Table 2.
Significantly differentially expressed genes between Mychigh and Myclow DLBCL (wild-type [WT] or mutated [MUT])
| WT-Mychigh versus WT-Myclow | MUT-Mychigh versus MUT-Myclow | ||||
|---|---|---|---|---|---|
| Functional categories |
Overall DLBCL (FDR < 0.01) |
GCB-DLBCL (FDR < 0.25) |
ABC-DLBCL (FDR < 0.05) | Overall DLBCL (FDR < 0.05) |
GCB-DLBCL (FDR < 0.25) |
| Signaling |
PAK1IP1 ↑ DIP2A ↓ |
VWCE ↑ RGS8 ↑ RANBP1 ↑ LRP5 ↑ TBC1D30 ↑ SLC6A2 ↑ SOSTDC1 ↑SKI ↓ IL10RA ↓ RAP2C ↓ ATXN1 ↓ IQSEC1 ↓ SOS2 ↓ TNFRSF25 ↓ |
ARHGAP24 ↑ VSNL1 ↑ ZDHHC21 ↑ PTPN11 ↑ LYN ↑ C9orf100 ↑ PAK1IP1 ↑ YWHAG ↑ TRIB3 ↑ GNB2L1 ↑ INVS ↑ TTC1 ↑ CSNK2A2 ↑ PIK3R2 ↑ ARHGAP25 ↑ FYN ↓ PRKCH ↓ CMTM3 ↓ DLG3 ↓ PSG1 ↓ TRPM8 ↓ |
DEPDC1 ↑ RITA1 ↑CXCL12 ↓ |
RITA1 ↑ PRSS12 ↑ SAFB ↑ TNKS ↑ MAP3K4 ↑TRAF7 ↑IL6ST ↓ CDGAP ↓ FYB ↓ PLXND1 ↓ |
|
Cell proliferation, cell cycle, DNA repair, gene expression regulation, ribosome biogenesis, DNA/RNA metabolisms, microRNA, differentiation |
MYC ↑ RUVBL2 ↑ CIRH1A ↑ RPLP0 ↑ MIR17HG ↑ BZW2 ↑ MATR3 ↑ NOP16 ↑ WDR12 ↑ APITD1 ↑ ANP32A ↑ MRPL3 ↑ EEF1B2 ↑ POLR1B ↑ EEF1E1 ↑ RPS21 ↑ FARSB ↑ MRPS33 ↑ GAR1 ↑ POLR1C ↑ STAT3 ↑ DDX21 ↑ NOP2 ↑ UTP20 ↑ MRPS12 ↑ RCL1 ↑ POLR3G ↑ MKI67IP ↑ MINA ↑ GTF2E2 ↑ PRMT1 ↑ NAT10 ↑ PRMT5 ↑ EXOSC2 ↑ APEX1 ↑ PA2G4 ↑ EIF3B ↑ PRPF4 ↑PHF1 ↓ |
MYC ↑ SMARCA4 ↑ RPS21 ↑ TTF2 ↑ BZW2 ↑ MKI67IP ↑ MARS2 ↑ PHB ↑ CAPRIN1 ↑ RPS16 ↑ TFDP1 ↑ EIF3B ↑ EXOSC2 ↑ EIF5A ↑ PPRC1 ↑ SLC29A2 ↑ MIR155HG ↓ TIAL1 ↓ ZBTB4 ↓ CDKN1B ↓ MBD5 ↓ ANKRD12 ↓ |
