Table III.
The summary of microarray data analysis results.
| Comparison | The smallest adjusted p-value (top gene) | The no. of DEGs (over-/underexpressed) | Overexpressed genes | Underexpressed genes |
|---|---|---|---|---|
| AML-PBMC vs. AML-BMMC | 0.11 (FAS) | 0 | FAS, DUSP2 | PRG1, THY1, STAT4, CTSG, CCL7, PRG2, SRGN, SRP9 |
| AML vs. HV | 1.67×10−10 (STMN1) | 163 (85/78) | Genes from Table IV, and ABL1, BCR, CBL, CCL24, CCND1, CCND2, CCNDBP1, CCR10, CD34, CD38, CDKN1A, CFL1, CLU, CTSG, DNAJB4, DNMT3B, GAB1, GSTP1, HOXB5, HOXC8, HPH, HSPA4L, IFNGR2, INPP5D, IRS2, JUNB, METTL3, MME, MT1H, NUP98, PHB2, PPIF, PRG2, RAF1, RHOH, SLC25A1, SLC7A5, SLITRK6, SMAD3, TLE1, TRAF4, ZEB2 | Genes from Table IV, and AIF1, CBFB, CRIP2, CSF3, CYBB, DRAP1, E2F1, FAS, FOSB, GDI1, HIF1A, HLA-DPA1, HLA-DRB1, IGHM, IL12B, KDR, LGALS3, MLLT10, MTMR11, MYLPF, NFKB2, PAK1, PHB2, PROCR, RHAG, S100A8, SHC1, SLC29A1, SULT1E1, TNFRSF10A, XCL1, XCR1, ZFP36 |
| AML-M1 vs. AML-M2 | 0.35 (IL5B) | 0 | IL5B, CASP2, LCP1, FLT3, BIRC2 | PRG1, CST7, MAPK6, SRGN, CTSG |
| AML-M1 vs. AML-M2a | 0.11 (CASP2) | 0 | CASP2, IL5B, BIRC2, FLT3, TPM1 | PRG1, CST7, MAPK6, CTSG, SRGN |
| AML-M1 vs. HV | 2.84×10−08 (STMN1) | 53 (28/25) | Set 1, and ARHGEF12, ERCC2, HSP90AB1, HSPA8, HSPA9, IGFBP7, ANGTP1, INPP5D, ITGB4, KIT, KITLG, MN1, MYB, RHOH | Set 3, and BIRC3, BTG1, CCL5, FCER1G, HCK, IFNA1, LYZ, NFKBIA, PGK1, S100A9, ACTB, CST7, LBD1 |
| AML-M2 vs. HV | 2.09×10−09 (STMN1) | 146 (74/72) | Set 2, and ABCF1, ABL1, ANGTP1, ARF1, ATP6V0C, BCR, CBL, CCL24, CCND2, CCR10, CD34, CDKN1A, CFL1, CTSD, CTSG, DNAJB4, DNMT3B, ETV6, GAB1, GAL, GAPDH, HIGD1A, HPH, HSPA4L, HSPD1, IFNGR2, ITGB4, KIT, KITLG, MAP7, METTL3, MME, MN1, MPO, MYB, MYH9, NPM1, PHB2, PPIF, PRG1, PRG2, RAF1, SLC7A5, SMAD3, TUBB, ZEB2 | Set 4, and BTG1, FCER1G, HCK, HLA-DPB1, PGK1, PLBD1, CBFB, CD44, CD52, CD74, CRIP2, CX3CR1, CYP2E1, DRAP1, FAS, HIF1A, HLA-DRB1, IGHM, JUN, KDR, LCP1, LGALS3, MLLT10, MYLPF, NFKB2, PAK1, PROCR, PTPRE, PXN, RARA, RHAG, RHOB, SLC29A1, SPTBN1, STAT5B, STAU2, SULT1E1, TNFRSF10B, TNFSF10, XCR1, ZFP36 |
| RUNX1/RUNX1T1+ | 1.75×10−06 (STMN1) | 13 (7/6) | STMN1, CDK6, MYC, RPLP0, MPO, HSPA8, ATP6V0C | TMSB4X, LTB, IFITM1, PF4, FCN1, CD44 |
| AML vs. HV FLT3+ AML vs. HV |
3.32×10−07 (CDK6) | 17 (10/7) | CDK6, STMN1, RPLP0, ANGTP1, SET, MCM5, ENO1, RASSF5, DNTT, MYL9 | TRADD, TMSB4X, CAPN10, LTB, PDGFRB, XBP1, SPTBN1 |
| NPM1+ AML vs. HV | 7.35×10−07 (STMN1) | 97 (50/47) | Set 2, and ABCF1, AK2, ANGTP1, ARHGAP4, BCR, DAD1, GAB1, GAL, GAPDH, HSPA1A, HSPD1, IFNGR2, ITGB4, MAP7, MN1, NPM1, NUP98, PRG1, RHOH, SLC25A1, TRAF2, TUBB | Set 4, and HCK, HLA-DPB1, PGK1, PLBD1, CD52, CEBPB, CYBB, FOSB, GJB1, IL12B, IL9, PAK1, PRODH, PTPRE, SPTBN1, SWAP70 |
