Table 1

Genes altered ≥4-fold after 5-Aza-CdR treatment of the LD419 fibroblast cell line

AccessionSymbolFunctionFold changea 3 days after treatmentFold changea 8 days after treatment5′ CpG island (CGI)
AverageExp 1Exp 2AverageExp 1Exp 2
Up-regulated genesb
 Genes inducible by interferonc
  K02765 C3 Complement component 21.2 ∼17.7 ∼24.6 29.0 ∼28.6 29.3 N
  Z19574 KRT17 Cytokeratin 13.6 ∼12.8 ∼14.4 19 ∼16.6 ∼21.4 N
  Y00503 KRT19 Cytokeratin2.52.22.77.18.75.4CGI
  M13955 KRT7 Cytokeratin2.81.44.111.95.318.5CGI
  X74929 KRT8 Cytokeratin18.5∼25.311.629∼40.317.7N
  M26167 PF4V1 Cytokine family2.3∼2.6∼1.95.4∼4.8∼6.0N
  J03474 SAA1 Cytokine stimulated3.3∼4.1∼2.418.2∼18.7∼17.7N
  X67325 IFI27 IFN induced18.8∼16.9∼20.742.1∼32.5∼51.7N
  D89050 OLR1 LDL receptor4.23.94.57.79.65.7N
  M97936 STAT1 Transcription factor11.3∼16.8∼5.814.8∼23.85.8CGI
 Other genes
  U07919 ALDH6 Aldehyde dehydrogenase3.33.43.14.64.94.3CGI
  L20591 ANXA3 Annexin2.92.5∼3.34.34.1∼4.4N
  X16662 ANXA8 Annexin4.1∼3.0∼5.210.6∼6.5∼14.6N
  U70063 ASAH Ceramidase0.5∼−1.01.96.0∼5.16.8CGI
  D13639 CCND2 Cyclin4.63.85.440.049.430.6CGI
  M83186 COX7A1 Cytochrome c oxidase3.41.15.612.05.3∼18.7CGI
  D55696 PRSC1 Endopeptidase4.9∼10.8−115.4∼22.88N
  Y08374 CHI3L1 Environment change Resp.16.213.818.518.517.119.9N
  U28727 PAPPA Growth factor activator3.74.72.711.1∼17.54.6N
  U90551 H2AFL Histone 3.3 2.5 ∼4.0 12.0 7.4 ∼16.6 N
  Z80780 H2BFH Histone 2.8 ∼1.6 ∼3.9 6.1 ∼7.4 4.8 N
  X57985 H2BFQ Histone4.5∼4.8∼4.16.7∼6.0∼7.4CGI
  M32053 H19 Imprinted gene 4.3 4 ∼4.6 9.5 5.5 ∼13.5 CGI
  U31201 LAMC2 Laminin−1.6∼−1.8∼−1.46.5∼4.3∼8.6N
  U41518 AQP1 Membrane protein4.45.23.623.019.226.7N
  D90224 TNFSF4 Membrane protein (type ii)4.5∼4.1∼4.88.6∼6.610.6N
  X05232 MMP3 Metalloproteinase 33.5∼4.0∼2.99.6∼8.8∼10.3N
  D45917 TIMP3 Metalloproteinase 3 inhibitor2.82.92.74.85.14.5CGI
  U37283 MAGP2 Microfibril-associated2.6∼2.9∼2.311.5∼9.5∼13.5N
  X13100 MYH3 Myosin2.7∼1.6∼3.78.6∼8.2∼9.0N
  Y00757 SGNE1 Neuroendocrine protein4.7∼1.8∼7.56.6∼6.4∼6.7N
  X17042 PRG1 Proteoglycan2.62.134.74.35.1N
  U10687 MAGEA4 Tumor transformation 4.1 2.1 ∼6.1 10.5 ∼8.8 ∼12.2 N
 Down-regulated genesb
  D21063_at MCM2 Cell cycle−14.4∼−19.2−9.5−22.4∼−24.4∼−20.4CGI
  X51688_at CCNA2 Cell cycle−11.3∼−11.2∼−11.3−11.15∼−12.7−9.6CGI
  X65550_at MKI67 Cell cycle−5.5∼−4.1∼−6.8−6.6∼−4.9∼−8.3CGI
  X85137_s_at KNSL1 Cell cycle−3.1−3.9−2.2−4.7−4.4−5N
  L25876_at CDKN3 Cell cycle−4.4−4.8−3.9−4.05−4−4.1N
  L36033_at CDF1 Cytokine−1.8−1.4−2.1−8.6∼−8.5−8.7CGI
  X62534_s_at HMG2 Nuclear protein−3.9−4−3.7−5.3−5.2−5.4CGI
  D82345_at TMSNB Thymosin β−4.2−3.5−4.9−7∼−8.0−6N
  U74612_at FOXM1 Transcription factor−7.9−9.2−6.6−9−11.6−6.4CGI
  U61145_at EZH2 Transcription factor−4.3∼−5.4−3.1−6.65∼−6.1∼−7.2CGI
  D14657_at KIAA0101 Unknown function−3−3.6−2.4−4.85−5.1−4.6N
  • a A “∼” preceding the fold change value indicates that the expression level for the untreated sample was under the calculated noise level; therefore, the fold change is an approximation.

  • b Bold represents genes induced in both LD419 and T24 cells.

  • c Based on a PubMed search; CGI, 5′ CpG island; Exp, experiment; N, no known 5′ CpG island.