Selected genes in DE_SigUp or MFUp that have not been previously described as differentially regulated in erythroblasts
| Gene . | Symbol . | List . | Largest significant FC between erythroid stages* . | Function . | DE in a reanalyzed dataset? (reference) . | DE in a previous cell line study? (reference) . |
|---|---|---|---|---|---|---|
| Carbonic anhydrase 3 | CA3 | DE_Sig | 177.7x C-I | Muscle-specific, catalyses reversible hydration of CO2, inhibits apoptosis | 9 | |
| Calbindin 1 | CALB1 | DE_Sig | 173.1x I-L | Inhibits apoptosis in osteoblasts by binding to and inhibiting caspase 3 | 12 | 8 |
| FK506 binding protein 1B, 12.6 kDa | FKBP1B | DE_Sig | 13.1x C-L | Inhibits the mTOR proliferation pathway | 12 | 7 |
| Intalectin 1 | ITLN1 | DE_Sig | 31.3x C-L | Binds cell surface galactofuronidase | 12 | |
| Multiple EGF-like-domains 9 | MEGF9 | DE_Sig | 18.1x C-L | Signaling molecule, regulated during development | ||
| N-myc downstream regulated 1 | NDRG1 | DE_Sig | 10.5x C-L | Involved in hypoxia response, cell differentiation, and cell growth arrest | ||
| PTEN-induced putative kinase 1 | PINK1 | DE_Sig | 11.5x C-L | Implicated in mitochondrial quality control | ||
| Regulatory factor X-associated protein | RFXAP | DE_Sig | −32.9x I-L | In association with NFY and Creb; involved in MHC class II activation | 12 | |
| S100 calcium binding protein A4 | S100A4 | DE_Sig | −24.5x P-L | Overexpression promotes metastasis, activates NF-κB; functions as a Ca2+-activated molecular switch, regulates macrophage recruitment and chemotaxis | ||
| SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 | SMARCA4 | DE_Sig | −11.0x C-L | Coactivates γ-globin gene | ||
| Transmembrane protein 140 | TMEM140 | DE_Sig | 26.6x C-L | Potential role in supporting HSC activity of a stromal cell line | 12 | |
| Zinc finger protein 451 | ZNF451 | DE_Sig | 11.5x C-L | ZNF451 is a novel PML body- and SUMO-associated transcriptional co-regulator | ||
| Histone cluster 1, H2bd | HIST1H2BD | DE_Sig & MFUp | 26.0x C-L | 9,12 | ||
| Bromodomain and WD repeat domain containing 3 | BRWD3 | MFUp | 6.7x C-L | May have a role in JAK/STAT signaling | ||
| Cathepsin L2 | CTSL2 | MFUp | 7.1x C-L | |||
| DnaJ (Hsp40) homolog, subfamily B, member 4 | DNAJB4 | MFUp | 15.3 C-L | A tumor suppressor activated by YY1 and AP1 | 8 | |
| Gasdermin B | GSDMB | MFUp | 8.8x C-L | Involved in regulation of apoptosis in the gastrointestinal epithelium | ||
| Importin 11 | IPO11 | MFUp | 12.1x C-L | Increases the intensity of pleiotrophic cytokine responses | ||
| Lin-7 homolog B (C elegans) | LIN7B | MFUp | 19.3 C-L | Involved in Ras signaling; effects include cell growth, differentiation, and survival | ||
| Nuclear paraspeckle assembly transcript 1 (non—protein-coding) | NEAT1 | MFUp | 28.7x C-L | RNA component of paraspeckles, ribonucleoprotein structures involved in regulating the expression of certain genes in differentiated cells by nuclear retention of RNA | ||
| Retinoic acid receptor responder (tazarotene induced) 3 | RARRES3 | MFUp | 5.2x C-L | Retinoid-inducible growth regulator, induces apoptosis | ||
| Rififylin | RFFL | MFUp | 7.7x C-L | Inhibits recycling from the endocytic recycling compartment | ||
| Ras-related associated with diabetes | RRAD | MFUp | 12.5x P-L | Involved in Ras signalling; effects include cell growth, differentiation, and survival | 12 | 7 |
| Lysine (K)-specific demethylase 6A | KDM6A | MFUp | 7.8x C-L | Involved in chromatin remodeling | ||
| Zinc finger protein 805 | ZNF805 | MFUp | 6.2x C-L |
| Gene . | Symbol . | List . | Largest significant FC between erythroid stages* . | Function . | DE in a reanalyzed dataset? (reference) . | DE in a previous cell line study? (reference) . |
