Genes with significantly higher average gene expression in AL plasma cells compared to MM
Gene symbol . | Name of gene . | Genes the focus gene regulates . | Genes by which the focus gene is regulated . | Genes the focus gene binds . | Value of the test statistic . |
|---|---|---|---|---|---|
| RARA | Retinoic acid receptor, alpha MMP11, FOS | RXRA, MYOD1, POU1F1, PKC, STAT5B, IL1B | IL3, NCOA3, RXRA, RARB, OXT, MYB | RXRA, NCOA1, NCOR1, 2, | 3.60 |
| RB1/Rb* | Retinoblastoma MAPK8 | HBP1, RNA Pol III, cyclin A, CDKn2A, p53, EGF | E2F1, TGFB1, IL3, BCL2, RBAK, MYC | E2F4; HDAC1, 2, 3; BRCA1 | 3.73 |
| CCND1* | Cyclin D1 CDK4, CCND3, CDKN1A | Cyclin A, RB1 (Rb), CDK2, TNF, CDKN1A, IL3, NFκB, PCNA, TGFBR2 | CDX1, CDKN1B, TGFB1, Rb, ER, CDK6, RELA ubiqultin | CDK4; CDKN1C, B, A; CDK2 | 5.07 |
| CDKN1B | Cyclin-dependent kinase inhibitor 1B | CDK4, CCDN1, IL4, MYC, Rb, CDKN1A | TGFB1, CCNE1, DC, DC25A, IL4, LMP1, MYC, IL3, IL7, p53, BCL2 | CCNA2, YWHAE, GRB2, CCND1, CDK4, XPO1, KIS | 3.95 |
| CDC25B | Cell division cycle 25B | CCND1, CDK2, MYC, Cyclin A, CDC2, p53 | CDKN1A, p53, CDC2, Proteasome | CCNB1, YWHAZ, CDC2 | 3.96 |
| JUN | v-jun sarcoma virus homolog | BCL3, CDKN1A, p53, BAX, MDM2, MSH2, SERPINE1, IGFBP1 | IL6; CEPBA; EGF; IL4; MAPK10; TGFB1, 3 | HOXD12; MMP1; TNFRSF6; ATF2; MAPK8, 9, 10; FOS; PGR | 6.58 |
| MAPK12 | Mitogen-activated protein kinase 12 | TNFSF6, p53, IL2, JUN, TNF, FOS, CCL5, THPO | EGF, TGFB1, CXCL12, VEGF, TNF, IL3, CCL5, THPO | MAP2K4, GRB2, MAP3K1, JUN, ATF2, p53, JUNB | 4.77 |
| RUNX2 | Runt-related transcription factor 2 | FN1, COL1A1, MYOD1, TNFRSF11B, MMP13, TPS1 | BMP2, TGFB1, VEGF, FGF2, TNF, MAPK, IGFBP5, IL7 | MADH3, MADh1, Osteocalcin, JUN, FOS, CEBPA, MMP13 | 3.74 |
| NFκB1A* | Inhibitor of nuclear factor of κ light chain gene enhancer in B cells | NFκB, ICAM1, TNF, CASP3, RELA, RELB | IL1B, TNF, Hsp70, IKBKB, IL2, p53 | MYOD1, RELA, XPO1, RELB, p53, JUN, IKK, IKBKB | 3.29 |
| IGFBP3 | Insulin-like growth factor binding protein 3 | AKT1, BCL2, IGF1R, BAX, BAD, BCL2L1 | IL1b, p53, TGFB1, IL6, EGF, PTEN | IGF2, p53, IGF1R, THBS1 | 5.38 |
| IGFBP5 | Insulin-like growth factor binding protein 5 | AKT, BCL2, CASP3, BCL2L1, Erk 1/2, p 38MAPK, RUNX2 | IGF1, TGFB1, IGFBP3, SERPING1, STAT3, PTEN, AKT1 | IGF1, 2; MYB; MYBL2; SERPINE2 | 3.87 |
| FGFR1 | Fibroblast growth factor receptor 1 | FGFR1, JUN, BMP4, AKT, PLCγ | IL3; FGF2, 1; VEGF; MMP2; CCND1; CDKN2A | FGFR2; FGF1, 7, 4; GRB7; CD44; FGF13 | 3.90 |
