List of genes and gene categories repressed by LMP2A
Murine bone marrow CD 19+ . | Murine spleen CD19+ . | Human BJAB + LMP2A . | Human LCL + LMP2A . |
|---|---|---|---|
| Cell cycle/apoptosis | |||
| SH3P9 myc box dependent interacting (Bin1) | SH3P9 myc box-dependent interacting (Bin1) | BTG family, member 3 (Btg3) | ATM kinase |
| Caspase-6 | B-cell translocation gene 2 (Btg2) | Cyclin A2 | RBP-1-like protein (Bcaa) |
| EGL nine homolog 1 (Egln 1) | p53 variant | Cell division cycle 2 (Cdc2) | pptase and tensin (PTEN) |
| Ubiquinol-cytochrome c reductase (Ubcr) | Proline-rich protein expressed in brain (Prtb) | CHK 1 checkpoint homolog (Chek1) | Retinoblastomaa susceptibility (Rbl) |
| Signal-induced proliferation associated (Spa-1) | CDC28 protein kinase 2 (Cks2) | ||
| (tre-2/USP6, BUB2, cdc16) domain (Tbc 1d1) | Defender against cell death 1 (Dad 1) | ||
| Transgene insert site 737 (TgN737) | Programmed cell death 4 (Pdcd4) | ||
| Pituitary tumor-transforming 1 (Pttg 1) | |||
| Ubiquinol-cytochrome C reductase (Ucrq) | |||
| YME1-like 1 (Yme 1I1) | |||
| DNA/RNA metabolism | |||
| Heterogeneous nuclear riboprotein H2 | H1 histone family, member 2 | Eukaryotic translation initiation factor (eIF2s2) | eIF-1A |
| H2B histone family, member S | Polymerase (RNA) II (DNA directed) | Eukaryotic translation initiation factor (eIF4a1) | Histone H2A/g (H2AFG) |
| DNA-binding nuclear protein NP220 | Polymerase (RNA) II (DNA directed) | High-mobility group box 2 (Hmgb2) | Histone H2A.2 (H2AFO) |
| Polymerase (RNA) II (DNA directed) | RAD50 homolog | Heterogeneous nuclear ribonucleoprotein (Hnrph1) | Histone H2A.X (H2AFX) |
| RADI homolog | Rael RNA export 1 homolog | Mitochondrial ribosomal protein 63 | Histone H2B/h |
| Trf-proximal protein homolog (Trfp) | Ribosomal protein L21 | Mitochondrial ribosomal protein L3 | Histone H2B/e |
| Zinc finger protein 292 | Zinc finger protein 36 (TISII) | High mobility group-like nuclear protein (Nhp2) | Histone H2B1 S |
| Zinc finger protein, subfamily 1A, 4 | Polymerase (RNA) II (DNA directed) polypeptide J | Histone H2BFC | |
| DNA repair protein rad18 | Histone H2BFD | ||
| RAD1 homolog | Histone H2B/k (H2BFK) | ||
| RNA-binding region containing (RNPI, RRM) | Histone H2BFL | ||
| Ribosomal protein L26-like 1 | Histone H2BFR | ||
| Ribosomal protein L38 | H4 histone family G (H4FG) | ||
| Zinc finger protein 9 | |||
| Inflammation/immunity | |||
| Colony-stimulating factor 1 receptor (Csf 1r) | Adenosine A2a receptor (Adora2a) | Allograft inflammatory factor 1 (Aif1) | Butyrophilin (BTF4) |
| Deoxynucleotidyltransferase, terminal (TdT) | Complement component 1r | Complement component 1q receptor 1 | CD69 |
| Histocompatibility 2, class II antigen A | CD19 antigen | Complement component 4A | IFN-induced leucine zipper protein 35 (Ifi35) |
| Histocompatibility 2, Q region locus 7 | CD22 antigen | Integrin, beta 2 (LFA-1) | IFN-induced protein 44 (Ifi44) |
| Interferon (alpha and beta) receptor 2 | Histocompatibility 2, D region locus 1 | Ig kappa chain V-I region (Igk) | IgG lambda light chain V-J-C region |
| Germ line immunoglobulin V(H)II gene | Histocompatibility 2, class II, locus DMa | T-cell receptor alpha locus (TCR alpha) | Interleukin-7 (IL-7) |