| CR AML vs. HV | 4.44×10−09 (STMN1) | 74 (31/43) | Set 1, and ADRA2C, HSP90AB1, HSPA8, HSPA9, IGFBP7, ANGTP1, ATP6V0C, GAL, GAPDH, HOXB5, HPH, ITGB4, KIT, MT1H, MYB, PRTN3, TUBB | Set 3, and ADD3, BTG1, CCL3, CCL5, CSF3R, FCER1G, HCK, HLA-DPB1, IFNA1, LYZ, NFKBIA, PLBD1, S100A9, XBP1, AGPAT1, AIF1, BIRC3, CBFB, CD74, CX3CR1, CYP2E1, HIF1A, PTPRE, RARA, RHOB, S100A8, SPTBN1, STAT5B, SULT1E1, TNFSF10 |
| RES AML vs. HV | 7.98×10−07 (STMN1) | 84 (41/43) | Set 2, and ABL1, ARF1, CBL, CD38, CDKN1A, DNAJB4, KIT, MYH9, PRG1, SMAD3, TBL1X, TLE1, TRAP1 | Set 3, and ADD3, BIRC3, CSF3, DUSP2, FCER1G, HLA-DPB1, IGF1, PGK1, PIM1, PLBD1, STK4, XBP1, CRIP2, CYP2E1, DRAP1, GDI1, HLA-DRB1, HOXA3, IGHM, IL8, KDR, MLLT10, NFKB2, PAK1, PXN, RARA, SLC29A1, STAU2, SWAP70, TNFSF10, XCR1 |
| X AML vs. HV | 5.57×10−07 (STMN1) | 79 (37/42) | Set 1, and ARHGEF12, ERCC2, HOXA10, HSPA8, IGFBP7, MYH11, PDE3B, PRKAR1B, ZNF22, ANGTP1, CD81, FUS, GAB1, HSPD1, IFNGR2, KIT, KITLG, MAP7, MN1, MYB, NPM1, RHOH, TUBB | Set 4, and BTG1, FCER1G, CD74, FOSB, IGHM, IL12B, PRAME, PXN, TIPARP, TNFRSF10A, ZFP36 |
| RUNX1/RUNX1T1+ AML vs. remaining AML | 0.99 (TERT) | 0 | TERT, MPO, OGFR, STK32B, CST7, IL5RA, SPI1, PLXNC1 | HPRT1, PML |
| RUNX1/RUNX1T1+ AML vs. remaining AMLa | 0.96 (HPRT1) | 0 | MPO, CXCL2, IL5RA, OGFR, STK32B, CST7, TERT, PLXNC1, SWAP70 | HPRT1 |
| FLT3+ AML vs. remaining AML | 0.48 (VIM) | 0 | VIM, DNTT, CDK6, CEACAM6 | IL4, G6PD, PSMA6, PMAIP1, TRADD, TUBB4 |
| FLT3+ AML vs. remaining AMLa | 0.088 (CDK6) | 0 | CDK6, VIM, CEACAM6, DNTT, CASP3 | PMAIP1, IL4, G6PD, MKI67, CDKN2A |
| NPM1+ AML vs. remaining AML | 0.99 (FOSB) | 0 | ANXA8, TRAF2, NAP1L1 | FOSB, HLA-DPA1, STOM, KLF4, MLLT1, PRODH, EBF1 |
| NPM1+ AML vs. remaining AMLa | 0.9 (FOSB) | 0 | TRAF2, ANXA8, RHOH, PGK2, HSPA1A | FOSB, KLF4, HLA-DPA1, EBF1, MLLT1 |
| NPM1+/FLT3+ AML vs. remaining AML | 0.26 (CPA3) | 0 | CPA3, CCL17, HOXA5, PLCG1, ANXA1, CLEC2B, TUBA1A, CCNG2, VIM | RTN2 |
| NPM1+/FLT3+ AML vs. remaining AMLa | 0.043 (CPA3) | 1 | CPA3, (CASP3, PKN2, CCL17, CLEC2B, PBX3, RB1) | PMAIP1, RTN2, LTA |
| NPM1+/FLT3− AML vs. remaining AML | 0.79 (TRAF2) | 0 | TRAF2, ANXA8, ITGB4, HSPA9, BCR, MYL9, RHOH | PRODH, GTF2E2, STOM |
| NPM1+/FLT3− AML vs. remaining AMLa | 0.28 (TRAF2) | 0 | TRAF2, RHOH, SLC25A1, ANXA8, NONO, ITGB4, ABCF1, BCR, MYL9 | PRODH |
| NPM1−/FLT3+ AML vs. remaining AML | 0.63 (PSMA6) | 0 | PTK7, SRP9, DNAJB5, CD247 | PSMA6, NUP88, CANX, NUBPL, BUD31, CASP2 |
| NPM1−/FLT3+ AML vs. remaining AMLa | 0.36 (CASP2) | 0 | PTK7, CDK6, CEACAM6, FGF13 | CASP2, APOC1, PSMA6, NUP88, NUBPL, CANX |
| NPM1+/FLT3− AML vs. NPM1−/FLT3+ AML | 0.77 (CANX) | 0 | CANX, PSMA6, NUP88, ITGB4, G6PD, TRAF2 | DNAJB5, CEACAM6, PTK7, CEBPB |