| TNFRSF1A | Tumor necrosis factor receptor superfamily 1A | CASP3, NFκB, IL1B, CXCL12, TNF, VEGF, TGFB1 | IFNγ, TNF, TRADD, TRAD2, p53, RELB | TRAF1, TRAF2, JAK1, JAK2, TNF, TRADD, FADD, DAXX, STAT1 | 3.78 |
| PDGRFB | Platelet derived growth factor receptor, beta polypeptide | SRC, SYK, FOS, PIP3K, Vav, PKC | FN1, GPCR, MYC, KRAS2 | PIK3R1, PDGFRA, PI3K, STAT5, GPRK2L | 3.53 |
| BCL6 | B-cell CLL/Lymphoma 6 | BAX; p38MAPK; BCL2; CCL-2, 6, and 7 | BCL6, MYOD1, MAPK | IRF4, JUN, BCL11A, BCL2L1 | 3.40 |
| APOE | Apolipoprotein E | APP, Fibrin, Ig, HMOX1, PPARγ, MMP9, CREB1 | APP, APOA1, RXRA, IL1B, LPL | APP, APOA1, LPL, TAU40, SERPINA3C | 4.82 |
| CD36 | Thrombospondin receptor | INS1 PPARγ, PPARα, CYCL12 | TGFB1, IL4, NFκB, IL6, | FYN, LYN, CD9, ITGB1, ITGA3 | 4.54 |
| CD44 | CD44 antigen | MMP9, FGFR1, LYN, MMP7, ETV5 | NFκB, MYC, THPO, JUN, IGF1, TNF, OSM, KRAS2 | GRB2, LCK, FYN, FGFR1, RELA, FN1 | 3.19 |
| CXCL12* | SDF-1 | AKT, ERK 1/2LCK, JAK1, JAK3, STAT3, STA5B, PI3K | TNF, TAT, KRAS2, MMP2, TGFB1, VEGF, MMP9, MMP1 | CXCR4, MMP2, FN1 | 5.95 |
| HMOX1 | Heme Oxygenase 1 | MAPK1, HMOX1, TNF, IL6 | TGFB1, IL1B, IL10, TNF | APP, NFκB, Ap2 | 4.12 |
| DCN | Decorin | ERBB3, ERBB4, CDKN1A, CDKN1B, Cyclin A, VEGF, AKT1, TGFB | LPL; TNF; DES; MMP2, 3, 7, 9; TGFB1; IL10; IL1B | WISP1, EGFR, Collagen, TNX, C1QA, Apoa | 3.94 |
| BTRC | Beta-transducin repeat containing | NFκB1A, NFκBIB, IκBKE, ATF4 | TNF, IκBKB, NFκBIA | NFκBIA, NFκB1, ATF4, UBQLN2, TNFRSF5 | 4.28 |
| APP | Amyloid beta (A4) precursor protein, appican | APOE, CACNL, CASP9, TNF, MMP9, SPNA2 | APOA1, SERPINA1, CASP8, APOE, PSEN1, TNF, IL1B | PSEN1, RXRA, APOA1, APBA2, LRP1 | 3.72 |
| A2M | Alpha 2-macroglobulin | IGFBP1, APP, PDGRFB, CREB1 | LIF, IL6, INS1, APP, IL1B, STAT3 | VEGF, APOE, IL2, IL6, TGFB1 | 3.91 |
| SERPINA1 | Serine proteinase inhibitor (α-anti-trypsin) | CCL2, IL2, APP, TGFB1, PDGF, NFκB | MMP9, ELA2, Proteasome, XBP1, PPARγ, MMP1 | NR5A2, CANX, ELA2, HSPA5 | 5.24 |
| TNFRSF6 | Tumor necrosis factor receptor superfamily, 6 | CASP3, CASP8, CASP9, NFκB1, MAPK8, TNFSF6, BID | IFNg, IL15, PTEN, TNF, MYC, NFκB, p53, IL10, LMP1 | TNFSF6, JUN, STAT3, p53, FADD, CASP10 TRADD | 4.49 |
Gene symbol . | Name of gene . | Genes the focus gene regulates . | Genes by which the focus gene is regulated . | Genes the focus gene binds . | Value of the test statistic . |
|---|---|---|---|---|---|