| Immunoglobulin lambda chain, variable 1 | IFN-γ inducible protein 30 (Ifi30) | Pre-B lymphocyte gene 3 (vpreB) | Interferon regulatory factor 7B (IRF7b) |
| Interleukin-16 (IL-16) | IFN-γ inducible protein (Ifi47) | Interferon-induced protein (IRF4/Pip/Isg15) | |
| Integrin beta 4 binding protein (Itgb4bp) | Delta-immunoglobulin (IgD) | Melanoma antigen rec by T cells (MART-1, Mlana) | |
| Immunoglobulin lambda 5 | IgE Fc receptor, low affinity II, alpha | B-lymphocyte cell-surface antigen B1 (CD20) | |
| Ig B-cell antigen receptor gene (mb-1) | Germ line IgH chain gene, DJC region | 2,5 oligoadenylate synthetase 2 (Oas2) | |
| Q2-k gene for class I antigen (MHC I) | Immunoglobulin heavy chain 6 of IgM | HLA-E, transketolase (Tkt) | |
| Recombinase activating gene-2 (Rag2) | IL-4-induced gene 1 (IL4i1) | Tumor necrosis factor receptor 1b (Tnfrsf1b) | |
| TRAF-interacting protein (Traip) | TNF-beta mRNA, lymphotoxin A | TNFR7, CD27 | |
| Uromodulin (Umod) | Lymphotoxin B | ||
| VpreB | Lymphocyte antigen 9 (Ly9) | ||
| Immunoglobulin-associated alpha (mb-1) | |||
| Myeloid-associated differentiation marker (Myadm) | |||
| TNF receptor superfamily (tnfrsf5, CD40) vpreB | |||
| Signaling | |||
| Raf-related oncogene (A-raf) | Adrenergic receptor, beta 2 (b2ar) | Casein kinase II (CKII) | Calmodulin 1 |
| Cornichon homolog (Cnih) | B lymphoid kinase (Blk) | Developmentally regulated GTP binding protein (Drg1) | Dual-specificity phosphatase 5 (Dusp5) |
| FK506 binding protein 1a (Flb 1a) | Bruton tyrosine kinase (Btk) | Growth factor receptor-bound protein 2 (Grb2) | Inositol 1,4,5 trisphosphate receptor (Itpr1) |
| Guanine nucleotide binding protein, alpha inhibiting (Gnai2) | Adapter protein CIKS (Act 1) | Hyaluronan-mediated motility receptor (RHAMM) | Phosphoinositide-binding protein (Pip3e) |
| Protein phosphatase 1B (Ppm1b) | tyr-thr dual specificity phosphatase PAC-1 (Dusp2) | Protein phosphatase 1, catalytic subunit (PP1) | Cytohesin binding protein HE (Pscdbp) |
| Pleckstrin homology, Sec7 and coiled/coil domain (Pscd3) | Growth hormone (Gh) | Receptor (calcitonin) activity modifying protein (Ramp2) | Ras-associated domain family 2 (Ral GDS/AF-6) |
| Rho interacting protein 3 (Rhoip3) | Glia maturation factor, gamma (Gmfγ) | RAS guanyl releasing protein 1 (Rasgrp1) | Wingless-type MMTV integration site (Wnt6) |
| Sel 1 inhibitor of Notch | Hematopoietic cell phosphatase (SHP) | Ras suppressor protein 1 (Rsp1) | |
| Serine/threonine kinase 10 (LOK, Stk 10) | Interferon regulatory factor 1 (IRF1) | vav 3 oncogene (Vav3) | |
| Spleen tyrosine kinase Syk | Lymphocyte antigen 57 (BLNK) | WW domain binding protein 11 (Wbp11) | |
| TPR-containing, SH2-binding phosphoprotein (Tsp) | Membrane-bound C2 domain containing (Mbc2) | ||
| Membrane-spanning 4-domains (Ms4a4d) | |||
| Nuclear receptor binding protein (Nrbp) | |||
| RAS p21 protein activator 3 (Rasa3) | |||
| Regulator of G-protein signaling 19 (Rgs19) | |||
| Ras-like without CAAX 1 (Rit1) | |||
| Small protein effector 1 of Cdc42 (Spec1) | |||
| SWAP complex protein, 70 kDa (Swap70) | |||
| Tubby-like protein 3 (Tulp3) | |||
| Transcription factors | |||
