Examples of known genes in subtracted cDNA library placed into functional categories
| Category/gene name . | Description . | Log2(EML24/EML0) . | Log2(LHLowRBright/LHLowRLow) . |
|---|---|---|---|
| Transcription factors/DNA binding proteins | |||
| Cbfb | Core binding factor β | — | − 0.9 ± 0.2 |
| Cebpa-rs1 | Transcription regulator related to C/ebp α | − 0.9 ± 0.3 | — |
| Cebpb | Transcription regulator C/ebp β | — | — |
| Cebpg | Controls the activity of IL-4 promoter activity | − 1.9 ± 0.68 | − 2.5 ± 0.29 |
| Crem | Transcriptional modulator of cAMP responsive genes | — | − 1.5 ± 0.7 |
| Elk4 | Member of ETS oncogene family | − 1.2 ± 0.5 | − 0.9 ± 0.08 |
| Fos | Part of AP1; propagation of mitogenic signals | − 1.2 ± 0.4 | − 2.0 ± 0.05 |
| Hmga1 | High-mobility group AT-hook 1 | — | — |
| Hoxa5 | Homeobox A5 | — | — |
| Jun | Jun oncogene, part of AP1 transcriptional complex with Fos | — | — |
| Klf9 | Erythroid-specific transcription | 1.8 ± 0.53 | − 2.5 ± 0.15 |
| Lrf | BTB-POZ transcription factor, dimerizes with Bcl6 | — | − 2.7 ± 0.1 |
| Mint | Organizes transcriptional complexes | 2.9 ± 0.3 | 2.5 ± 0.7 |
| Mlf2 | Related to Mlf1, a partner in t(3;5) with Npm in leukemia | − 2.9 ± 0.45 | − 2.4 ± 0.3 |
| Nkx2-3 | Regulates emigration of circulating leukocytes | − 1.6 ± 1.0 | — |
| Sox4 | Important for very early B-cell differentiation | − 2.1 ± 1.1 | − 2.7 ± 0.26 |
| Sox5 | SRY-box containing gene 5 | — | − 3.1 ± 0.22 |
| Tal1 | T-cell acute lymphocytic leukemia 1 | — | — |
| Xbp1 | Essential for plasma cell differentiation, liver development | 1.6 ± 0.4 | − 1.1 ± 0.5 |
| Signaling proteins | |||
| Arhgef1 | Rho guanine nucleotide exchange factor (GEF) 1 | − 0.9 ± 0.58 | — |
| Calm | Calmodulin, component of calcium signaling pathway | — | − 1.2 ± 0.13 |
| Calr | Calreticuin, major ER calcium-binding protein | — | − 2.2 ± 0.3 |
| Camkk2 | CaM-kinase kinase β, regulates calcium signaling | — | − 3.1 ± 0.2 |
| Ccnd1 | Cyclin D1, cell cycle regulation | − 1.7 ± 1.0 | − 2.7 ± 0.2 |
| Csnk1a | Casein kinase i, α isoform | — | − 2.9 ± 0.45 |
| Hus1 | Cell cycle checkpoint protein | − 1.4 ± 0.07 | − 3.1 ± 0.32 |
| Iqgap | IQ motif containing GTPase-activating protein 1 | — | — |
| Itpr3 | Inositol 1, 4, 5-triphosphate receptor 3 | — | — |
| Lats1 | Large tumor suppressor, modulates CDC2 activity | — | — |
| Map2k3 | Mitogen-activated protein kinase kinase 3 | — | — |
| Nsp3 | Novel SH2-protein; couples Eph receptors to R-Ras | — | − 2.1 ± 0.06 |
| Parg1 | PTPL1-associated RhoGAP 1; activates Rho | ND | − 2.7 ± 0.55 |
| Pde4b | Phosphodiesterase 4B, cAMP specific | — | — |
| Pde8a | Phosphodiesterase 8A, cAMP specific | — | — |
| Rala | Ras-related GTPase | — | − 0.74 ± 0.22 |
| Rangap1 | RAN GTPase-activating protein 1 | — | — |
| Tax1bp1 | Antiapoptotic; involved in IL-1 signaling pathway | 0.6 ± 0.35 | — |
| Tpd52 | Regulator of cell proliferation, gene transcription | − 2.4 ± 0.2 | − 0.9 ± 0.02 |
| Traf1 | TNF receptor-associated factor 1 | — | — |
| Traf6 | TNF receptor-associated factor 6 | — | — |
| Tyk2 | Plays a restricted role in IFNα signaling | − 2.1 ± 0.2 | − 2.6 ± 0.2 |
| Vav3 | Activates Rho GTP-binding proteins | — | — |
| Wnk1 | Serine/threonine protein kinase | − 1.9 ± 0.5 | − 2.5 ± 0.4 |
| Growth factors | |||
