Table 3. The 40 most strongly up-regulated genes in KBM7-NuKO cells.
| Gene id | Approved gene name | Fold change | FDR-P, KO vs WT1 | FPKM WT2 | FPKM KO2 |
|---|---|---|---|---|---|
| LINC01224 | long intergenic non-protein coding RNA 1224 | 1832.2 | 1.56E-149 | 0.000 | 10.839 |
| ZNF483 | zinc finger protein 483 | 1649.2 | 9.98E-143 | 0.000 | 2.201 |
| OVOL1 | ovo-like zinc finger 1 | 718.9 | 5.18E-50 | 0.000 | 1.434 |
| FAM162B | family with sequence similarity 162, member B | 323.3 | 3.96E-30 | 0.000 | 2.382 |
| NAP1L2 | nucleosome assembly protein 1-like 2 | 280.2 | 9.86E-180 | 0.018 | 5.828 |
| ZNF544 | zinc finger protein 544 | 264.4 | 1.02E-171 | 0.007 | 1.991 |
| SLC1A1 | solute carrier family 1 | 110.2 | 1.06E-11 | 0.000 | 0.211 |
| TACC2 | transforming, acidic coiled-coil containing protein 2 | 107.6 | 8.60E-11 | 0.000 | 0.043 |
| ATP10B | ATPase, class V, type 10B | 76.2 | 3.91E-08 | 0.000 | 0.051 |
| EMC10 | ER membrane protein complex subunit 10 | 67.6 | 1.74E-172 | 0.021 | 1.475 |
| SGPP2 | sphingosine-1-phosphate phosphatase 2 | 62.5 | 2.32E-41 | 0.013 | 0.992 |
| GALNT5 | polypeptide N-acetylgalactosaminyltransferase 5 | 59.8 | 1.73E-25 | 0.006 | 0.465 |
| NHSL2 | NHS-like 2 | 51.9 | 9.76E-06 | 0.000 | 0.098 |
| ECT2L | epithelial cell transforming 2 like | 49.5 | 1.28E-05 | 0.000 | 0.080 |
| SERPINB10 | serpin peptidase inhibitor, clade B, member 10 | 47.1 | 2.28E-05 | 0.000 | 0.131 |
| HLA-DOA | major histocompatibility complex, class II, DOA | 47.0 | 9.78E-05 | 0.000 | 0.088 |
| FAM155A | family with sequence similarity 155, member A | 42.5 | 0.000444026 | 0.000 | 0.038 |
| PAK3 | p21 protein (Cdc42/Rac)-activated kinase 3 | 42.2 | 7.28E-05 | 0.000 | 0.030 |
| DNMT3L | DNA (cytosine-5-)-methyltransferase 3-like | 39.8 | 0.000129366 | 0.000 | 0.159 |
| THY1 | Thy-1 cell surface antigen | 39.8 | 0.000129366 | 0.000 | 0.050 |
| ABCA8 | ATP-binding cassette, sub-family A (ABC1), 8 | 37.8 | 0.002009234 | 0.000 | 0.025 |
| CYP26B1 | cytochrome P450, family 26B, polypeptide 1 | 37.4 | 0.000229216 | 0.000 | 0.055 |
| ANXA3 | annexin A3 | 35.3 | 0.002276797 | 0.000 | 0.052 |
| BASP1 | brain abundant, membrane attached signal protein 1 | 35.2 | 0 | 4.294 | 151.21 |
| MIXL1 | Mix paired-like homeobox | 35.0 | 0.000407311 | 0.000 | 0.129 |
| SDC4 | syndecan 4 | 34.8 | 1.39E-55 | 0.053 | 1.918 |
| CELA1 | chymotrypsin-like elastase family, member 1 | 32.9 | 0.009226334 | 0.000 | 0.259 |
| TMEM176B | transmembrane protein 176B | 32.8 | 3.69E-09 | 0.011 | 0.502 |
| SNX19 | sorting nexin 19 | 32.8 | 0.011374951 | 0.000 | 0.030 |
| NAV3 | neuron navigator 3 | 32.6 | 0.00158859 | 0.000 | 0.022 |
| LINC01124 | long intergenic non-protein coding RNA 1124 | 32.6 | 0.001588576 | 0.000 | 0.115 |
| HS6ST3 | heparan sulfate 6-O-sulfotransferase 3 | 32.5 | 0.000722541 | 0.000 | 0.031 |
| PAK6 | p21 protein (Cdc42/Rac)-activated kinase 6 | 32.5 | 0.000722541 | 0.000 | 0.037 |
| LINC00925 | long intergenic non-protein coding RNA 925 | 32.0 | 8.37E-20 | 0.006 | 0.233 |
| AOC1 | amine oxidase, copper containing 1 | 30.6 | 2.14E-58 | 0.059 | 1.881 |
| C1orf204 | chromosome 1 open reading frame 204 | 30.2 | 0.001942513 | 0.000 | 0.091 |
| NDRG4 | NDRG family member 4 | 30.1 | 0.00128289 | 0.000 | 0.023 |
| NHS | Nance-Horan syndrome | 30.1 | 0.001597534 | 0.000 | 0.022 |
| NIM1K | NIM1 serine/threonine protein kinase | 29.3 | 6.57E-17 | 0.012 | 0.429 |
| A4GALT | alpha 1,4-galactosyltransferase | 29.1 | 3.48E-08 | 0.008 | 0.301 |
1False discovery rate-adjusted P-value
2Fragments per kilobase of transcript per million mapped reads, a measure of transcript abundance in KBM7 wild type (WT) and KBM7-NuKO (KO) knockout cells