| E2A transcription factor | B-cell leukemia/lymphoma 6 (Bcl-6) | C-terminal binding protein 1 (CTBP1) | Capicua homolog (Cic) |
| E4F transcription factor 1 (E4f1) | E2A transcription factor | Early growth response 4 (Egr4) | HB9 homeobox transcription factor (H1xb9) |
| Early B-cell factor (EBF) | Early B-cell factor (EBF) | Enhancer of rudimentary homolog (Erh) | Sex comb on midleg-like 2 (Scml2) |
| Early development regulator 2 (Edr2, Mph2) | Kruppel-like factor LKLF mRNA (Kif2) | Nuclear receptor subfamily 4 (Nur77, Nr4a1) | RP58, zinc finger protein (Znf238) |
| E26 avian leukemia oncogene 2 (Ets2) | LIM only 2 (Lmo2) | PBX/knotted 1 homeobox 2 (KN1, Pknox2) | |
| Host cell factor C1 transcription factor (Hcfc1) | Max dimerization protein 4 (Mad4) | Wilms tumor 1-associating protein (Wtap) | |
| Lymphoid enhancer factor-1 (LEF-1) | Nuclear factor of kappa in B cells 2 (Nfkb2) | ||
| Nuclear transcription factor-Y gamma (NF-Yγ) | pax-5 transcription factor | ||
| Pax-5 | SCAN-KRAB-zinc finger gene 1 (Skz1) | ||
| Ets transcription factor PU.1 | SpiB Ets family member | ||
| Transcription factor-like 1 (YL-1, Tcfl1) | Tripartite motif protein 21 (Trim21) | ||
| T-cell leukemia, homeobox 2, hox11L1 (Tlx2) | |||
| Tripartite motif protein 25 (Trim25) | |||
| Ubiquitination | |||
| Autophagy 12-like (Apg121) | WW domain-containing protein 4 (Wwp2) | ||
| Ubiquilin 1 (Ubqln1) | |||
| Ubiquitin-specific protease 15 (Usp15) |
Murine bone marrow CD 19+ . | Murine spleen CD19+ . | Human BJAB + LMP2A . | Human LCL + LMP2A . |
|---|---|---|---|
| Cell cycle/apoptosis | |||
| SH3P9 myc box dependent interacting (Bin1) | SH3P9 myc box-dependent interacting (Bin1) | BTG family, member 3 (Btg3) | ATM kinase |
| Caspase-6 | B-cell translocation gene 2 (Btg2) | Cyclin A2 | RBP-1-like protein (Bcaa) |
| EGL nine homolog 1 (Egln 1) | p53 variant | Cell division cycle 2 (Cdc2) | pptase and tensin (PTEN) |
| Ubiquinol-cytochrome c reductase (Ubcr) | Proline-rich protein expressed in brain (Prtb) | CHK 1 checkpoint homolog (Chek1) | Retinoblastomaa susceptibility (Rbl) |
| Signal-induced proliferation associated (Spa-1) | CDC28 protein kinase 2 (Cks2) | ||
| (tre-2/USP6, BUB2, cdc16) domain (Tbc 1d1) | Defender against cell death 1 (Dad 1) | ||
| Transgene insert site 737 (TgN737) | Programmed cell death 4 (Pdcd4) | ||
| Pituitary tumor-transforming 1 (Pttg 1) | |||
| Ubiquinol-cytochrome C reductase (Ucrq) | |||
| YME1-like 1 (Yme 1I1) | |||
| DNA/RNA metabolism | |||
| Heterogeneous nuclear riboprotein H2 | H1 histone family, member 2 | Eukaryotic translation initiation factor (eIF2s2) | eIF-1A |
| H2B histone family, member S | Polymerase (RNA) II (DNA directed) | Eukaryotic translation initiation factor (eIF4a1) | Histone H2A/g (H2AFG) |
| DNA-binding nuclear protein NP220 | Polymerase (RNA) II (DNA directed) | High-mobility group box 2 (Hmgb2) | Histone H2A.2 (H2AFO) |
| Polymerase (RNA) II (DNA directed) | RAD50 homolog | Heterogeneous nuclear ribonucleoprotein (Hnrph1) | Histone H2A.X (H2AFX) |
| RADI homolog | Rael RNA export 1 homolog | Mitochondrial ribosomal protein 63 | Histone H2B/h |
| Trf-proximal protein homolog (Trfp) | Ribosomal protein L21 | Mitochondrial ribosomal protein L3 | Histone H2B/e |
