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Table 3 Most prominent altered genes after in vitro interventions of human transformed germinal centre B cells investigated in gene expression profiles of primary samples of aggressive Non-Hodgkin Lymphoma

From: Global gene expression changes of in vitro stimulated human transformed germinal centre B cells as surrogate for oncogenic pathway activation in individual aggressive B cell lymphomas

  BAFF   CD40L   anti-IgM   IL21   LPS  
  Gene symbols log2FC Gene symbols log2FC Gene symbols log2FC Gene symbols log2FC Gene symbols log2FC
1 ID1 −2,07 ID1 −2,007 CYP26A1 −2,752 BCL6 −1,904 ID1 −1,9
2 ID4 −0,92 C3orf37 −1,432 ID4 −2,687 SOX2* −1,805 RGS18* −0,853
3 BNIP3 −0,79 SMAD1* −1,182 BEST3* −2,41 DNAJB4 −1,589 C3orf37 −0,85
4 TXNIP −0,74 DEPTOR −1,159 IL7R* −2,399 ID3 −1,534 DDIT4 −0,83
5 BNIP3L −0,72 CAB39L −1,086 BMP7 −2,373 DDIT4 −1,514 ID3 −0,811
6 PFKFB4* −0,71 CD83 −1,017 SOX4 −2,343 ID1 −1,493 METTL7A −0,8
7 GPER −0,68 METTL7A −1,005 TNFSF8* −2,264 RGCC −1,239 CAB39L* −0,799
8 PNOC −0,67 ANKRD36BP2* −0,983 RNF144B* −2,213 IL7R −1,152 TXNIP −0,786
9 RGS18* −0,66 ID3 −0,983 DNAJB4 −2,156 HEY2* −1,136 BNIP3 −0,776
10 P4HA1 −0,654 ENPP3* −0,937 ID1 −2,093 VEGFA −1,115 ID4 −0,776
11 CCNG2 −0,635 IRF8 −0,924 BCL6 −2,037 GADD45A −0,982 CCNG2 −0,721
12 HILPDA −0,631 RGS18* −0,919 RHOH −2,005 CYTIP −0,93 PFKFB4* −0,709
13 ID2 −0,585 FAM167A* −0,909 RGCC −1,946 PCDH9 −0,914 KDM3A −0,69
14 SAMD13* −0,582 AICDA −0,864 NCKAP1 −1,857 CCNG2 −0,889 HILPDA* −0,678
15 CD24 −0,578 GPER −0,852 IKZF1* −1,845 TXNIP −0,872 FAM167A* −0,673
16 ID3 −0,564 ID4 −0,835 HEY2* −1,761 BICD2 −0,868 PTPRC −0,665
17 C3orf37 −0,56 PDZRN4 −0,809 PCDH9 −1,751 RGS18* −0,861 STAT2* −0,649
18 GPR18 −0,541 BNIP3 −0,785 SOX2* −1,723 ANKRD37* −0,852 SAMD13* −0,631
19 ALDOC −0,516 VEGFA −0,777 MYCT1* −1,716 TRIM8 −0,836 ENPP3* −0,609
20 BBOX1 −0,516 TP53INP1* −0,776 RGS18* −1,715 KIAA0907 −0,786 SMAD1* −0,593
21 CD83 −0,509 PTPRC −0,77 SMAD1 −1,679 NEDD9 0,787 P4HA1 −0,593
22 POLD4 −0,494 RASSF6* −0,767 MLLT3 −1,656 RELB 0,79 VEGFA −0,592
23 HBP1 −0,484 CCNG2 −0,761 KIF20A −1,631 PAPD5* 0,791 KLRC3 −0,591
24 FAM167A* −0,476 CLEC2B −0,74 FAM214A* −1,612 ZNFX1* 0,794 GPER −0,588
25 EVI2A −0,476 BMP7 −0,735 BCL2 1,618 B3GNT2* 0,797 ZNF385B* −0,588
26 TP53INP1* −0,474 TLR1 −0,732 PSAT1* 1,62 HIF1A 0,814 TP53INP1* −0,583
27 YPEL5 −0,467 SATB1 −0,731 LOC285628* 1,637 KIF26B 0,814 UBE2H* −0,581
28 TRIM22 −0,464 BTG2 −0,726 FAIM3 1,641 MMD 0,82 TRIM22 −0,571
29 TLR1 −0,463 PCDH9 −0,725 MAP2K3 1,644 AICDA* 0,822 PIK3C2B −0,571
30 CLEC2B −0,463 PRKACB −0,724 PPP1R15A 1,662 EPSTI1* 0,837 STAP1 −0,564
