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Table 3 Human gene expression data by Affymetrix microarray and qRT-PCR,

From: In Vivo Topoisomerase I Inhibition Attenuates the Expression of Hypoxia-Inducible Factor 1α Target Genes and Decreases Tumor Angiogenesis

   

Affymetrix microarray

qRT-PCR

Probe set ID

Gene symbol

Gene name

Mean fold-change, T versus, C

Mean fold-change, R versus C

P(T versus C)

Reference gene

Mean fold-change, T versus C

Mean fold-change, R versus C

P (T versus C)

Downregulated (>2.0-fold)

         

227337_at

* ANKRD37

Ankyrin repeat domain 37

−4.8

1.2

0.018

HMBS

−3.4

1.4

0.018

      

KRT19

−3.4

1.3

0.018

222088_s_at

* SLC2A3

Solute carrier family 2 (facilitated glucose transporter), member 3

−3.7

1.3

0.018

HMBS

−2.8

1.2

0.043

      

KRT19

−2.8

1.2

0.043

202887_s_at

* DDIT4

DNA-damage-inducible transcript 4

−3.6

1.0

0.018

HMBS

−2.8

1.3

0.018

      

KRT19

−2.7

1.2

0.018

201169_s_at

* BHLHB2

Basic helix-loop-helix domain containing, class B, 2

−3.3

1.2

0.018

HMBS

−2.3

1.1

0.018

201170_s_at

  

−2.5

1.0

0.018

KRT19

−2.2

1.2

0.018

201313_at

* ENO2

Enolase 2 (gamma, neuronal)

−3.1

1.0

0.018

HMBS

−2.8

1.3

0.018

      

KRT19

−2.7

1.2

0.018

207543_s_at

* P4HA1

Procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), a polypeptide 1

−2.9

1.0

0.018

HMBS

−2.4

1.2

0.018

      

KRT19

−2.3

1.2

0.018

202620_s_at

* PLOD2

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2

−2.8

1.1

0.018

HMBS

−2.2

1.1

0.018

      

KRT19

−2.1

1.2

0.018

202022_at

* ALDOC

Aldolase C, fructose-bisphosphate

−2.8

1.1

0.018

HMBS

−3.3

1.1

0.018

      

KRT19

−3.1

1.1

0.018

240991_at

* NDRG1

N-myc downstream regulated gene 1

−2.7

1.1

0.018

HMBS

−4.6

1.3

0.018

200632_s_at

  

−2.5

1.1

0.018

KRT19

−4.4

1.3

0.018

211527_x_at

* VEGFA

Vascular endothelial growth factor A

−2.4

1.3

0.018

HMBS

−2.0

1.1

0.018

212171_x_at

  

−2.0

1.1

0.018

KRT19

−1.9

1.1

0.018

221479_s_at

* BNIP3L

BCL2/adenovirus E1B 19kDa interacting protein 3-like

−2.4

1.1

0.018

HMBS

−1.9

1.4

0.018

221478_at

  

−2.3

1.1

0.018

KRT19

−1.9

1.4

0.018

201250_s_at

* SLC2A1

Solute carrier family 2 (facilitated glucose transporter), member 1

−2.4

1.1

0.018

HMBS

−2.2

1.2

0.018

201249_at

  

−2.0

1.1

0.018

KRT19

−2.1

1.2

0.018

202973_x_at

FAM13A1

Family with sequence similarity 13, member A1

−2.4

1.7

0.018

HMBS

NA

NA

217047_s_at

  

−2.2

1.6

0.018

KRT19

   

226390_at

STARD4

StAR-related lipid transfer (START) domain containing 48

−2.4

1.0

0.018

HMBS

−2.4

1.2

0.018

      

KRT19

−2.3

1.2

0.027

202219_at

* SLC6A8

Solute carrier family 6 (neurotransmitter transporter, creatinine), member 8

−2.3

1.1

0.018

HMBS

−2.7

1.1

0.028

      

KRT19

−2.7

1.2

0.028

202464_s_at

* PFKFB3

6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 3

−2.3

1.0

0.018

HMBS

−2.2

1.1

0.018

      

KRT19

−2.0

1.2

0.018

202912_at

* ADM

Adrenomedullin

−2.3

1.3

0.018

HMBS

−2.2

1.6

0.018

      

