Genes with significantly lower average gene expression in AL plasma cells than in MM cells
Gene symbol . | Name of gene . | Genes the focus gene regulates . | Genes by which the focus gene is regulated . | Genes the focus genes binds . | Value of the test statistic . |
|---|---|---|---|---|---|
| MYC* | v-myc myelocytomatosis viral oncogene homolog | CSK2, CDKN1A, NFκB, CDC25A, PDGFRB | RGFB1, IL3, CDKN1B, EPO, KRAS2, RELA | TRADD; RBL1; E2F1, 2, 3, 4, and 5 | –3.78 |
| p53* | Tumor protein p53 | JUN, CDKN1A, IGFBP3, NFκB1, RELA, CREBBP | IL3, ATM, ETS1, NFκB, MAPK8 | MDM2, CREB, CDKN2A, CREBBP | –3.54 |
| E2A* | E2A Ig enhancer binding factor (E12/E47) | CDKN1a, PAX-5, RAG1, VPREB1, CD79A | EBP, PAX3, IL6, PIP, NOTCH1 | HOXB7, HOXB8, HOXA5, MYOG, MYOD1, RB1, EBF | –4.17 |
| XRCC4 | X-ray repair factor 4 | POLM, LIG4 | POLM, KITLG | LIG4, XRCC5, PRKDC, DNA Ligase | –3.43 |
| XRCC5* | Ku 80 | Osteocalcin, DNA-PK, RNA Pol II | LOX, CXCL12, p53, DNA-PK | XRCC4, PCNA, Telomerase | –3.99 |
| TXN | Thioredoxin | VEGF, CD4, PTEN, IL2, NFκB, BCL2, TRAF6 | ILlb, MYC, ATM | CREB3, PTEN, NFκB | –5.88 |
| IL6ST* | IL6 signal transducer | IL6, JUNB, JAK1, 2, STAT1, 3, 5B | TNF, IL6, OSM, IL6R, SOCS | STAT3; SOCS3; IL11; IL6; JAK1, 2; STAT1 | –3.71 |
| TGFB1 | Transforming growth factor B1 | CDK2, CDKN1A, Cyclin D, CDK6, CDKN1B, MYC | IL4, IL13, TNF | TGFBR, EGR1, ITGAV, A2M | –3.21 |
| CASP3* | Caspase 3 | CASP8, 9, BID, CASP6, SSB | AKT1, BID, TNF | CASP1, CDKN1A, BCL2L1, STAT1, CCND3 | –3.00 |
| RELA | NFκB p65 subunit | JUNB, CD86, CD44, TNFRSF5, CCR7, ICAM, BCL2L1, TNFRSF6 | PPARγ, TNF, FADD, TRADD, TNFRSF1A, p53, IKBKB | MMP9, NFKB1A, IFNG, IL6, IL4, IL12B | –3.91 |
| CD47 | CD47 antigen | THBS1, PTPN2 | ERBB2, HOXa11, CSCL12 | UBQLN1, SRC, LICAM | –4.33 |
| CDK4* | Cyclin-dependent kinase 4 | RBL1; CDK2; MYC; RB1; CDKN1B, C; DKN1A; CDK6 | IL4, MYC, CDKN1A, CDKN1B, BCL2, PPAR6, BCL2L1 | PCNA, MDM2, p53, CCND1, CDKN1C, CDKN1A, CDKN1B, CDK6, CCND2 | –4.69 |
| CDK5 | Cyclin-dependent kinase 5 | MYC, JUN, MAPK10, APP | CDK5R1, Laminin 1, PHO80 | CCND1, SET, ACTN1, PHO80 | –3.61 |
| CDK9 | Cyclin-dependent kinase 9 | MYC, RB1, MBP, MYOD1 | Alkaline phosphatase, PTEN, IL6, TAT | TAT, RB1, MYC, RELA, Hsp90, MYOD1, NFκB1 | –4.42 |
| CDC37 | Cell division cycle 37 homolog | CDK4, Hsp90 | CDKN2A, LCK, CCL5 | CCND1, CDK6, Hsp90, TRAF3, SRC, IKBKG | –3.63 |
| CCNB1 | Cyclin B1 | RB1, CDC25A, CDKN1B, p53, GRO | TGFB1, CDC25A, CDKN1A, MYC, PTEN, p53 | CDC2, CDC25A, CDKN1A, RELA, PAP, MYC, ERBB2 | –4.06 |
| PSEN1 | Presenilin 1 | LRP1, APP, Gamma secretase, JUN, CCND1, NOTCH1 | ETS1, p53, PSEN2, CASP3, IL1B, GSK3B | APBA1, APBA2, NOTCH1, APP, Alpha catenin, NOTCH2 and 3 | –3.82 |
| PSEN2 | Presenilin 2 | APP, NOTCH1, ERBB4, BAX, PSEN1, p53, BCL2, CASP3 | PSEN1, p53, CASP3, Ubiquilin, NCSTN | NOTCH1, APP, PEN2, PSEN1, Gamma secretase, PSEN2, BCL2L1 | –3.36 |
| UCHL1 | Ubiquitin carboxyl-terminal esterase L1 | Ubiquitin | HNF4a, MYCN | Ubiquitin, CDKN1B, SNCA | –3.12 |
| PTEN | Phosphatase and tensin homolog | BCL2, CASP3, TNFRSF6, AKT1, CSN2 | ERBB2, BCL2, TGFB1, HBX, EGR1 | MAGI-3, AIP1, TXN, p53 | –3.90 |
Gene symbol . | Name of gene . | Genes the focus gene regulates . | Genes by which the focus gene is regulated . | Genes the focus genes binds . | Value of the test statistic . |
|---|---|---|---|---|---|