31 HLA-C 0,457 GPM6A −0,721 FAM208B 1,674 RAB11FIP1 0,844 BNIP3L −0,558
32 ACTR3* 0,46 STAT2* −0,72 SIAH2 1,676 RAB30 0,845 MYBL1 −0,556
33 NAF1* 0,46 CLIP2 0,721 HIVEP3* 1,679 SIN3A* 0,847 GPM6A −0,549
34 PSMD12 0,461 ARHGAP17 0,727 METRNL* 1,711 PLEK 0,854 ANKRD37* −0,548
35 NUDT5* 0,461 CFLAR 0,74 HERPUD1 1,727 IFITM1 0,863 SPG11 −0,537
36 TESC 0,463 FYTTD1* 0,743 KLF10 1,749 PRDM2 0,885 NARF −0,536
37 CCAR1* 0,464 HLA-DMB 0,747 LTA 1,753 DUSP10 0,888 ABCA1 −0,531
38 ANKRD33B* 0,465 MTMR10* 0,749 GPR18 1,769 FAM100B* 0,892 SEC14L1 −0,531
39 RILPL2* 0,466 HLA-F 0,754 IFRD1 1,777 FAS 0,894 IL7R −0,522
40 PLCB1 0,467 PLEK 0,757 CD274* 1,785 IL7 0,896 H1FX −0,52
41 NFKBIE 0,47 PPP1R9B* 0,759 SLC3A2 1,79 CD69 0,921 ASF1A −0,511
42 DDX21 0,47 TESC 0,764 HSPA5 1,8 B4GALT1* 0,923 GLCCI1* −0,509
43 TAPBP 0,471 IGLL1 0,765 ATF3 1,834 BCL2L1 0,924 EVI2A −0,508
44 RBBP6 0,474 SNX20* 0,765 DENND4A 1,848 CD40 0,934 VGLL4 −0,507
45 SOGA2 0,474 CREM* 0,77 ARHGAP25 1,849 TET3* 0,951 PRKACB −0,503
46 HINT1* 0,474 IKBKE 0,782 TOR3A 1,85 SOCS1 0,962 LRP4 −0,499
47 SRRM1 0,475 FAS 0,788 IRF2BP2* 1,868 NFKBID* 0,983 PLCXD1 −0,498
48 PHACTR4 0,475 CIITA 0,788 SLC30A1 1,886 SRSF5 0,996 CLEC2B −0,497
49 AK3* 0,476 TAP1 0,789 TNF 1,905 MASTL* 1,011 LOC440864* −0,494
50 KPNB1 0,477 NOTCH2NL* 0,797 CTH 1,91 TLR7 1,036 SLC44A1* −0,493
51 GTF2H2B* 0,477 RFX5 0,806 APOBEC3B 1,928 MCL1 1,04 TSPAN11* −0,484
52 TAF1D 0,477 FDXR 0,81 NFKB1 1,94 PIM2 1,06 BTN2A2 0,488
53 CSF2RB 0,479 NFKBIE 0,827 CD58 1,946 IER2 1,067 NFKBIE 0,493
54 MYBBP1A 0,481 MIR155HG* 0,829 NFKBIE 1,958 ZFP36L1 1,072 HLA-C 0,495
55 YY1* 0,483 LOXL2 0,829 NAB2 1,984 IFIT2* 1,072 LSS 0,502
56 FLVCR1* 0,488 HLA-B 0,831 JUND 2,024 SNX11 1,078 FDXR 0,502
57 NAA16 0,49 VAV2* 0,832 ARL4C 2,026 TAP1 1,086 KLHDC5* 0,505
58 SRRT 0,491 ZNF385C* 0,836 UPP1 2,029 JUNB 1,088 HLA-B 0,511
59 TNRC6A* 0,493 RASSF2 0,841 CDKN1A 2,033 LRRC32 1,1 CCDC28B 0,514
60 FNBP1 0,494 HLA-E 0,843 FAM100B* 2,059 NA 1,101 HLA-DMB 0,517
61 CIZ1 0,495 BIRC3 0,845 MDFIC 2,091 MARCKS 1,108 CUX2 0,519
62 TOMM40 0,495 ANKRD33B* 0,847 IER2 2,137 DUSP2 1,134 DUSP22* 0,523
63 TBC1D24* 0,498 ANXA7 0,85 DUSP10 2,144 NUDT4 1,139 RPS6KA1 0,527
64 ILF3 0,498 HVCN1* 0,85 FAM102A 2,198 CXCR5 1,155 HLA-DOA* 0,527
65 NFKB2 0,501 EPB41L4B* 0,86 RAB8B* 2,198 IER5 1,155 SYNCRIP 0,528
66 TFDP1* 0,505 PIK3CD 0,864 PTGER4 2,204 BCL3 1,16 ZNF385C* 0,533
67 ZNF385C* 0,508 LAT2 0,871 HLA-DQB1 2,206 SAMSN1 1,18 DENND4A 0,535
68 LYAR* 0,508 HCP5 0,884 ARAP2 2,214 NFKBIZ* 1,2 PDLIM3* 0,535
69 BIRC3 0,508 HLA-DOA* 0,894 SLC7A11 2,215 IL2RA 1,211 FYTTD1* 0,536
