Table 2. The 40 most strongly down-regulated genes in KBM7-NuKO cells.
| Gene id | Approved gene name | Fold change | FDR-P, KO vs WT1 | FPKM WT2 | FPKM KO2 |
|---|---|---|---|---|---|
| GFRA1 | GDNF family receptor alpha 1 | 3221.0 | 4.38E-298 | 2.548 | 0.000 |
| ZNF660 | zinc finger protein 660 | 1785.1 | 5.30E-174 | 2.094 | 0.000 |
| DZIP1 | DAZ interacting zinc finger protein 1 | 1364.6 | 0.00E+00 | 10.206 | 0.007 |
| CROT | carnitine O-octanoyltransferase | 623.2 | 2.81E-60 | 0.958 | 0.000 |
| EDIL3 | EGF-like repeats and discoidin I-like domains 3 | 590.1 | 3.02E-68 | 0.785 | 0.000 |
| PHACTR3 | phosphatase and actin regulator 3 | 566.5 | 9.06E-65 | 0.711 | 0.000 |
| NUDT2 | nudix (NDP- linked moiety X)-type motif 2 | 545.0 | 1.03E-181 | 13.295 | 0.018 |
| RAB42 | RAB42, member RAS oncogene family | 267.5 | 3.31E-31 | 0.936 | 0.000 |
| MPZL2 | myelin protein zero-like 2 | 260.3 | 0.00E+00 | 10.580 | 0.039 |
| IFI44L | interferon-induced protein 44-like | 224.3 | 0.00E+00 | 5.862 | 0.026 |
| GALM | galactose mutarotase (aldose 1-epimerase) | 203.4 | 1.84E-77 | 1.908 | 0.006 |
| CRISP3 | cysteine-rich secretory protein 3 | 161.1 | 9.10E-96 | 3.206 | 0.017 |
| TP53TG1 | TP53 target 1 (non-protein coding) | 160.9 | 7.09E-19 | 1.194 | 0.000 |
| MGMT | O-6-methylguanine-DNA methyltransferase | 157.9 | 1.56E-18 | 0.337 | 0.000 |
| LUM | lumican | 142.9 | 9.87E-15 | 0.360 | 0.000 |
| misc_RNA | Y-RNA-like misc_RNA, chromosome 8 | 137.3 | 1.76E-15 | 9.261 | 0.000 |
| BRINP3 | bone morphogenetic/retinoic acid inducible protein 3 | 135.8 | 0.00E+00 | 32.885 | 0.243 |
| NKX2-2 | NK2 homeobox 2 | 125.3 | 8.96E-15 | 0.457 | 0.000 |
| IGF2BP1 | insulin-like growth factor 2 mRNA binding protein 1 | 121.7 | 0.00E+00 | 8.783 | 0.071 |
| GJA1 | gap junction protein, alpha 1, 43kDa | 120.4 | 3.14E-174 | 4.721 | 0.037 |
| ABCC6 | ATP-binding cassette, sub-family C, member 6 | 110.5 | 4.57E-13 | 0.111 | 0.000 |
| GYPE | glycophorin E (MNS blood group) | 110.5 | 2.42E-12 | 0.418 | 0.000 |
| ADGRL3 | adhesion G protein-coupled receptor L3 | 109.0 | 6.96E-33 | 0.203 | 0.001 |
| RAG2 | recombination activating gene 2 | 107.5 | 4.59E-160 | 4.217 | 0.037 |
| FIGN | fidgetin | 87.7 | 1.97E-38 | 0.394 | 0.004 |
| CPED1 | cadherin-like and PC-esterase domain containing 1 | 87.1 | 4.13E-63 | 0.925 | 0.009 |
| TMEM254 | transmembrane protein 254 | 84.4 | 9.42E-90 | 2.303 | 0.025 |
| GLDC | glycine dehydrogenase (decarboxylating) | 83.9 | 5.13E-10 | 0.136 | 0.000 |
| JCHAIN | joining chain of multimeric IgA and IgM | 74.6 | 4.58E-27 | 1.160 | 0.011 |
| CNTNAP5 | contactin associated protein-like 5 | 72.1 | 3.90E-08 | 0.101 | 0.000 |
| TM4SF1 | transmembrane 4 L six family member 1 | 70.3 | 4.74E-24 | 0.502 | 0.005 |
| CXCL10 | chemokine (C-X-C motif) ligand 10 | 66.1 | 1.78E-181 | 30.704 | 0.463 |
| KYNU | kynureninase | 64.5 | 1.46E-162 | 0.845 | 0.013 |
| EVA1A | eva-1 homolog A (C. elegans) | 57.3 | 4.61E-30 | 0.929 | 0.014 |
| CNTNAP4 | contactin associated protein-like 4 | 54.8 | 2.13E-33 | 0.378 | 0.006 |
| HPGD | hydroxyprostaglandin dehydrogenase 15-(NAD) | 52.1 | 5.40E-19 | 0.246 | 0.003 |
| TSPAN7 | tetraspanin 7 | 51.4 | 7.66E-06 | 0.125 | 0.000 |
| CD200 | CD200 molecule | 51.1 | 1.26E-98 | 2.669 | 0.051 |
| OAS2 | 2'-5'-oligoadenylate synthetase 2, 69/71kDa | 49.4 | 4.24E-278 | 5.029 | 0.100 |
| CXCL11 | chemokine (C-X-C motif) ligand 11 | 47.1 | 4.54E-120 | 6.138 | 0.128 |
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