| Zinc finger protein 292 | Zinc finger protein 36 (TISII) | High mobility group-like nuclear protein (Nhp2) | Histone H2B1 S |
| Zinc finger protein, subfamily 1A, 4 | Polymerase (RNA) II (DNA directed) polypeptide J | Histone H2BFC | |
| DNA repair protein rad18 | Histone H2BFD | ||
| RAD1 homolog | Histone H2B/k (H2BFK) | ||
| RNA-binding region containing (RNPI, RRM) | Histone H2BFL | ||
| Ribosomal protein L26-like 1 | Histone H2BFR | ||
| Ribosomal protein L38 | H4 histone family G (H4FG) | ||
| Zinc finger protein 9 | |||
| Inflammation/immunity | |||
| Colony-stimulating factor 1 receptor (Csf 1r) | Adenosine A2a receptor (Adora2a) | Allograft inflammatory factor 1 (Aif1) | Butyrophilin (BTF4) |
| Deoxynucleotidyltransferase, terminal (TdT) | Complement component 1r | Complement component 1q receptor 1 | CD69 |
| Histocompatibility 2, class II antigen A | CD19 antigen | Complement component 4A | IFN-induced leucine zipper protein 35 (Ifi35) |
| Histocompatibility 2, Q region locus 7 | CD22 antigen | Integrin, beta 2 (LFA-1) | IFN-induced protein 44 (Ifi44) |
| Interferon (alpha and beta) receptor 2 | Histocompatibility 2, D region locus 1 | Ig kappa chain V-I region (Igk) | IgG lambda light chain V-J-C region |
| Germ line immunoglobulin V(H)II gene | Histocompatibility 2, class II, locus DMa | T-cell receptor alpha locus (TCR alpha) | Interleukin-7 (IL-7) |
| Immunoglobulin lambda chain, variable 1 | IFN-γ inducible protein 30 (Ifi30) | Pre-B lymphocyte gene 3 (vpreB) | Interferon regulatory factor 7B (IRF7b) |
| Interleukin-16 (IL-16) | IFN-γ inducible protein (Ifi47) | Interferon-induced protein (IRF4/Pip/Isg15) | |
| Integrin beta 4 binding protein (Itgb4bp) | Delta-immunoglobulin (IgD) | Melanoma antigen rec by T cells (MART-1, Mlana) | |
| Immunoglobulin lambda 5 | IgE Fc receptor, low affinity II, alpha | B-lymphocyte cell-surface antigen B1 (CD20) | |
| Ig B-cell antigen receptor gene (mb-1) | Germ line IgH chain gene, DJC region | 2,5 oligoadenylate synthetase 2 (Oas2) | |
| Q2-k gene for class I antigen (MHC I) | Immunoglobulin heavy chain 6 of IgM | HLA-E, transketolase (Tkt) | |
| Recombinase activating gene-2 (Rag2) | IL-4-induced gene 1 (IL4i1) | Tumor necrosis factor receptor 1b (Tnfrsf1b) | |
| TRAF-interacting protein (Traip) | TNF-beta mRNA, lymphotoxin A | TNFR7, CD27 | |
| Uromodulin (Umod) | Lymphotoxin B | ||
| VpreB | Lymphocyte antigen 9 (Ly9) | ||
| Immunoglobulin-associated alpha (mb-1) | |||
| Myeloid-associated differentiation marker (Myadm) | |||
| TNF receptor superfamily (tnfrsf5, CD40) vpreB | |||
| Signaling | |||
| Raf-related oncogene (A-raf) | Adrenergic receptor, beta 2 (b2ar) | Casein kinase II (CKII) | Calmodulin 1 |
| Cornichon homolog (Cnih) | B lymphoid kinase (Blk) | Developmentally regulated GTP binding protein (Drg1) | Dual-specificity phosphatase 5 (Dusp5) |
| FK506 binding protein 1a (Flb 1a) | Bruton tyrosine kinase (Btk) | Growth factor receptor-bound protein 2 (Grb2) | Inositol 1,4,5 trisphosphate receptor (Itpr1) |
| Guanine nucleotide binding protein, alpha inhibiting (Gnai2) | Adapter protein CIKS (Act 1) | Hyaluronan-mediated motility receptor (RHAMM) | Phosphoinositide-binding protein (Pip3e) |