CDCA7L ↑ HNRNPA1 ↑ RUVBL2 ↑ MAD2L1 ↑ MIS18A ↑ ERCC1 ↑ RPLP0 ↑ RPS15 ↑ DCAF13 ↑ PRMT5 ↑ MYC ↑ CIRH1A ↑ RPSA ↑ EEF1E1 ↑ GINS1 ↑ LRPPRC ↑ ZNF410 ↑ RPLP1 ↑ ZWINT ↑ PABPC1 ↑ ADSL ↑ SPIB ↑ PDCD2L ↑ TOP2A ↑ TRMT10C ↑ IARS2 ↑ MRPL47 ↑ PRKDC ↑ GAR1 ↑ NOP16 ↑ MKI67IP ↑ RPL13A/RPL13AP5/RPL13AP6 ↑ URI1 ↑ KARS ↑ TLK1 ↑ ARPP19 ↑ ESPL1 ↑ POLR1B ↑ DDX21 ↑ TRIP13 ↑ POLR3E ↑ PRIM1 ↑ RPS19 ↑ ZNF22 ↑ RPL13A ↑ HELLS ↑ MATR3/SNHG4 ↑ TAF5 ↑ WDR12 ↑ TFAM ↑ ANP32A ↑ BZW2 ↑ NOP56 ↑ MRPL32 ↑ POLG ↑ UTP20 ↑ EIF3M ↑ CHEK1 ↑ NOLC1 ↑ GTF2E2 ↑ RPL17 ↑ HAUS6 ↑ NOP2 ↑ IRF2BP2 ↑ DENR ↑ PURB ↑ MIS18A ↑ SFRS1 ↑ HIVEP1 ↑ MTPAP ↑ EIF2A ↑ CNP ↑ CDCA5 ↑ RPL24 ↑ HNRNPA0 ↑ FANCI ↑ CDK1 ↑ ZNF511 ↑ MRPS12 ↑ GUF1 ↑ FARSB ↑ RPS3A ↑ MINA ↑ NAP1L1 ↑ EIF4B ↑ MRPL4 ↑ TARBP1 ↑ PRMT1 ↑ RPS16 ↑ NUP93 ↑ POLR1C ↑ HNRNPL ↑ BXDC2 ↑ SPAG5 ↑ NUP205 ↑ FTSJ1 ↑ RPA3 ↑ LUC7L3 ↑ DDX39 ↑ NR2C2AP ↑ DDX18 ↑ RPL37A ↑ DENR ↑ PQBP1 ↑ RPS2 ↑ RAD50 ↑ MTA1 ↑ RPS29 ↑ BARD1 ↑ MIS18A ↑ EXOSC8 ↑ EIF4B ↑ RPL4 ↑ ZNF274 ↑ XPOT ↑ MRPS16 ↑ RPS6KB1 ↑ APEX1 ↑ NAT10 ↑ PTBP1 ↑ POLB ↑ ZNF131 ↑ RPS17 ↑ TEFM ↑ TRMT61B ↑ NCBP2 ↑ DCP1A ↑ RPL38 ↑ MRPS22 ↑ DBF4 ↑ RPS13 ↑ DIMT1L ↑ KANSL2 ↑ RPS28 ↑ PLRG1 ↑ RPP40 ↑ ZNF805 ↑ HAUS4 ↑ CEP295 ↑ KIF23 ↑ EEF2 ↑ RFC1 ↑PATL2 ↓ ARNT ↓ NFATC3 ↓ PHF1 ↓ C19orf40 ↓ ASXL3 ↓ |
MYC ↑ ELAC2 ↑ SRPK1 ↑ EZH2 ↑ CIRH1A ↑ MATR3 ↑ RPS10 ↑ SLC25A33 ↑ RPL5 ↑ DDX21 ↑ EIF3M ↑ TTF2 ↑ SUV39H2 ↑ NOLC1 ↑ MRPL3 ↑ NOP56 ↑ SERBP1 ↑ MIR17HG ↑ NOP58 ↑ ZNF131 ↑ RPS10 ↑ CBX3 ↑ PMS1 ↑ HELLS ↑ EIF2S1 ↑ ZNF138 ↑ RBMX ↑ RRS1 ↑ BUB3 ↑ RPL36A ↑ RPS13 ↑ FARSB ↑ RP9 ↑ RPL5 ↑ RPS10 ↑ TIMELESS ↑ PTCD1 ↑ HNRNPA1 ↑ CCND2 ↓ NR2F2 ↓ JUND ↓ |
BACH2 ↑ MORF4L2 ↑ ZNF675 ↑ ZBTB3 ↑ TTF2 ↑ ZNF331 ↑ CDK1 ↑ ZNF138 ↑ CNOT1 ↑ RBMX ↑ ZNF780B ↑ RPL15 ↑ SKA3 ↑ MRGBP ↑ ZNF480 ↑ HMGA1 ↑ DDX51 ↑ RPS2 ↑ ATRX ↑ RRP36 ↑ STRA13 ↑ COMMD5 ↑ ZBED3 ↑ KHSRP ↑ MRPL19 ↑ NUP54 ↑ ZNF215 ↑ RPL37A ↑ TAF13 ↓ STAT3 ↓ PARP14 ↓ CCND1 ↓ MARCA2 ↓ ZNF205 ↓ CSRP2 ↓ |
