Table 1 Top ten genes originally calculated using S/N (for edgeR-normalized data; first ten rows) and top ten genes calculated using FDR for DE (edgeR P values; second ten rows). The table includes the counts-per-million table (A = GM12892 and B = H1-hESC), S/N and estimated false discovery rate (FDR) for edgeR and limma-voom for the ENCODE dataset comparing three replicates of GM12892 to four replicates of H1-hESC
Id | A1 | A2 | A3 | B1 | B2 | B3 | B4 | edgeR S/N | edgeR FDR | voom S/N | voom FDR |
|---|---|---|---|---|---|---|---|---|---|---|---|
MIPOL1 | 0.0 | 0.0 | 0.0 | 237.1 | 232.5 | 226.0 | 227.5 | 45.75 | 7.47e −31 | 3.79 | 3.32e −07 |
AQP4 | 0.0 | 0.0 | 0.0 | 46.1 | 45.0 | 46.7 | 44.4 | 43.87 | 1.44e −14 | 3.90 | 1.99e −06 |
FAM19A4 | 0.0 | 0.0 | 0.0 | 142.1 | 131.1 | 143.8 | 131.4 | 20.21 | 1.91e −24 | 4.06 | 4.72e −07 |
C17orf66 | 2.3 | 2.1 | 2.1 | 0.0 | 0.0 | 0.0 | 0.0 | 16.96 | 1.89e −02 | 2.72 | 7.40e −04 |
TM4SF19 | 3.5 | 3.2 | 3.2 | 0.0 | 0.0 | 0.0 | 0.0 | 16.96 | 3.00e −03 | 2.72 | 2.39e −04 |
SOX1 | 0.0 | 0.0 | 0.0 | 7.5 | 6.7 | 6.5 | 6.3 | 13.02 | 8.37e −05 | 4.33 | 1.27e −04 |
HPGD | 0.0 | 0.0 | 0.0 | 22.6 | 21.0 | 19.6 | 19.0 | 12.97 | 5.08e −09 | 4.56 | 7.48e −06 |
LOC100131176 | 0.0 | 0.0 | 0.0 | 17.9 | 15.3 | 18.7 | 17.2 | 12.02 | 5.14e −08 | 3.51 | 1.49e −05 |
ZNF385D | 0.0 | 0.0 | 0.0 | 135.5 | 155.0 | 155.0 | 132.3 | 11.80 | 2.60e −25 | 4.67 | 3.70e −07 |
NPY1R | 0.0 | 0.0 | 0.0 | 209.8 | 179.9 | 179.3 | 208.5 | 11.38 | 1.33e −27 | 2.95 | 6.77e −07 |
PLEK | 25 082.8 | 12 622.5 | 11 394.8 | 0.0 | 0.0 | 0.0 | 0.0 | 2.16 | 1.79e −216 | 16.11 | 9.36e −09 |
MS4A1 | 25 455.1 | 14 937.7 | 12 886.8 | 0.0 | 0.0 | 0.0 | 0.0 | 2.63 | 2.62e −215 | 7.26 | 1.60e −08 |
SLAMF1 | 7 407.2 | 4 859.3 | 4 283.2 | 0.0 | 0.0 | 0.0 | 0.0 | 3.32 | 2.98e −165 | 5.11 | 2.53e −08 |
CCL3 | 11 057.5 | 3 413.1 | 3 544.1 | 0.0 | 0.0 | 0.0 | 0.0 | 1.37 | 4.62e −165 | 5.13 | 2.15e −08 |
FCRLA | 7 742.0 | 2 979.1 | 3 879.8 | 0.0 | 0.0 | 0.0 | 0.0 | 1.92 | 1.01e −161 | 6.08 | 1.84e −08 |
RGS1 | 9 939.5 | 9 967.3 | 7 741.6 | 0.0 | 0.0 | 0.0 | 0.0 | 7.22 | 4.53e −159 | 2.66 | 1.44e −07 |
DPPA4 | 0.0 | 0.0 | 0.0 | 14 580.2 | 15 215.1 | 14 745.3 | 10 617.3 | 6.47 | 2.37e −158 | 12.02 | 1.84e −08 |
TDGF1 | 0.0 | 0.0 | 0.0 | 15 699.8 | 15 481.1 | 13 374.5 | 8 522.5 | 3.98 | 6.37e −157 | 15.48 | 1.84e −08 |
SFRP2 | 0.0 | 0.0 | 0.0 | 14 673.3 | 15 229.5 | 13 067.2 | 7 234.4 | 3.43 | 1.84e −153 | 9.87 | 2.15e −08 |
BLK | 9 943.0 | 2 954.7 | 2 351.8 | 0.0 | 0.0 | 0.0 | 0.0 | 1.20 | 2.98e −147 | 3.28 | 5.17e −08 |