| Protein phosphatase 1B (Ppm1b) | tyr-thr dual specificity phosphatase PAC-1 (Dusp2) | Protein phosphatase 1, catalytic subunit (PP1) | Cytohesin binding protein HE (Pscdbp) |
| Pleckstrin homology, Sec7 and coiled/coil domain (Pscd3) | Growth hormone (Gh) | Receptor (calcitonin) activity modifying protein (Ramp2) | Ras-associated domain family 2 (Ral GDS/AF-6) |
| Rho interacting protein 3 (Rhoip3) | Glia maturation factor, gamma (Gmfγ) | RAS guanyl releasing protein 1 (Rasgrp1) | Wingless-type MMTV integration site (Wnt6) |
| Sel 1 inhibitor of Notch | Hematopoietic cell phosphatase (SHP) | Ras suppressor protein 1 (Rsp1) | |
| Serine/threonine kinase 10 (LOK, Stk 10) | Interferon regulatory factor 1 (IRF1) | vav 3 oncogene (Vav3) | |
| Spleen tyrosine kinase Syk | Lymphocyte antigen 57 (BLNK) | WW domain binding protein 11 (Wbp11) | |
| TPR-containing, SH2-binding phosphoprotein (Tsp) | Membrane-bound C2 domain containing (Mbc2) | ||
| Membrane-spanning 4-domains (Ms4a4d) | |||
| Nuclear receptor binding protein (Nrbp) | |||
| RAS p21 protein activator 3 (Rasa3) | |||
| Regulator of G-protein signaling 19 (Rgs19) | |||
| Ras-like without CAAX 1 (Rit1) | |||
| Small protein effector 1 of Cdc42 (Spec1) | |||
| SWAP complex protein, 70 kDa (Swap70) | |||
| Tubby-like protein 3 (Tulp3) | |||
| Transcription factors | |||
| E2A transcription factor | B-cell leukemia/lymphoma 6 (Bcl-6) | C-terminal binding protein 1 (CTBP1) | Capicua homolog (Cic) |
| E4F transcription factor 1 (E4f1) | E2A transcription factor | Early growth response 4 (Egr4) | HB9 homeobox transcription factor (H1xb9) |
| Early B-cell factor (EBF) | Early B-cell factor (EBF) | Enhancer of rudimentary homolog (Erh) | Sex comb on midleg-like 2 (Scml2) |
| Early development regulator 2 (Edr2, Mph2) | Kruppel-like factor LKLF mRNA (Kif2) | Nuclear receptor subfamily 4 (Nur77, Nr4a1) | RP58, zinc finger protein (Znf238) |
| E26 avian leukemia oncogene 2 (Ets2) | LIM only 2 (Lmo2) | PBX/knotted 1 homeobox 2 (KN1, Pknox2) | |
| Host cell factor C1 transcription factor (Hcfc1) | Max dimerization protein 4 (Mad4) | Wilms tumor 1-associating protein (Wtap) | |
| Lymphoid enhancer factor-1 (LEF-1) | Nuclear factor of kappa in B cells 2 (Nfkb2) | ||
| Nuclear transcription factor-Y gamma (NF-Yγ) | pax-5 transcription factor | ||
| Pax-5 | SCAN-KRAB-zinc finger gene 1 (Skz1) | ||
| Ets transcription factor PU.1 | SpiB Ets family member | ||
| Transcription factor-like 1 (YL-1, Tcfl1) | Tripartite motif protein 21 (Trim21) | ||
| T-cell leukemia, homeobox 2, hox11L1 (Tlx2) | |||
| Tripartite motif protein 25 (Trim25) | |||
| Ubiquitination | |||
| Autophagy 12-like (Apg121) | WW domain-containing protein 4 (Wwp2) | ||
| Ubiquilin 1 (Ubqln1) | |||
| Ubiquitin-specific protease 15 (Usp15) |
At least 2 separate, identical experiments comparing gene transcription in LMP2A-positive versus LMP2A-negative cells were performed for each cell type. Statistical analyses of the arrays were performed as described in “Materials and methods.” Genes with probability values of less than .01 and differential ratios of less than 1.1 in LMP2A-positive cells compared with LMP2A-negative cells are listed.