| RARA | Retinoic acid receptor, alpha MMP11, FOS | RXRA, MYOD1, POU1F1, PKC, STAT5B, IL1B | IL3, NCOA3, RXRA, RARB, OXT, MYB | RXRA, NCOA1, NCOR1, 2, | 3.60 |
| RB1/Rb* | Retinoblastoma MAPK8 | HBP1, RNA Pol III, cyclin A, CDKn2A, p53, EGF | E2F1, TGFB1, IL3, BCL2, RBAK, MYC | E2F4; HDAC1, 2, 3; BRCA1 | 3.73 |
| CCND1* | Cyclin D1 CDK4, CCND3, CDKN1A | Cyclin A, RB1 (Rb), CDK2, TNF, CDKN1A, IL3, NFκB, PCNA, TGFBR2 | CDX1, CDKN1B, TGFB1, Rb, ER, CDK6, RELA ubiqultin | CDK4; CDKN1C, B, A; CDK2 | 5.07 |
| CDKN1B | Cyclin-dependent kinase inhibitor 1B | CDK4, CCDN1, IL4, MYC, Rb, CDKN1A | TGFB1, CCNE1, DC, DC25A, IL4, LMP1, MYC, IL3, IL7, p53, BCL2 | CCNA2, YWHAE, GRB2, CCND1, CDK4, XPO1, KIS | 3.95 |
| CDC25B | Cell division cycle 25B | CCND1, CDK2, MYC, Cyclin A, CDC2, p53 | CDKN1A, p53, CDC2, Proteasome | CCNB1, YWHAZ, CDC2 | 3.96 |
| JUN | v-jun sarcoma virus homolog | BCL3, CDKN1A, p53, BAX, MDM2, MSH2, SERPINE1, IGFBP1 | IL6; CEPBA; EGF; IL4; MAPK10; TGFB1, 3 | HOXD12; MMP1; TNFRSF6; ATF2; MAPK8, 9, 10; FOS; PGR | 6.58 |
| MAPK12 | Mitogen-activated protein kinase 12 | TNFSF6, p53, IL2, JUN, TNF, FOS, CCL5, THPO | EGF, TGFB1, CXCL12, VEGF, TNF, IL3, CCL5, THPO | MAP2K4, GRB2, MAP3K1, JUN, ATF2, p53, JUNB | 4.77 |
| RUNX2 | Runt-related transcription factor 2 | FN1, COL1A1, MYOD1, TNFRSF11B, MMP13, TPS1 | BMP2, TGFB1, VEGF, FGF2, TNF, MAPK, IGFBP5, IL7 | MADH3, MADh1, Osteocalcin, JUN, FOS, CEBPA, MMP13 | 3.74 |
| NFκB1A* | Inhibitor of nuclear factor of κ light chain gene enhancer in B cells | NFκB, ICAM1, TNF, CASP3, RELA, RELB | IL1B, TNF, Hsp70, IKBKB, IL2, p53 | MYOD1, RELA, XPO1, RELB, p53, JUN, IKK, IKBKB | 3.29 |
| IGFBP3 | Insulin-like growth factor binding protein 3 | AKT1, BCL2, IGF1R, BAX, BAD, BCL2L1 | IL1b, p53, TGFB1, IL6, EGF, PTEN | IGF2, p53, IGF1R, THBS1 | 5.38 |
| IGFBP5 | Insulin-like growth factor binding protein 5 | AKT, BCL2, CASP3, BCL2L1, Erk 1/2, p 38MAPK, RUNX2 | IGF1, TGFB1, IGFBP3, SERPING1, STAT3, PTEN, AKT1 | IGF1, 2; MYB; MYBL2; SERPINE2 | 3.87 |
| FGFR1 | Fibroblast growth factor receptor 1 | FGFR1, JUN, BMP4, AKT, PLCγ | IL3; FGF2, 1; VEGF; MMP2; CCND1; CDKN2A | FGFR2; FGF1, 7, 4; GRB7; CD44; FGF13 | 3.90 |
| TNFRSF1A | Tumor necrosis factor receptor superfamily 1A | CASP3, NFκB, IL1B, CXCL12, TNF, VEGF, TGFB1 | IFNγ, TNF, TRADD, TRAD2, p53, RELB | TRAF1, TRAF2, JAK1, JAK2, TNF, TRADD, FADD, DAXX, STAT1 | 3.78 |