| Metabolism |
TMEM97 ↑ CYB5R2 ↑ LDHB ↑ NME1 ↑ NDUFA8 ↑ ATIC ↑ QDPR ↑ MAT2A ↑ SLC7A1 ↑ |
SHMT2 ↑ ARSB ↑ ACLY ↑ PPAT ↑ FADS2 ↑ AHCY ↑ SRXN1 ↑ ATAD3A ↑ |
CYB5R2 ↑ MTHFD2 ↑ ESD ↑ TMEM97 ↑ HINT1 ↑NDUFA12 ↑ USMG5 ↑ NDUFA8 ↑ ATP5S ↑ ADK ↑ NOC3L ↑ LDHB ↑ PIGW ↑ LYPLA1 ↑ DTYMK ↑ PFKM ↑ SFXN4 ↑ LDHB ↑ NME1 ↑ PLA2G5 ↑ ATP5C1 ↑ NDUFB6 ↑ CISD1 ↑ NDUFA9 ↑ QDPR ↑ GOT1 ↑ ATIC ↑ MAT2A ↑ NME1/NME1- NME2/NME2 ↑ PASK ↑ COX7C ↑ PUS1 ↑ PMM2 ↑ COQ3 ↑ PTCD2 ↑ATP6V1G3 ↓ IDH1 ↓ |
TMEM97 ↑ LRPPRC ↑ BDH1 ↑ DCTPP1 ↑ ATIC ↑ MAT2A ↑ AHCY ↑ ATP5J2 ↑ ST3GAL3 ↑ |
BCAT2 ↑ ATP2A3 ↑ DIO3 ↑ HPDL ↑ UGCG ↓ RNASEK ↓ ARG2 ↓ SLC39A6 ↓ |
| Protein folding. chaperon, trafficking, degradation |
PPIA ↑ FKBP4 ↑ CCT2 ↑ CHCHD4 ↑ |
HSPD1 ↑ NUP35 ↑ CHCHD4 ↑ USP36 ↑ TIMM8B ↑ IPO11 ↑ |
TIMM23 ↑ CLNS1A ↑ C15orf63 ↑ CUEDC2 ↑ CCT4 ↑ HSPA14 ↑ COMMD2 ↑ PCBP2 ↑ IPO7 ↑ SLC25A3 ↑ UBA2 ↑ SNX5 ↑ SACS ↑ CSE1L ↑ UBLCP1 ↑ DNAJA3 ↑ TIMM9 ↑ PSME3 ↑ SKP2 ↑ GRPEL1 ↑ IPO4 ↑ TEX10 ↑ PFDN4 ↑ TUBGCP5 ↑ LARP4 ↑ AIMP2 ↑ BAG2 ↑ TOMM40 ↑ NSF ↑ CBLL1 ↑ PPIA ↑USP7 ↓ RNPEP ↓ |
UCHL5 ↑ TIMM23 ↑ FBXO11 ↑ NPM3 ↑ IPO4 ↑ AKAP1 ↑ RAD23A ↑ UBE2G2 ↑ UBQLN4 ↑TNS1 ↓ |
GORASP2 ↑ FBXO41 ↑ TIMM22 ↑ UBQLN4 ↑ SH3GL3 ↑PACS1 ↓ |
| Apoptosis | PDCD5 ↑ | PDCD5 ↑ | BID ↑ GNL3 ↑ |
HRK ↑ FASTKD3 ↑ |
CARD16/CASP1 ↓ RASSF4 ↓ DAPK1 ↓ |
| Adhesion, cell interaction with extracellular matrix, cytoskeleton, transport, motility, membrane/vesicular trafficking and exocytosis |
C14orf104 ↑ SYNE1 ↓ |
SSX2IP ↑ TUBB3 ↑ITM2A ↓ ITM2B ↓ |
DCTN5 ↑ MTMR12 ↑ TUBB ↑ RTTN ↑ RAB3GAP2 ↑ DNAAF2 ↑APOL6 ↓ LAMA3 ↓ PAPPA ↓ |