| MYC* | v-myc myelocytomatosis viral oncogene homolog | CSK2, CDKN1A, NFκB, CDC25A, PDGFRB | RGFB1, IL3, CDKN1B, EPO, KRAS2, RELA | TRADD; RBL1; E2F1, 2, 3, 4, and 5 | –3.78 |
| p53* | Tumor protein p53 | JUN, CDKN1A, IGFBP3, NFκB1, RELA, CREBBP | IL3, ATM, ETS1, NFκB, MAPK8 | MDM2, CREB, CDKN2A, CREBBP | –3.54 |
| E2A* | E2A Ig enhancer binding factor (E12/E47) | CDKN1a, PAX-5, RAG1, VPREB1, CD79A | EBP, PAX3, IL6, PIP, NOTCH1 | HOXB7, HOXB8, HOXA5, MYOG, MYOD1, RB1, EBF | –4.17 |
| XRCC4 | X-ray repair factor 4 | POLM, LIG4 | POLM, KITLG | LIG4, XRCC5, PRKDC, DNA Ligase | –3.43 |
| XRCC5* | Ku 80 | Osteocalcin, DNA-PK, RNA Pol II | LOX, CXCL12, p53, DNA-PK | XRCC4, PCNA, Telomerase | –3.99 |
| TXN | Thioredoxin | VEGF, CD4, PTEN, IL2, NFκB, BCL2, TRAF6 | ILlb, MYC, ATM | CREB3, PTEN, NFκB | –5.88 |
| IL6ST* | IL6 signal transducer | IL6, JUNB, JAK1, 2, STAT1, 3, 5B | TNF, IL6, OSM, IL6R, SOCS | STAT3; SOCS3; IL11; IL6; JAK1, 2; STAT1 | –3.71 |
| TGFB1 | Transforming growth factor B1 | CDK2, CDKN1A, Cyclin D, CDK6, CDKN1B, MYC | IL4, IL13, TNF | TGFBR, EGR1, ITGAV, A2M | –3.21 |
| CASP3* | Caspase 3 | CASP8, 9, BID, CASP6, SSB | AKT1, BID, TNF | CASP1, CDKN1A, BCL2L1, STAT1, CCND3 | –3.00 |
| RELA | NFκB p65 subunit | JUNB, CD86, CD44, TNFRSF5, CCR7, ICAM, BCL2L1, TNFRSF6 | PPARγ, TNF, FADD, TRADD, TNFRSF1A, p53, IKBKB | MMP9, NFKB1A, IFNG, IL6, IL4, IL12B | –3.91 |
| CD47 | CD47 antigen | THBS1, PTPN2 | ERBB2, HOXa11, CSCL12 | UBQLN1, SRC, LICAM | –4.33 |
| CDK4* | Cyclin-dependent kinase 4 | RBL1; CDK2; MYC; RB1; CDKN1B, C; DKN1A; CDK6 | IL4, MYC, CDKN1A, CDKN1B, BCL2, PPAR6, BCL2L1 | PCNA, MDM2, p53, CCND1, CDKN1C, CDKN1A, CDKN1B, CDK6, CCND2 | –4.69 |
| CDK5 | Cyclin-dependent kinase 5 | MYC, JUN, MAPK10, APP | CDK5R1, Laminin 1, PHO80 | CCND1, SET, ACTN1, PHO80 | –3.61 |
| CDK9 | Cyclin-dependent kinase 9 | MYC, RB1, MBP, MYOD1 | Alkaline phosphatase, PTEN, IL6, TAT | TAT, RB1, MYC, RELA, Hsp90, MYOD1, NFκB1 | –4.42 |
| CDC37 | Cell division cycle 37 homolog | CDK4, Hsp90 | CDKN2A, LCK, CCL5 | CCND1, CDK6, Hsp90, TRAF3, SRC, IKBKG | –3.63 |
| CCNB1 | Cyclin B1 | RB1, CDC25A, CDKN1B, p53, GRO | TGFB1, CDC25A, CDKN1A, MYC, PTEN, p53 | CDC2, CDC25A, CDKN1A, RELA, PAP, MYC, ERBB2 | –4.06 |
| PSEN1 | Presenilin 1 | LRP1, APP, Gamma secretase, JUN, CCND1, NOTCH1 | ETS1, p53, PSEN2, CASP3, IL1B, GSK3B | APBA1, APBA2, NOTCH1, APP, Alpha catenin, NOTCH2 and 3 | –3.82 |
| PSEN2 | Presenilin 2 | APP, NOTCH1, ERBB4, BAX, PSEN1, p53, BCL2, CASP3 | PSEN1, p53, CASP3, Ubiquilin, NCSTN | NOTCH1, APP, PEN2, PSEN1, Gamma secretase, PSEN2, BCL2L1 | –3.36 |
| UCHL1 | Ubiquitin carboxyl-terminal esterase L1 | Ubiquitin | HNF4a, MYCN | Ubiquitin, CDKN1B, SNCA | –3.12 |
| PTEN | Phosphatase and tensin homolog | BCL2, CASP3, TNFRSF6, AKT1, CSN2 | ERBB2, BCL2, TGFB1, HBX, EGR1 | MAGI-3, AIP1, TXN, p53 | –3.90 |
Twenty genes, identified for further analysis from 5 networks using the Ingenuity Analysis software, had lower average expression in patients with AL (or higher average expression in patients with MM). The table is a partial list of dynamic interactions between these 20 focus genes and other genes that critically influence the function of the focus genes. 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 and MM, including MYC, p53, E2A, XRCC5 (Ku 80), IL6-ST, CASP3, and CDK4