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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.