| PDGRFB | Platelet derived growth factor receptor, beta polypeptide | SRC, SYK, FOS, PIP3K, Vav, PKC | FN1, GPCR, MYC, KRAS2 | PIK3R1, PDGFRA, PI3K, STAT5, GPRK2L | 3.53 |
| BCL6 | B-cell CLL/Lymphoma 6 | BAX; p38MAPK; BCL2; CCL-2, 6, and 7 | BCL6, MYOD1, MAPK | IRF4, JUN, BCL11A, BCL2L1 | 3.40 |
| APOE | Apolipoprotein E | APP, Fibrin, Ig, HMOX1, PPARγ, MMP9, CREB1 | APP, APOA1, RXRA, IL1B, LPL | APP, APOA1, LPL, TAU40, SERPINA3C | 4.82 |
| CD36 | Thrombospondin receptor | INS1 PPARγ, PPARα, CYCL12 | TGFB1, IL4, NFκB, IL6, | FYN, LYN, CD9, ITGB1, ITGA3 | 4.54 |
| CD44 | CD44 antigen | MMP9, FGFR1, LYN, MMP7, ETV5 | NFκB, MYC, THPO, JUN, IGF1, TNF, OSM, KRAS2 | GRB2, LCK, FYN, FGFR1, RELA, FN1 | 3.19 |
| CXCL12* | SDF-1 | AKT, ERK 1/2LCK, JAK1, JAK3, STAT3, STA5B, PI3K | TNF, TAT, KRAS2, MMP2, TGFB1, VEGF, MMP9, MMP1 | CXCR4, MMP2, FN1 | 5.95 |
| HMOX1 | Heme Oxygenase 1 | MAPK1, HMOX1, TNF, IL6 | TGFB1, IL1B, IL10, TNF | APP, NFκB, Ap2 | 4.12 |
| DCN | Decorin | ERBB3, ERBB4, CDKN1A, CDKN1B, Cyclin A, VEGF, AKT1, TGFB | LPL; TNF; DES; MMP2, 3, 7, 9; TGFB1; IL10; IL1B | WISP1, EGFR, Collagen, TNX, C1QA, Apoa | 3.94 |
| BTRC | Beta-transducin repeat containing | NFκB1A, NFκBIB, IκBKE, ATF4 | TNF, IκBKB, NFκBIA | NFκBIA, NFκB1, ATF4, UBQLN2, TNFRSF5 | 4.28 |
| APP | Amyloid beta (A4) precursor protein, appican | APOE, CACNL, CASP9, TNF, MMP9, SPNA2 | APOA1, SERPINA1, CASP8, APOE, PSEN1, TNF, IL1B | PSEN1, RXRA, APOA1, APBA2, LRP1 | 3.72 |
| A2M | Alpha 2-macroglobulin | IGFBP1, APP, PDGRFB, CREB1 | LIF, IL6, INS1, APP, IL1B, STAT3 | VEGF, APOE, IL2, IL6, TGFB1 | 3.91 |
| SERPINA1 | Serine proteinase inhibitor (α-anti-trypsin) | CCL2, IL2, APP, TGFB1, PDGF, NFκB | MMP9, ELA2, Proteasome, XBP1, PPARγ, MMP1 | NR5A2, CANX, ELA2, HSPA5 | 5.24 |
| TNFRSF6 | Tumor necrosis factor receptor superfamily, 6 | CASP3, CASP8, CASP9, NFκB1, MAPK8, TNFSF6, BID | IFNg, IL15, PTEN, TNF, MYC, NFκB, p53, IL10, LMP1 | TNFSF6, JUN, STAT3, p53, FADD, CASP10 TRADD | 4.49 |
Twenty-six genes, identified for further analysis from 5 networks using the Ingenuity Analysis software, had higher average expression in patients with AL. The table shows a partial list of dynamic interactions between these 26 focus genes and other genes that critically influence their function. The value of the test statistic is shown as a comparison of AL and MM plasma cells.
Genes in these rows may be particularly relevant to the pathogenesis of AL, including RB, CCND1, NFκB1A, and CXCL12