| Efnb1 | Ephrin B1, cek5 receptor ligand | — | — |
| Hdgf | Hepatoma-derived growth factor; a mitogen for fibroblasts | — | − 1.4 ± 0.04 |
| Hegfl | Heparin-binding EGF-like, potent mitogen | — | − 3.2 ± 0.12 |
| Scgf | Controls the proliferation of hematopoietic stem cells | − 1.4 ± 0.17 | 0.93 ± 0.04 |
| Surface molecules/membrane proteins | |||
| Fgfr1 | Basic fibroblast growth factor receptor 1 precursor | — | − 3.1 ± 0.1 |
| Gpr21 | G protein–coupled receptor 21 (GPR21) | — | − 0.65 ± 0.1 |
| H2-K | Class I antigen of MHC, mediates transplant rejection | — | − 1.5 ± 0.08 |
| Hegfl | Heparin-binding EGF-like growth factor | — | — |
| Itm1 | Intergral membrane protein 1; unknown function | — | − 1.5 ± 0.08 |
| Ncam2 | Neural cell adhesion molecule 2 | — | — |
| Oprs1 | Opioid receptor, ς1 | — | — |
| Tnfrsf1b | TNF receptor superfamily, member 1b | — | — |
| Related to blood cell function | |||
| Gpx1 | Glutathione peroxidase; red cell antioxidant defense | 1.2 ± 1.0 | — |
| H2-Aa | Histocompatibility 2, class II antigen A, α | — | — |
| Ncf1 | NADPH oxidase subunit (47 kd) | — | 0.14 ± 0.1 |
| Prg2 | Eosinophil major basic protein | ||
| Scya19 | Small inducible cytokine A19 | — | − 2.8 ± 0.3 |
| Category/gene name . | Description . | Log2(EML24/EML0) . | Log2(LHLowRBright/LHLowRLow) . |
|---|---|---|---|
| Transcription factors/DNA binding proteins | |||
| Cbfb | Core binding factor β | — | − 0.9 ± 0.2 |
| Cebpa-rs1 | Transcription regulator related to C/ebp α | − 0.9 ± 0.3 | — |
| Cebpb | Transcription regulator C/ebp β | — | — |
| Cebpg | Controls the activity of IL-4 promoter activity | − 1.9 ± 0.68 | − 2.5 ± 0.29 |
| Crem | Transcriptional modulator of cAMP responsive genes | — | − 1.5 ± 0.7 |
| Elk4 | Member of ETS oncogene family | − 1.2 ± 0.5 | − 0.9 ± 0.08 |
| Fos | Part of AP1; propagation of mitogenic signals | − 1.2 ± 0.4 | − 2.0 ± 0.05 |
| Hmga1 | High-mobility group AT-hook 1 | — | — |
| Hoxa5 | Homeobox A5 | — | — |
| Jun | Jun oncogene, part of AP1 transcriptional complex with Fos | — | — |
| Klf9 | Erythroid-specific transcription | 1.8 ± 0.53 | − 2.5 ± 0.15 |
| Lrf | BTB-POZ transcription factor, dimerizes with Bcl6 | — | − 2.7 ± 0.1 |
| Mint | Organizes transcriptional complexes | 2.9 ± 0.3 | 2.5 ± 0.7 |
| Mlf2 | Related to Mlf1, a partner in t(3;5) with Npm in leukemia | − 2.9 ± 0.45 | − 2.4 ± 0.3 |
| Nkx2-3 | Regulates emigration of circulating leukocytes | − 1.6 ± 1.0 | — |
| Sox4 | Important for very early B-cell differentiation | − 2.1 ± 1.1 | − 2.7 ± 0.26 |
| Sox5 | SRY-box containing gene 5 | — | − 3.1 ± 0.22 |
| Tal1 | T-cell acute lymphocytic leukemia 1 | — | — |
| Xbp1 | Essential for plasma cell differentiation, liver development | 1.6 ± 0.4 | − 1.1 ± 0.5 |
| Signaling proteins | |||
| Arhgef1 | Rho guanine nucleotide exchange factor (GEF) 1 | − 0.9 ± 0.58 | — |
| Calm | Calmodulin, component of calcium signaling pathway | — | − 1.2 ± 0.13 |
| Calr | Calreticuin, major ER calcium-binding protein | — | − 2.2 ± 0.3 |
| Camkk2 | CaM-kinase kinase β, regulates calcium signaling | — | − 3.1 ± 0.2 |
| Ccnd1 | Cyclin D1, cell cycle regulation | − 1.7 ± 1.0 | − 2.7 ± 0.2 |
| Csnk1a | Casein kinase i, α isoform | — | − 2.9 ± 0.45 |
| Hus1 | Cell cycle checkpoint protein | − 1.4 ± 0.07 | − 3.1 ± 0.32 |
