Table 1.

Top 49 probe sets sorted by frequency of how often they are ranked as no. 1 in 50,000 iterations

Probe set IDRankingTop 1Top 10%Top 50%Top 100%Top 500%Top 1,000%Gene symbol
216836_s_at13.67%9.73%20.06%31.23%59.96%69.08%ERBB2
205440_s_at21.20%9.75%20.21%24.74%43.51%53.57%NPY1R
221811_at30.81%4.53%13.45%20.72%42.55%56.41%PERLD1
203569_s_at40.58%2.89%7.77%11.76%22.76%26.32%OFD1
212070_at50.58%2.20%3.20%4.36%11.94%16.61%GPR56
200029_at60.57%1.65%5.14%8.21%16.67%23.76%RPL19
210828_s_at70.53%3.67%11.32%15.53%24.72%28.47%ARNT
55616_at80.47%3.04%11.17%18.34%40.70%54.78%PERLD1
205590_at90.47%2.67%7.42%10.92%27.39%42.29%RASGRP1
212196_at100.46%3.21%5.76%7.66%18.91%26.87%IL6ST
216835_s_at110.45%3.22%7.84%11.35%21.79%28.06%DOK1
218094_s_at120.40%1.19%3.03%4.96%13.92%21.62%C20orf35
203685_at130.39%2.19%5.13%6.53%12.27%21.11%BCL2
201011_at140.37%1.62%3.80%5.35%13.60%19.57%RPN1
213712_at150.36%2.50%7.40%11.30%24.76%33.20%ELOVL2
203439_s_at160.34%2.25%9.79%18.73%52.53%63.92%STC2
219359_at170.34%3.94%7.43%8.14%11.51%14.99%FLJ22635
205354_at180.29%0.95%2.67%4.15%11.68%19.46%GAMT
218153_at190.28%0.93%1.44%1.82%4.66%7.92%FLJ12118
201255_x_at200.27%1.29%2.98%4.23%10.20%14.67%BAT3
205225_at210.27%1.19%1.72%2.35%5.06%9.18%ESR1
204699_s_at220.27%0.62%1.21%1.59%3.83%6.86%C1orf107
209140_x_at230.26%1.20%2.51%3.34%7.24%10.99%HLA-B
208715_at240.24%0.77%1.58%2.35%7.55%14.75%TMCO1
208962_s_at250.23%0.81%1.96%2.97%7.47%11.53%FADS1
203929_s_at260.23%3.59%14.67%22.21%42.84%51.38%MAPT
200070_at270.23%0.40%0.65%1.04%3.42%6.30%C2orf24
207332_s_at280.22%1.31%3.27%4.88%11.40%17.25%TFRC
36994_at290.22%1.37%3.95%6.10%15.37%22.04%ATP6V0C
202411_at300.22%1.03%2.27%3.50%11.67%18.72%IFI27
218276_s_at310.22%1.16%2.87%4.28%11.51%18.13%SAV1
210761_s_at320.21%0.99%3.64%6.65%31.35%50.79%GRB7
220414_at330.20%0.69%1.10%1.39%3.03%4.46%CALML5
200837_at340.19%0.50%0.82%1.35%5.08%8.91%BCAP31
219872_at350.19%2.91%8.83%13.03%30.64%40.52%DKFZp434L142
209016_s_at360.19%1.63%5.75%9.19%21.98%25.92%KRT7
210930_s_at370.18%0.40%0.96%1.92%11.01%20.81%ERBB2
220038_at380.18%1.73%5.43%8.72%24.36%36.14%SGK3
204029_at390.18%1.82%5.95%8.95%21.28%29.60%CELSR2
203627_at400.17%1.31%3.39%5.37%16.33%24.20%IGF1R
219197_s_at410.17%2.00%6.37%9.78%20.93%26.66%SCUBE2
221727_at420.17%1.10%3.42%6.01%20.81%30.72%SUB1
205186_at430.17%0.79%2.03%3.09%9.41%15.47%DNALI1
219155_at440.17%1.30%3.15%4.39%10.17%16.23%PITPNC1
209007_s_at450.16%0.64%1.17%1.49%3.38%6.32%C1orf63
204686_at460.16%0.71%1.63%2.72%10.66%19.20%IRS1
209485_s_at470.16%0.54%1.85%3.01%9.11%15.53%OSBPL1A
211176_s_at480.16%2.36%8.27%11.89%24.40%30.64%PAX4
216580_at490.16%1.03%2.72%4.06%10.16%15.70%RPL7
  • NOTE: There are two probe sets that target the HER-2 transcript. Probe set “216836_s_at” is ranked no. 1 most often, in 3.67% of all iterations. However, the second probe set “210930_s_at” makes it to the top only 0.18% of the time (ranked 37th). This is most likely because it targets the HER-2 transcripts further 5′ and its median overall expression intensity is only 80.2 compared with 670.6 for probe 216836_s_at.