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Table 1 Candidates for sequencing analysis in the LNCaP and 22Rv1 selected using GINI.

From: Par-3 partitioning defective 3 homolog (C. elegans) and androgen-induced prostate proliferative shutoff associated protein genes are mutationally inactivated in prostate cancer cells

  GENE Symbol Probe set ID 22Rv1 LNCaP
    Log2 (signal) Log2 Accumulation Log2 Degradation Log2 (signal) Log2 Accumulation Log2 Degradation
  PARD3 221526_x_at 7.1 0.9 0.1 3.2 2.9 1.6
  ANKRD28 213035_at 8.2 0.4 0.4 5.6 1.7 1.5
  CLPTM1 211136_s_at 9.7 -0.5 -0.6 4.3 1.6 1.8
LNCaP candidate VRK3 221999_at 6.5 0.3 0.5 3.9 1.5 2.5
s GTPBP2 221050_s_at 8.2 0.2 0.2 5.2 1.5 2.1
  LOC692247 1561355_at 6.9 0.1 0.3 3.9 1.5 1.5
  AFF1 227198_at 10.5 -0.6 0.7 5.4 1.3 1.4
  AS3 207956_x_at 5.9 2.6 1.4 10.0 0.1 0.3
22RV1 TTLL7 219882_at 3.6 2.0 1.4 7.6 0.3 0.9
candidate PDSB5 204742_s_at 3.9 1.9 1.3 7.8 -0.6 -0.6
s EIF5 208708_x_at 9.2 1.7 2.5 11.3 0.7 0.9
  EIF2C2 225827_at 3.5 1.6 1.9 6.1 -0.6 0.1
  1. RNAs from LNCaP and 22Rv1 cells were analyzed using Afffymetrix GeneChip Human Genome U133Plus 2.0 Array hybridization after the following treatments: 1) no treatment, 2) incubation with caffeine for four hours, 3) incubation with caffeine and actinomicin D following caffeine treatment for four hours and 4) incubation with actinomycin D following caffeine treatment for four hours. The candidates for sequencing analysis for LNCaP cells were selected by sorting the normalized, Log2 transformed hybridization signal values data using the following criteria: 1) expression of the candidate gene in the untreated LNCaP cells is more than four-times lower than in the untreated 22Rv1 cells used as a control, i.e., Log2(signal LNCaP) - Log2(signal 22Rv1) <2.0; 2). The mRNA level accumulation for candidate genes following incubation with caffeine for four hours should be more than threefold and less than twofold in the LNCaP and 22Rv1 cells, respectively: i.e., Log2 (Accumulation LNCaP) >1.3 and Log2(Accumulation 22Rv1) <1.0; 3). The mRNA levels for candidates after inhibiting both mRNA synthesis and mRNA degradation with actinomycin D and caffeine should be more than threefold and less than twofold higher than after inhibiting mRNA synthesis only with actinomycin D for the LNCaP and 22Rv1 cells, respectively: i.e., Log2 (Degradation LNCaP) >1.3 and Log2 (Degradation22Rv1) <1.0. Candidates for the 22Rv1 cells were selected in the same way, using the LNCaP cell as a control. Five probes for the 22Rv1 and seven probes for the LNCaP cells satisfied the described selection criteria.