Table 1.
NFBD1 shRNA-regulated genes identified by microarray analysis
| Pathway | Symbol | Description | 0 Gy
|
5 Gy
|
||||
|---|---|---|---|---|---|---|---|---|
| log2FC NFBD1 | log2FC p53 | log2FC NFBD1/p53 | log2FC NFBD1 | log2FC p53 | log2FC NFBD1/p53 | |||
| focal adhesion | CAV2 | caveolin 2 | −0.973 | −0.899 | −0.839 | −0.852 | ||
| CAV2 | caveolin 2 | −0.716 | −0.743 | −0.662 | −0.664 | |||
| PPP1CC | Protein phosphatase 1, catalytic subunit, gamma isoform | −0.534 | −0.516 | −0.786 | −0.504 | |||
| CAV1 | Caveolin 1, caveolae protein, 22kDa | −0.664 | −0.656 | −0.604 | −0.498 | |||
| CAV1 | Caveolin 1, caveolae protein, 22kDa | −0.537 | −0.482 | −0.664 | ||||
| PTEN | Phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | −0.425 | −0.374 | −0.373 | −0.448 | |||
| PTEN | Phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | −0.293 | −0.324 | −0.431 | −0.389 | |||
| LAMA5 | Laminin, alpha 5 | −0.661 | −0.519 | |||||
| LAMB3 | Laminin, beta 3 | −0.319 | −0.239 | −0.346 | −0.392 | |||
| LAMB2 | Laminin, beta 2 (laminin S) | −0.267 | −0.347 | |||||
| RAF1 | v-raf-1 murine leukemia viral oncogene homolog 1 | −0.349 | −0.353 | |||||
| CCND2 | Cyclin D2 | 0.340 | 0.232 | |||||
| THBS3 | Thrombospondin 3 | −0.266 | ||||||
| TLN2 | Talin 2 | −0.243 | ||||||
| COL5A1 | Collagen, type V, alpha 1 | −0.492 | −0.536 | |||||
| GRB2 | Growth factor receptor-bound protein 2 | −0.254 | ||||||
| CAPN2 | Calpain 2, (m/II) large subunit | −0.191 | −0.180 | |||||
| PDGFRB | Platelet-derived growth factor receptor, beta polypeptide | −0.242 | −0.271 | |||||
| Jak-STAT | BCL2L1 | BCL2-like 1 | −0.541 | −0.232 | −0.560 | −0.523 | −0.343 | −0.771 |
| BCL2L1 | BCL2-like 1 | −0.443 | 0.179 | −0.351 | −0.523 | −0.263 | −0.394 | |
| IFNAR1 | Interferon (alpha, beta and omega) receptor 1 | −0.292 | −0.438 | |||||
| IL12A | Interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35) | 0.180 | 0.294 | 0.186 | ||||
| STAM | Signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 | −0.598 | −0.559 | −0.593 | −0.442 | |||
| LEPR | Leptin receptor | −0.360 | −0.307 | |||||
| IL21R | Interleukin 21 receptor | 0.115 | 0.171 | |||||
| IL7R | Interleukin 7 receptor | −0.277 | −0.230 | −0.364 | ||||
| IL11 | Interleukin 11 | 0.179 | 0.133 | 0.162 | ||||
| CCND2 | Cyclin D2 | 0.395 | 0.340 | 0.232 | ||||
| CCND2 | Cyclin D2 | 0.499 | ||||||
| IL13RA2 | Interleukin 13 receptor, alpha 2 | 0.245 | ||||||
| GRB2 | Growth factor receptor-bound protein 2 | −0.254 | ||||||
| GHR | Growth hormone receptor | −0.201 | ||||||
| SOCS2 | Suppressor of cytokine signaling 2 | 0.157 | ||||||
| Insulin | PPP1CC | Protein phosphatase 1, catalytic subunit, gamma isoform | −0.534 | −0.516 | −0.786 | −0.504 | ||
| NRAS | Neuroblastoma RAS viral (v-ras) oncogene homolog | −0.448 | −0.430 | −0.459 | −0.316 | |||
| IRS1 | Insulin receptor substrate 1 | −0.382 | −0.353 | −0.347 | 0.288 | |||
| EXOC7 | Exocyst complex component 7 | −0.532 | ||||||
| RAF1 | v-raf-1 murine leukemia viral oncogene homolog 1 | −0.349 | −0.353 | |||||
| GRB2 | Growth factor receptor-bound protein 2 | −0.254 | ||||||
| MKNK2 | MAP kinase interacting serine/threonine kinase 2 | 0.160 | ||||||
| TSC1 | Tuberous sclerosis 1 | −0.221 | ||||||
| PRKAR2A | Protein kinase, cAMP-dependent, regulatory, type II, alpha | −0.267 | ||||||
| SOCS2 | Suppressor of cytokine signaling 2 | 0.57 | ||||||