70 LRP8 0,513 SYNGR2 0,901 MIR155HG* 2,249 PARP9* 1,212 ELL2* 0,537
71 CCDC28B 0,514 ALCAM 0,905 CD69 2,278 USP18 1,229 HLA-E 0,539
72 C8orf12* 0,514 WNT5A 0,916 TSC22D3 2,287 MAP3K8 1,333 IRF2BP2* 0,539
73 HLA-B 0,519 RUNX3 0,932 RGS16 2,316 ZC3H12A 1,38 DNAJB1 0,54
74 HSP90B1 0,523 BMP2K* 0,935 ZFP36L1 2,331 NFKBIA 1,435 IGLL1 0,545
75 KLHDC5* 0,525 CTSH 0,935 TRIB3 2,354 RGS16 1,437 TFDP1* 0,558
76 RP9* 0,526 PLEKHO1 0,94 IL21R* 2,373 GADD45B 1,481 PSPC1* 0,56
77 PEA15 0,528 RPS6KA1 0,956 KLF6* 2,383 MIR155HG* 1,498 ANKRD33B* 0,562
78 MT1X 0,534 DUSP22 0,963 PHACTR1 2,423 LINC00158* 1,525 CREBZF 0,565
79 MAN1A1 0,539 IFIH1 0,991 SESN2* 2,446 PTGER4 1,563 IRF4 0,575
80 DNAJB1 0,543 OLFML2A 0,994 TNFAIP3 2,612 DTX3L* 1,58 C8orf12* 0,579
81 SOGA1* 0,554 HLA-DQB1 0,994 CD1C 2,662 CXCL10 1,616 FNBP1 0,617
82 CENPV* 0,555 COL1A1* 1,003 PLEK 2,716 TNFAIP3 1,636 ANXA7 0,641
83 ICAM1 0,567 ICAM1 1,006 FAM46C* 2,926 MX1 1,638 MT1X 0,67
84 CD58 0,568 NFKB2 1,009 CD83 2,973 STAT1 1,659 BATF 0,702
85 NCOR2 0,578 NEIL2* 1,021 DDIT3 2,977 BIRC3 1,66 CALR 0,703
86 SNHG12* 0,585 FNBP1 1,041 DUSP2 3,004 EGR2 1,69 HLA-DQA1* 0,706
87 SLC23A2 0,586 BATF 1,061 SQSTM1 3,036 NFKBIE 1,765 OLFML2A 0,714
88 OLFML2A 0,588 CCDC28B 1,066 PHLDA1 3,048 IFIT5 1,913 UMODL1* 0,716
89 LRRFIP1 0,59 MAN1A1 1,082 BHLHE40 3,141 BCL2A1 1,942 HLA-DQB1 0,723
90 DENND4A 0,599 CUX2 1,089 SLAMF7* 3,147 IRF1 1,965 IKBKE 0,723
91 IGLL1 0,614 HLA-DQA1* 1,092 CCR7 3,572 SLC30A1 1,969 NEIL2* 0,726
92 OVOS2* 0,63 DENND4A 1,101 NA* 3,693 IFIT3* 1,973 RILPL2* 0,779
93 C1orf63 0,649 HLA-DPA1 1,105 LINC00158* 3,798 IRF4 2,167 MAN1A1 0,781
94 EIF5B 0,681 RILPL2* 1,117 LY9* 4,131 IFIT1 2,186 CREM 0,795
95 RUNX3 0,702 DOCK10 1,202 EGR1* 4,232 CMPK2* 2,253 HLA-DPA1 0,816
96 NA 0,704 BTN2A2 1,254 BCL2A1 4,295 BATF 2,3 ACTR3* 0,833
97 HLA-DQB1 0,726 NA 1,262 EGR2 4,518 CD83 2,705 CD58 0,834
98 HLA-DQA1 0,731 ELL2* 1,467 SGK1 4,84 SGK1 2,798 NA 0,952
99 TCOF1 0,744 CD58 1,62 DUSP5 5,011 ICAM1 2,918 LINC00158* 0,954
100 ELL2* 0,747 LINC00158* 1,793 RGS1 5,476 IRF9 3,155 IFIT3* 1,051
  1. Two independent patients cohort were tested. The gene expression from 219 primary lymphoma samples described by Hummel et al. (MMML-1 cohort) and 99 primary lymphoma samples published by Dave et al. (LLMPP-cohort) were compared to global gene expression changes described within the text [20, 21]. The deviation from the TOP100 LIMMA gene lists from in vitro interventions is determined by the absence of hybridization probes on the microarrays used for lymphoma gene expression description. In addition multiple hybridization probes for one gene were condensed into a single event.