C21orf59 ↑ |
PICK1 ↑ MYH7 ↑ ITGB1 ↓ DPYSL3 ↓ PALLD ↓ MARCKS ↓ CALD1 ↓ TPM1 ↓ ANXA4 ↓ ANXA7 ↓ NID1 ↓ RAB13 ↓ RAB12 ↓ RAB6A ↓ ASAP1 ↓ SH3PXD2A ↓ TNS1 ↓ SYNPO ↓ MYL12A/MYL12B ↓ VPS37C ↓ SLC39A13 ↓ SYNPR ↓ |
| Immune responses, tumor microenvironment |
NCR3LG1 ↑ |
ERAP2 ↑ C1QBP ↑GIMAP1 ↓ TRA@ ↓ FOXP3 ↓ CD4 ↓ |
MS4A2 ↑IL18BP ↓ | ||
| RNA gene; unknown function |
SNHG4 ↑ SNHG1 ↑ RBM26 ↑ KIAA0114 ↑ C4orf43 ↑ GAS5 ↑ C21orf45 ↑ WDR43 ↑ CCDC58 ↑ GRPEL1 ↑ LYAR ↑ NOC3L ↑ KIAA0020 ↑ SNHG8 ↑ C12orf24 ↑ SNORA21 ↑ FAM86A ↑ TRBC1 ↓ GLCCI1 ↓ LOC100233209 ↓ |
SNHG1 ↑ SNHG12 ↑ SNORA21 ↑ TTLL12 ↑ KIAA0020 ↑ RMND5A ↑ UBXN10 ↑ C9orf93 ↑ ZNRD1-AS1 ↑ TRBC1 ↓ EVI2B ↓ SECISBP2L ↓ KIAA1551 ↓ LOC401320 ↓ ZBED2 ↓ CCDC92 ↓ LOC440944 ↓ LOC651250 ↓ N4BP2L2 ↓ |
KLHL23 ↑ LOC100291837/RPS21 ↑ PUS7 ↑ CCDC86 ↑ RBM26 ↑ C4orf43 ↑ SNHG1 ↑ KIAA0114 ↑ LRRC58 ↑ GAS5 ↑ C3orf26 ↑ METTL9 ↑ZFAS1 ↑ URB1 ↑ WDR75 ↑ SNHG8 ↑ METTL5 ↑ WDR43 ↑ KBTBD8 ↑ CCDC58 ↑ C18orf19 ↑ NOC4L ↑ DYRK4 ↑ LYAR ↑ ATP5SL ↑ C12orf73 ↑ TMEM128 ↑ C19orf48 ↑ LSM12 ↑FAM13AOS ↓ C5orf4 ↓ LOC100233209 ↓ LAMB2L ↓ |
GAS5 ↑ SNHG4 ↑ LOC100127980 ↑ LOC100294028 ↑ C14orf2 ↑ SNHG1 ↑ RPS10P5 ↑ SNHG10 ↑ MARS2 ↑ LOC100288418 ↑ LOC440552 ↑ RRP1B ↑ NOC3L ↑ NUDCD1 ↑ CCDC93 ↑WWC2 ↓ |
ZFAS1 ↑ MATR3/SNHG4 ↑ MPHOSPH9 ↑ ZC3H3 ↑ C19orf43 ↑ C17orf86 ↑ CCDC51 ↑ PREPL ↑ SSBP4 ↑ LOC148189 ↑ LY6H ↑ FLJ40125 ↑ UBE2NL ↑ LOC731424 ↑ DDX60L ↓ EPSTI1 ↓ MEIS3P1 ↓ LOC100133790 ↓ C22orf42 ↓ |
Abbreviations: FDR, false discovery rate. GCB, germinal center B-cell–like; ABC, activated B-cell–like. Note: the genes are listed in the order according to the fold changes in Mychigh versus Myclow group.