH2
| ||
211450_s_at | 2956 |
MSH6
|
Hybridization and raw data collection
Data normalization
Selection of optimal probe design
Comparative analysis of Ziplex and Affymetrix data
Quality control of Ziplex array data
Results
Correlation of Affymetrix U133A and Ziplex array expression profiles
Comparative analysis of fold changes of Affymetrix U133A and Ziplex array expression profiles
Affymetrix U133A Array | Ziplex Automated Workstation | Platform Comparison | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |