Table 2. Stable reference gene selection based on 28 FF-FFPE pairs (56 samples).
| Gene name | Illumina code | Average probe intensity | GeNorm | NormFinder | Intragroup | Intergroup | |||
|---|---|---|---|---|---|---|---|---|---|
| M-Value | SD | Accumulated SD | FF | FFPE | FF | FFPE | |||
| ACTB * | ILMN_1343291 | 7733 | 0.35 | 0.32 | 0.20 | 0.10 | 0.12 | -0.08 | 0.08 |
| ATP5B | ILMN_2038778 | 9027 | 0.41 | 0.53 | 0.13 | 0.09 | 0.26 | -0.32 | 0.32 |
| B2M | ILMN_2094718 | 3452 | 0.53 | 0.52 | 0.13 | 0.27 | 0.29 | -0.06 | 0.06 |
| EEF1A1 * | ILMN_203877 | 19568 | 0.23 | 0.37 | 0.15 | 0.10 | 0.19 | 0.00 | 0.00 |
| GAPDH | ILMN_1713369 | 9813 | 0.47 | 0.41 | 0.14 | 0.05 | 0.26 | 0.15 | -0.15 |
| HMBS | ILMN_1693311 | 5024 | 0.50 | 0.42 | 0.13 | 0.08 | 0.29 | 0.00 | 0.00 |
| HPRT1 | ILMN_2331501 | 3189 | 0.60 | 0.59 | 0.13 | 0.11 | 0.44 | 0.28 | -0.28 |
| RPL13A | ILMN_2191428 | 1766 | 0.57 | 0.57 | 0.13 | 0.16 | 0.37 | 0.25 | -0.25 |
| TPT1 | ILMN_1772132 | 21641 | 0.23 | 0.25 | 0.25 | 0.05 | 0.09 | -0.06 | 0.06 |
| UBB | ILMN_1726306 | 6839 | 0.44 | 0.35 | 0.16 | 0.08 | 0.19 | -0.04 | 0.04 |
| UBC | ILMN_2148459 | 10474 | 0.29 | 0.33 | 0.17 | 0.05 | 0.15 | -0.14 | 0.14 |
| median 11 selected reference genes | 7517 | 0.29 | 0.17 | 0.17 | -0.05 | 0.05 | 0.04 | 0.03 | |
| ACTN1 * | ILMN_2216852 | 22697 | 0.84 | 1.10 | 0.14 | 0.54 | 0.63 | -0.76 | 0.76 |
| AKR1D1 * | ILMN_1722634 | 16970 | 0.80 | 0.88 | 0.13 | 0.09 | 0.57 | -0.65 | 0.65 |
| ALAS1 | ILMN_1681374 | 3647 | 0.69 | 0.64 | 0.13 | 0.23 | 0.58 | 0.13 | -0.13 |
| ALDOA * | ILMN_1801928 | 5516 | 0.98 | 1.54 | 0.16 | 1.80 | 2.24 | 0.61 | -0.61 |
| G6PD | ILMN_2051232 | 6690 | 0.92 | 1.39 | 0.15 | 1.02 | 0.46 | -1.04 | 1.04 |
| GUSB | ILMN_1669878 | 3186 | 0.73 | 0.79 | 0.13 | 0.08 | 0.84 | 0.41 | -0.41 |
| HSP90AB1 | ILMN_2385647 | 9113 | 0.67 | 0.73 | 0.13 | 0.10 | 0.79 | 0.31 | -0.31 |
| NUCB1 * | ILMN_1673711 | 23216 | 0.78 | 0.83 | 0.13 | 0.08 | 0.59 | -0.58 | 0.58 |
| PGK1 | ILMN_2347949 | 2145 | 0.71 | 0.68 | 0.13 | 0.20 | 0.64 | -0.23 | 0.23 |
| PUM1 | ILMN_2056975 | 5360 | 0.75 | 0.83 | 0.13 | 0.09 | 0.56 | 0.58 | -0.58 |
| SDHA | ILMN_1783424 | 3830 | 0.87 | 1.15 | 0.14 | 0.19 | 1.68 | 0.61 | -0.61 |
| TMBIM6 | ILMN_2157277 | 11760 | 0.65 | 0.64 | 0.13 | 0.16 | 0.59 | 0.22 | -0.22 |
| YWHAZ | ILMN_2232177 | 9990 | 0.62 | 0.62 | 0.13 | 0.06 | 0.38 | 0.40 | -0.40 |
All samples from Table 1 were used. In case of duplicate hybridizations, the sample with the highest median value for the reference genes was selected. GeNorm and NormFinder software were used to calculate the stability of genes. M-value; the average expression stability value, for which an arbitrarily cut-off at 0.6 was used to assign genes as stably expressed or not. ACTB = Actin-Beta; ATP5B = ATP Synthase Subunit Beta; B2M = beta-2-microglobin; EEF1A1 = eukaryotic translation elongation factor 1 alpha 1; GAPDH = Glyceraldehyde-3-Phosphate Dehydrogenase; HMBS = hydroxymethylbilane synthase; HPRT1 = hypoxanthine phosphoribosyltransferase 1; RPL13A = ribosomal protein L13a; TPT1 = tumor protein, translationally-controlled 1; UBB = ubiquitin B; UBC = ubiquitin C; ACTN1 = actinin, alpha 1; AKR1D1 = aldo-keto reductase family 1, member D1; ALAS1 = aminolevulinate, delta-, synthase 1; ALDOA = aldolase A, fructose-bisphosphate; G6PD = glucose-6-phosphate dehydrogenase; GUSB = glucuronidase, beta; HSP90AB1 = heat shock protein 90kDa alpha (cytosolic), class B member 1; NUCB1 = nucleobindin 1; PGK1 = phosphoglycerate kinase 1; PUM1 = pumilio RNA-binding family member 1; SDHA = succinate dehydrogenase complex, subunit A, flavoprotein (Fp); TMBIM6 = transmembrane BAX inhibitor motif containing 6; YWHAZ = tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta.
* Belong to the housekeeping gene set of Illumina.