| NPM1+/FLT3− AML vs. NPM1−/FLT3+ AMLa | 0.42 (CDK6) | 0 | CASP2, CANX, APOC1, TRAF2, HSPA8, PSMA6 | CDK6, CEACAM6, PTK7, DNAJB5 |
| NPM1+/FLT3− AML vs. NPM1+/FLT3+ AML | 0.56 (RTN2) | 0 | RTN2, IL4, PKLR | CPA3, CCL17, PLCG1, GTF2E2, ITGA4, CCL1, RNH1 |
| NPM1+/FLT3− AML vs. NPM1+/FLT3+ AMLa | 0.17 (PMAIP1) | 0 | PMAIP1, RTN2, IL4 | CPA3, PRKCQ, CCL17, CCL1, PKN2, CASP3, PLCG1 |
| NPM1−/FLT3+ AML vs. NPM1+/FLT3+ AML | 0.83 (DNAJB5) | 0 | DNAJB5, FGF13, CD247 | APOC1, NUBPL, PKN2, NAP1L1 FOXP1, CCL17, BUD31 |
| NPM1−/FLT3+ AML vs. NPM1+/FLT3+ AMLa | 0.09 (PKN2) | 0 | DNAJB5, FGF13, ABR | PKN2, APOC1, CPA3, CASP2, NUBPL, JUN, CCL1 |
| CR AML vs. RES AML | 0.52 (TRAP1) | 0 | GAPDH, HOP, TERT, PXN, MT1H | TRAP1, NFKBIA, ABL1, AGPAT1, NUBPL |
| CR AML vs. RES | 0.46 (GAPDH) | 0 | GAPDH, MT1H, TERT, TUBA1 | NFKBIA, NUBPL, TRAP1, TBL1X, CFLAR, PRDX2 |
| CR AML vs. X AML | 0.72 (ARHGEF12) | 0 | PRAME, ROBO1, RBPMS, TERT | ARHGEF12, MEIS1, PTPN6, EPHB2, ANXA8, AVEN |
| CR AML vs. X AMLa | 0.71 (MEIS1) | 0 | PRAME, ROBO1, IGHM, IL6 | MEIS1, ARHGEF12, ERCC2, PTPN6, CFLAR, HIF1A |
| RES AML vs. X AML | 0.98 (AZU1) | 0 | AZU1, LYZ, SIRPA, STOM, GP1BB, TOP2B, HPH | MAFB, MLLT10, CACNA2D2 |
| RES AML vs. X AMLa | 0.95 (AZU1) | 0 | AZU1, HPH, TOP2B, SIRPA, CD7 | CD81, CACNA2D2, MLLT10, MAFB, BIRC2 |
| CR_long AML vs. CR_short AML | 0.98 (CAST) | 0 | CAST, BIRC5, MAF, FBXL10, PTPRC, SHQ1, MYH11, NPM1 | CRIP2, CREBBP |
| CR_long AML vs. CR_short AMLa | 0.98 (CRIP2) | 0 | CAST, BIRC5, MAF, HMGA2, MCM3, SHQ1, PTPRC | CRIP2, ID1, SQSTM1 |
a
The analysis repeated with AML samples only (without HV). All analyses were performed with the use of Bioconductor limma package and linear models. Differentially expressed genes (DEGs) were identified with a significance level of α 0.05. p-values were corrected for multiple testing. When no statistically significant genes were identified in a comparison, the table includes the top 10 genes ranked according to p-value (in parentheses). The sets of genes common for multiple comparisons - set 1: CDK6, CEBPA, EEF1G, ENO1, GSN, HOXB6, KRAS, MCM5, MYC, PKM2, RASSF5, RPLP0, SET, STMN1 (14 overexpressed genes common for 7 comparisons); set 2: set 1 and ADRA2C, ARHGEF12, ERCC2, HOXA10, HSP90AB1, HSPA8, HSPA9, IGFBP7, JUNB, MYH11, PDE3B, PRKAR1B, SRGN, ZNF22 (28 overexpressed genes common for 4 comparisons); set 3: B2M, CAPN10, CCL19, FCN1, HOXA9, IFITM1, LTB, MAP4K2, PDGFRB, PF4, TMSB4X, TRADD (12 underexpressed genes common for 7 comparisons); set 4: set 3 and ADD3, BIRC3, CCL3, CCL5, CSF3, CSF3R, DUSP2, E2F1, HLA-DPA1, IFNA1, IGF1, LYZ, NFKBIA, PIM1, RALGDS, S100A9, SHC1, STK4, XBP1 (31 underexpressed genes common for 4 comparisons).