KRT19

−2.2

1.6

0.027

218498_s_at

* ERO1L

ERO1-like (S. cerevisiae)

−2.3

1.1

0.018

HMBS

−2.2

1.4

0.018

222646_s_at

  

−2.1

1.1

0.018

KRT19

−2.0

1.3

0.018

213562_s_at

SQLE

Squalene epoxidase

−2.3

1.1

0.018

HMBS

−1.6

1.4

0.043

      

KRT19

−1.5

1.3

0.043

230710_at

cDNA FLJ41489 fis, clone BRTHA2004582

−2.3

1.2

0.018

HMBS

NA

NA

      

KRT19

   

216607_s_at

CYP51A1

Cytochrome P450, family 51, subfamily A, polypeptide 1

−2.2

1.0

0.018

HMBS

−2.2

1.3

0.018

      

KRT19

−2.1

1.3

0.018

238551_at

FUT11

Fucosyltransferase 11 (α (1,3) fucosyltransferase)

−2.2

1.0

0.018

HMBS

−1.8

1.1

0.018

      

KRT19

−1.7

1.0

0.026

216915_s_at

PTPN12

Protein tyrosine phosphatase, non-receptor type 12

−2.2

1.3

0.018

HMBS

1.0

1.1

0.612

      

KRT19

1.0

1.2

0.398

213349_at

TMCC1

Transmembrane and coiled-coil domain family 1

−2.2

1.1

0.018

HMBS

NA

NA

      

KRT19

   

243543_at

SC4MOL

Sterol-C4-methyl oxidase-like

−2.1

1.0

0.018

HMBS

−2.1

1.1

0.018

      

KRT19

−2.0

1.1

0.018

201037_at

* PFKP

Phosphofructokinase, platelet

−2.0

1.1

0.018

HMBS

−1.9

1.2

0.028

      

KRT19

−1.9

1.2

0.028

200738_s_at

* PGK1

Phosphoglycerate kinase 1

−2.0

1.0

0.018

HMBS

−1.7

1.1

0.018

      

KRT19

−1.5

1.1

0.043

Upregulated (>2-fold)

         

1552411_at

DEFB106A/B

Defensin, β 106A/defensin, β 106B

2.8

−1.3

0.018

HMBS

NA

NA

      

KRT19

   

216500_at

2.3

1.1

0.018

HMBS

NA

NA

      

KRT19

   

218543_s_at

PARP12

Poly (ADP-ribose) polymerase family, member 12

2.2

1.1

0.018

HMBS

2.0

1.2

0.028

      

KRT19

2.1

1.2

0.028

Downregulated (<2.0-fold)

         

224657_at

* ERRFI1

ERBB receptor feedback inhibitor 1

−1.8

1.2

0.018

HMBS

−1.4

1.4

0.091

      

KRT19

−1.2

1.5

0.150

218507_at

* HIG2

Hypoxia-inducible protein 2

−1.8

1.1

0.018

HMBS

−1.3

1.6

0.043

1554452_a_at

  

−1.8

1.2

0.018

KRT19

−1.2

1.4

0.236

1569020_at

* NEDD9

Neural precursor cell expressed, developmentally downregulated 9

−1.8

1.1

0.018

HMBS

−1.6

1.3

0.063

      

KRT19

−1.5

1.4

0.034

225366_at

PGM2

Phosphoglucomutase 2

−1.5

1.1

0.018

HMBS

1.0

1.1

0.600

      

KRT19

1.0

1.1

0.340

Upregulated (<2.0-fold)

         

231974_at

MLL2

Myeloid/lymphoid or mixed-lineage leukemia 2

1.7

−1.1

0.018

HMBS

1.3

1.0

0.499

      

KRT19

1.4

1.1

0.596

No change

         

200989_at

HIF1A

Hypoxia-inducible factor 1, a subunit (basic helix-loop-helix transcription factor)

−1.1

−1.1

0.176

HMBS

1.0

1.2

1.000

      

KRT19

1.2

1.2

0.446

  1. Asterisks (*) indicate hypoxia-induced or HIF1A target genes. HMBS and KRT19 genes were used as endogenous references for qRT-PCR. P values were calculated using Wilcoxon signed-rank tests. NA, not applicable.