Table 2 of
Rozsa, Mol Vis 2006;
12:125-141.Table 2 of
Rozsa, Mol Vis 2006;
12:125-141.
Table 2. Validation of microarray results by quantitative PCR
A: Genes with three fold increase in signal intensity after dexamethasone treatment by both microarray and qPCR analysis for all three TM Cell lines. B: Genes with three fold decrease in signal intensity after dexamethasone treatment by both microarray and qPCR analysis for all three TM cell lines. C: Genes with a qPCR fold change less than three fold in one or more TM cell lines. Quantitative PCR performed using intron-spanning primers are shown by asterisks. In the microarray analysis (P) and (A) indicate whether the signal was scored as present or absent, respectively.
A:
Microarray
Microarray qPCR signal Microarray
Affymetrix fold fold mean signal mean
probe GenBank Gene title (symbol) change change untreated dex-treated
----------- --------- ------------------------- ---------- ------- ---------- -----------
214456_x_at M23699 serum amyloid A1 (SAA1) 218.7 338.4* 91 (A) 19873 (P)
206423_at NM_021146 angiopoietin-like 7 187.0 365.3 112 (A) 20939 (P)
(ANGPTL7)
208607_s_at NM_030754 serum amyloid A2 (SAA2) 114.0 2852.0* 56 (A) 6405 (P)
202376_at NM_001085 serine (or cysteine) 48.2 150.9 1436 (P) 69260 (P)
proteinase inhibitor,
clade A, member 3
(SERPINA3)
203021_at NM_003064 secretory leukocyte 34.2 1706.8 527 (A) 18023 (P)
protease inhibitor (SLPI)
204363_at NM_001993 coagulation factor 26.2 15.9 137 (A) 3592 (P)
III (F3)
205403_at NM_004633 interleukin 1 receptor, 22.9 26.4 44 (A) 1000 (P)
type II (IL1R2)
204560_at NM_004117 FK506 binding protein 5 19.9 6.5 144 (A) 2873 (P)
(FKBP5)
210155_at D88214 myocilin, trabecular 16.7 191.3 4688 (P) 78368 (P)
meshwork inducible
glucocorticoid response
(MYOC)
205883_at NM_006006 zinc finger and BTB 13.6 734.3 365 (A) 4950 (P)
domain containing 16
(ZBTB16)
212741_at AA923354 monoamine oxidase A 13.1 16.2 353 (A) 4612 (P)
(MAOA)
218723_s_at NM_014059 response gene to 12.3 17.5 1441 (P) 17743 (P)
complement 32 (RGC32)
206024_at NM_002150 4-hydroxyphenylpyruvate 11.9 7.7 1018 (P) 12132 (P)
dioxygenase (HPD)
221541_at AL136861 cysteine-rich secretory 10.6 12.9 706 (P) 7459 (P)
protein LCCL domain
containing 2 (CRISPLD2)
217546_at R06655 metallothionein 1M (MT1M) 8.9 36.8* 486 (A) 4297 (P)
202409_at X07868 insulin-like growth 7.8 32.2* 384 (P) 2987 (P)
factor II (IGF2)
208763_s_at AL110191 TSC22 domain family, 6.8 8.8 1496 (P) 10171 (P)
member 3 (TSC22D3)
205422_s_at NM_004791 integrin, beta-like 1 6.4 9.4 760 (P) 4883 (P)
(ITGBL1)
201525_at NM_001647 apolipoprotein D (APOD) 5.3 16.0 2920 (P) 15340 (P)
200974_at NM_001613 actin, alpha 2, smooth 4.6 8.4 8108 (P) 37623 (P)
muscle, aorta (ACTA2)
203961_at AL157398 nebulette (NEBL) 4.4 12.0 145 (A) 642 (P)
204627_s_at M35999 integrin, beta 3 3.9 4.6 188 (A) 737 (P)
(ITGB3)
204326_x_at NM_002450 metallothionein 1X (MT1X) 3.7 5.9 10597 (P) 39047 (P)