| Iqgap | IQ motif containing GTPase-activating protein 1 | — | — |
| Itpr3 | Inositol 1, 4, 5-triphosphate receptor 3 | — | — |
| Lats1 | Large tumor suppressor, modulates CDC2 activity | — | — |
| Map2k3 | Mitogen-activated protein kinase kinase 3 | — | — |
| Nsp3 | Novel SH2-protein; couples Eph receptors to R-Ras | — | − 2.1 ± 0.06 |
| Parg1 | PTPL1-associated RhoGAP 1; activates Rho | ND | − 2.7 ± 0.55 |
| Pde4b | Phosphodiesterase 4B, cAMP specific | — | — |
| Pde8a | Phosphodiesterase 8A, cAMP specific | — | — |
| Rala | Ras-related GTPase | — | − 0.74 ± 0.22 |
| Rangap1 | RAN GTPase-activating protein 1 | — | — |
| Tax1bp1 | Antiapoptotic; involved in IL-1 signaling pathway | 0.6 ± 0.35 | — |
| Tpd52 | Regulator of cell proliferation, gene transcription | − 2.4 ± 0.2 | − 0.9 ± 0.02 |
| Traf1 | TNF receptor-associated factor 1 | — | — |
| Traf6 | TNF receptor-associated factor 6 | — | — |
| Tyk2 | Plays a restricted role in IFNα signaling | − 2.1 ± 0.2 | − 2.6 ± 0.2 |
| Vav3 | Activates Rho GTP-binding proteins | — | — |
| Wnk1 | Serine/threonine protein kinase | − 1.9 ± 0.5 | − 2.5 ± 0.4 |
| Growth factors | |||
| Efnb1 | Ephrin B1, cek5 receptor ligand | — | — |
| Hdgf | Hepatoma-derived growth factor; a mitogen for fibroblasts | — | − 1.4 ± 0.04 |
| Hegfl | Heparin-binding EGF-like, potent mitogen | — | − 3.2 ± 0.12 |
| Scgf | Controls the proliferation of hematopoietic stem cells | − 1.4 ± 0.17 | 0.93 ± 0.04 |
| Surface molecules/membrane proteins | |||
| Fgfr1 | Basic fibroblast growth factor receptor 1 precursor | — | − 3.1 ± 0.1 |
| Gpr21 | G protein–coupled receptor 21 (GPR21) | — | − 0.65 ± 0.1 |
| H2-K | Class I antigen of MHC, mediates transplant rejection | — | − 1.5 ± 0.08 |
| Hegfl | Heparin-binding EGF-like growth factor | — | — |
| Itm1 | Intergral membrane protein 1; unknown function | — | − 1.5 ± 0.08 |
| Ncam2 | Neural cell adhesion molecule 2 | — | — |
| Oprs1 | Opioid receptor, ς1 | — | — |
| Tnfrsf1b | TNF receptor superfamily, member 1b | — | — |
| Related to blood cell function | |||
| Gpx1 | Glutathione peroxidase; red cell antioxidant defense | 1.2 ± 1.0 | — |
| H2-Aa | Histocompatibility 2, class II antigen A, α | — | — |
| Ncf1 | NADPH oxidase subunit (47 kd) | — | 0.14 ± 0.1 |
| Prg2 | Eosinophil major basic protein | ||
| Scya19 | Small inducible cytokine A19 | — | − 2.8 ± 0.3 |
The Log2 ratios of EML24/EML0 and LHLowRBright/LRLowHLowwere the average values of 3 experiments and normalized the signal intensity of each hybridization to internal control glyceraldehyde-3-phosphate dehydrogenase. A minus sign in front of a Log2 raio indicates downregulation (and the absence of a minus sign indicates upregulation) of (1) gene expression when EML cells were treated with all ATRA/IL-3 for 24 hours, or (2) in primary sorted bone marrow cells, LHLowRLow relative to LHLowRBright. A data cell containing only a minus sign indicates no change.
LRLowHLow indicates lineage-minus (Lin−)rhodamineLowHoechstLow; LHLowRBright, Lin−HoechstLowrhodamineBright; cAMP, cyclic adenosine monophosphate; GTPase, guanosine 5′-triphosphatase; Eph, ephrin; TNF, tumor necrosis factor; IFN, interferon; GTP, guanosine 5′-triphosphate; EGF, epidermal growth factor; MHC, major histocompatibility complex; and NADPH, nicotinamide adenine dinucleotide phosphate.