| FLOT2 | Flotillin 2 | −0.276 | ||||||
| TGF-beta | INHBE | Inhibin, beta E | 0.670 | 0.471 | 0.461 | 0.572 | ||
| TGFBR3 | Transforming growth factor, beta receptor III | −0.505 | ||||||
| TIAF1 | TGFB1-induced anti-apoptotic factor 1 | −0.517 | ||||||
| SMAD6 | SMAD family member 6 | −0.280 | −0.386 | |||||
| SMAD3 | SMAD family member 3 | −0.474 | ||||||
| SKP1 | S-phase kinase-associated protein 1 | −0.420 | −0.321 | 0.249 | −0.365 | −0.290 | ||
| PPP2R2C | Protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform | −0.354 | ||||||
| THBS3 | Thrombospondin 3 | −0.266 | ||||||
| TGFBR1 | Transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kDa) | −0.109 | ||||||
| carbohydrate metabolism | ADRA1B | Adrenergic, alpha-1B-, receptor | −0.447 | 0.240 | −0.396 | −0.227 | ||
| CS | Citrate synthase | −0.580 | −0.511 | −0.559 | −0.483 | |||
| IDH1 | Isocitrate dehydrogenase 1 (NADP+), soluble | −0.476 | −0.537 | −0.352 | −0.477 | |||
| LAMP2 | Lysosomal-associated membrane protein 2 | −1.257 | −1.225 | −1.014 | −1.065 | |||
| LAMP2 | Lysosomal-associated membrane protein 2 | −1.121 | −0.813 | −0.911 | −1.001 | |||
| PGM3 | Phosphoglucomutase 3 | −0.389 | −0.362 | −0.415 | −0.478 | |||
| PPP1CC | Protein phosphatase 1, catalytic subunit, gamma isoform | −0.786 | −0.504 | −0.534 | −0.516 | |||
| SLC2A3 | Solute carrier family 2 (facilitated glucose transporter), member 3 | −0.495 | −0.471 | −0.749 | −0.409 | −0.444 | −0.710 | |
| B4GALT4 | UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 | −0.292 | −0.377 | −0.402 | −0.439 | |||
| B4GALT4 | UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4 | −0.730 | −0.569 | −0.646 | −0.536 | |||
| SUCLA2 | Succinate-CoA ligase, ADP-forming, beta subunit | −0.349 | −0.348 | −0.400 | −0.413 | |||
| SUCLA2 | Succinate-CoA ligase, ADP-forming, beta subunit | −0.466 | −0.246 | −0.392 | −0.362 | |||
| POFUT1 | Protein O-fucosyltransferase 1 | −1.046 | −1.012 | −0.906 | −0.864 | |||
| PGM2 | Phosphoglucomutase 2 | −0.413 | −0.378 | −0.385 | −0.405 | |||
| RNA splicing | NCBP1 | Nuclear cap binding protein subunit 1, 80kDa | −0.732 | −0.462 | −0.567 | −0.533 | ||
| PPP1R8 | Protein phosphatase 1, regulatory (inhibitor) subunit 8 | −0.301 | 0.249 | −0.261 | 0.188 | |||
| PTBP1 | Polypyrimidine tract binding protein 1 | −0.613 | −0.506 | −0.332 | −0.254 | |||
| PTBP1 | Polypyrimidine tract binding protein 1 | −0.599 | −0.353 | |||||
| RBM9 | RNA binding motif protein 9 | 0.208 | −0.222 | −0.201 | −0.102 | |||
| PTBP2 | Polypyrimidine tract binding protein 2 | 0.601 | 0.530 | 0.800 | 0.522 | |||
| PTBP2 | Polypyrimidine tract binding protein 2 | 0.534 | 0.448 | 0.635 | 0.591 | |||
| THOC3 | THO complex 3 | −0.631 | −0.568 | −0.724 | −0.722 | |||
| THOC3 | THO complex 3 | −0.607 | −0.417 | −0.712 | −0.687 | |||
NOTE: NFBD1 shRNA-regulated genes identified by Illumina microarray analysis are listed (second and third columns from the left). Genes with the highest fold change and representative pathways (leftmost column) are listed. The log2 fold change caused by NFBD1 or p53 shRNA is indicated in the presence and absence of IR (6 rightmost columns). If the gene did not appear in the list of top 1000 most significant (based on the P-value of the three biological replicates) genes regulated by a given shRNA or IR condition, the entry is left blank. “FC” = fold change.