|
B:
Microarray
Microarray qPCR signal Microarray
Affymetrix fold fold mean signal mean
probe GenBank Gene title (symbol) change change untreated dex-treated
----------- --------- -------------------------- ---------- ------- ---------- -----------
209821_at AB024518 chromosome 9 open reading -17.1 -92.6* 1850 (P) 108 (P)
frame 26 (C9orf26)
209541_at AI972496 insulin-like growth factor -13.1 -34.8 3515 (P) 268 (P)
1 (IGF1)
205825_at NM_000439 proprotein convertase -11.7 -12.5* 6342 (P) 544 (P)
subtilisin/kexin type 1
(PCSK1)
210119_at U73191 potassium -8.8 -12.8 2715 (P) 308 (P)
inwardly-rectifying
channel, subfamily J,
member 15 (KCNJ15)
204948_s_at NM_013409 follistatin (FST) -8.7 -20.7 21126 (P) 2443 (P)
206022_at NM_000266 Norrie disease (NDP) -7.7 -34.7 2036 (P) 265 (P)
221577_x_at AF003934 growth differentiation -7.3 -7.3 6564 (P) 897 (P)
factor 15 (GDF15)
206326_at NM_002091 gastrin-releasing peptide -6.8 -34.8* 3806 (P) 562 (A)
(GRP)
205266_at NM_002309 leukemia inhibitory -6.8 -13.3 4422 (P) 655 (P)
factor (LIF)
204933_s_at NM_002546 tumor necrosis factor -6.6 -11.3 3312 (P) 500 (A)
receptor superfamily,
member 11b (TNFRSF11B)
204135_at NM_014890 downregulated in ovarian -5.9 -9.1 6348 (P) 1084 (P)
cancer 1 (DOC1)
210511_s_at M13436 inhibin, beta A (INHBA) -4.8 -6.3 7409 (P) 1554 (P)
201830_s_at NM_005863 neuroepithelial cell -4.4 -5.8 3943 (P) 897 (P)
transforming gene 1 (NET1)
204846_at NM_000096 ceruloplasmin (CP) -4.3 -5.2* 662 (P) 153 (A)
205127_at NM_000962 prostaglandin-endoperoxide -4.3 -8.2 1064 (P) 246 (A)
synthase 1 (PTGS1)
209960_at X16323 hepatocyte growth -4.2 -7.5 5066 (P) 1218 (P)
factor (HGF)
205207_at NM_000600 interleukin 6 (interferon, -3.7 -4.6 4562 (P) 1231 (P)
beta 2) (IL6)
205289_at AA583044 bone morphogenetic protein -3.6 -4.4* 779 (P) 215 (P)
2 (BMP2)
|
C:
Microarray qPCR signal Microarray
Affymetrix fold fold mean signal mean
probe GenBank Gene title (symbol) change change untreated dex-treated
----------- --------- ------------------------- ---------- ------- ---------- -----------
206637_at NM_014879 purinergic receptor P2Y, 7.5 2.4* 103 (A) 772 (P)
G-protein coupled, 14
(P2RY14)
201481_s_at NM_002862 phosphorylase, glycogen; 6.9 1.7* 743 (A) 5111 (P)
brain (PYGB)
206114_at NM_004438 EPH receptor A4 (EPHA4) 6.4 2.3* 341 (A) 2201 (P)
205082_s_at AB046692 aldehyde oxidase 1 (AOX1) 5.5 2.4* 649 (P) 3551 (P)
208613_s_at AV712733 filamin B, beta (FLNB) 4.8 2.9 534 (A) 2557 (P)
219028_at NM_022740 homeodomain interacting 4.3 3.0 768 (P) 3298 (P)
protein kinase 2 (HIPK2)
205547_s_at NM_003186 transgelin (TAGLN) 3.5 3.4 12015 (P) 42093 (P)
202861_at NM_002616 period homolog 1 (PER1) 3.4 8.8* 278 (A) 954 (P)
201744_s_at NM_002345 lumican (LUM) -4.8 -9.9* 8833 (P) 1861 (P)
216546_s_at AJ251847 chitinase 3-like 1 -6.1 -2.7* 3101 (P) 505 (A)
(CHI3L1)
203917_at NM_001338 coxsackie virus and -7.2 -7.1* 8188 (P) 1139 (P)
adenovirus receptor
(CXADR)
|