|---|---|---|---|---|---|---|
| Carbonic anhydrase 3 | CA3 | DE_Sig | 177.7x C-I | Muscle-specific, catalyses reversible hydration of CO2, inhibits apoptosis | 9 | |
| Calbindin 1 | CALB1 | DE_Sig | 173.1x I-L | Inhibits apoptosis in osteoblasts by binding to and inhibiting caspase 3 | 12 | 8 |
| FK506 binding protein 1B, 12.6 kDa | FKBP1B | DE_Sig | 13.1x C-L | Inhibits the mTOR proliferation pathway | 12 | 7 |
| Intalectin 1 | ITLN1 | DE_Sig | 31.3x C-L | Binds cell surface galactofuronidase | 12 | |
| Multiple EGF-like-domains 9 | MEGF9 | DE_Sig | 18.1x C-L | Signaling molecule, regulated during development | ||
| N-myc downstream regulated 1 | NDRG1 | DE_Sig | 10.5x C-L | Involved in hypoxia response, cell differentiation, and cell growth arrest | ||
| PTEN-induced putative kinase 1 | PINK1 | DE_Sig | 11.5x C-L | Implicated in mitochondrial quality control | ||
| Regulatory factor X-associated protein | RFXAP | DE_Sig | −32.9x I-L | In association with NFY and Creb; involved in MHC class II activation | 12 | |
| S100 calcium binding protein A4 | S100A4 | DE_Sig | −24.5x P-L | Overexpression promotes metastasis, activates NF-κB; functions as a Ca2+-activated molecular switch, regulates macrophage recruitment and chemotaxis | ||
| SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 | SMARCA4 | DE_Sig | −11.0x C-L | Coactivates γ-globin gene | ||
| Transmembrane protein 140 | TMEM140 | DE_Sig | 26.6x C-L | Potential role in supporting HSC activity of a stromal cell line | 12 | |
| Zinc finger protein 451 | ZNF451 | DE_Sig | 11.5x C-L | ZNF451 is a novel PML body- and SUMO-associated transcriptional co-regulator | ||
| Histone cluster 1, H2bd | HIST1H2BD | DE_Sig & MFUp | 26.0x C-L | 9,12 | ||
| Bromodomain and WD repeat domain containing 3 | BRWD3 | MFUp | 6.7x C-L | May have a role in JAK/STAT signaling | ||
| Cathepsin L2 | CTSL2 | MFUp | 7.1x C-L | |||
| DnaJ (Hsp40) homolog, subfamily B, member 4 | DNAJB4 | MFUp | 15.3 C-L | A tumor suppressor activated by YY1 and AP1 | 8 | |
| Gasdermin B | GSDMB | MFUp | 8.8x C-L | Involved in regulation of apoptosis in the gastrointestinal epithelium | ||
| Importin 11 | IPO11 | MFUp | 12.1x C-L | Increases the intensity of pleiotrophic cytokine responses | ||
| Lin-7 homolog B (C elegans) | LIN7B | MFUp | 19.3 C-L | Involved in Ras signaling; effects include cell growth, differentiation, and survival | ||
| Nuclear paraspeckle assembly transcript 1 (non—protein-coding) | NEAT1 | MFUp | 28.7x C-L | RNA component of paraspeckles, ribonucleoprotein structures involved in regulating the expression of certain genes in differentiated cells by nuclear retention of RNA | ||
| Retinoic acid receptor responder (tazarotene induced) 3 | RARRES3 | MFUp | 5.2x C-L | Retinoid-inducible growth regulator, induces apoptosis | ||
| Rififylin | RFFL | MFUp | 7.7x C-L | Inhibits recycling from the endocytic recycling compartment | ||
| Ras-related associated with diabetes | RRAD | MFUp | 12.5x P-L | Involved in Ras signalling; effects include cell growth, differentiation, and survival | 12 | 7 |
| Lysine (K)-specific demethylase 6A | KDM6A | MFUp | 7.8x C-L | Involved in chromatin remodeling | ||
| Zinc finger protein 805 | ZNF805 | MFUp | 6.2x C-L |
The largest significant fold change between stages of our maturing erythroblasts is indicated with a brief summary of the function and whether it was differentially expressed in any of the reanalyzed datasets listed in Table 1, or any of the previous erythroid cell line studies. References for gene function are given in supplemental Table 8B.
C indicates CFU-E; P, Pro-E; I, Int-E; and L, Late-E.