Skip to main content

Table 1 mRNA levels and copy number determination of differentially expressed genes in HT29 MTX-resistant cells.

From: Role of Caveolin 1, E-Cadherin, Enolase 2 and PKCalpha on resistance to methotrexate in human HT29 colon cancer cells

GenBank

Gene Name

Chromosome

Copy Number (Q-PCR)

Expression

Gene Function

    

Microarrays

Validation (RT-PCR)

 

NM_002961

S100A4

1

0.85 ± 0.1

3.7 (p = 5.5e-6)

5.68 ± 0.4

Angiogenesis

BU078629

ZFYVE16

5

16.81 ± 2.1

6.1 (p = 7.7e-6)

6.7 ± < 0.1

Zinc ion binding

AI144299

DHFR

5

16.09 ± 1.4

7.1 (p = 1.2e-7)

11.05 ± 0.5

Nucleotide metabolism

NM_002439

MSH3

5

4.97 ± 0.5

3.9 (p = 5.5e-6)

4.23 ± 0.4

Missmatch repair

AI912976

RASGRF2

5

17.76 ± 0.4

4.6(p = 8.9e-5)

6.10 ± 0.5

MAPK signaling

AF912976

SSBP2

5

10.27 ± 0.7

2.4 (p = 3.4e-3)

2.96 ± 0.2

ss DNA binding

NM_022406

XRCC4

5

17.31 ± 1.1

7.1 (p = 4.7e-6)

8.90 ± 2.3

ds break repair

U43328

HAPLN1

5

11.55 ± < 0.1

147 (p = 2.9e-10)

1111.9 ± 80.7

Cell adhesion

AA053711

EDIL3

5

14.3 ± 0.7

157 (p = 9.1e-8)

N/D

Cell adhesion

U17496

PSMB8

6

0.91 ± < 0.1

0.1 (p = 0.01)

N/D

Proteasome subunit

NM_004666

VNN1

6

0.84 ± < 0.1

0.04 (p = 0.01)

N/D

Nitrogen metabolism

AU147399

CAV1

7

1.14 ± < 0.1

10.9 (p = 1.5e-4)

15.00 ± 0.8

Integ. plasma membr.

BE552421

MTUS1

8

3.52 ± 0.1

3.4 (p = 1.8e-6)

N/D

Mitoc. tumor suppressor

U05598

AKR1C1

10

0.94 ± < 0.1

4,6 (p = 3.9e-6)

6.72 ± 0.7

Xenobiotics metabolism

NM_001975

ENO2

12

0.92 ± < 0.1

6.0 (p = 4.6e-6)

3.90 ± 0.1

Glycolisis

AK000345

DHRS2

14

0.97 ± < 0.1

0.12 (p = 0.01)

N/D

Oxidoreductase

L08599

CDH1

16

0.33 ± < 0.1

0.19 (p = 0.01)

0.15 ± < 0.1

Cell adhesion

AI471375

PRKCA

17

1.05 ± < 0.1

4.2 (p = 1.7e-5)

2.55 ± 0.2

Regulation cell cycle

BQ003811

SLC19A1

21

0.84 ± < 0.1

0.1 (p = 0.01)

N/D

Cell adhesion

NM_001569

IRAK1

X

1.25 ± < 0.1

0.26 (p = 7.3e-3)

N/D

IL1 receptor Kinase

NM_004135

IDH3G

X

0.85 ± < 0.1

0.28 (p = 7.3e-8)

N/D

TCA cycle

NM_001183

ATP6AP1

X

0.68 ± < 0.1

0.3 (p = 0.01)

N/D

ATP biosynthesis

  1. Twenty-two genes belonging to the 3-fold differentially expressed list were selected according to their possible relation with drug resistance and/or chromosomal localization. It is shown the GenBank accession number of all genes next to their common name, and their chromosome number. Real-Time PCR was used to determine their copy number, and the expression levels for all them are presented both as the values found in the microarrays (in fold changes relative to the control; t-test p-values included) and as validated mRNA levels (using RT-Real-Time PCR). All experimental results are expressed as fold changes referred to the sensitive cells and values are the mean of triplicate experiments ± SE. The last column indicates the functional categories of the genes. N/D, nondetermined value.