Table 1

Prednisolone-induced changes in gene expression in pediatric ALL

Probe IDAccession no.Gene name*DescriptionNo. of patient samples†Fold change‡P
Up-regulated genes 
    204560_at NM_004117 FKBP5 FK506-binding protein 5 10 35.4 < .001 
    205883_at NM_006006 ZBTB16 (PLZF) Zinc finger and BTB domain containing 16 10 8.8 < .001 
    201008_s_at AI439556 TXNIP (VDUP) Thioredoxin-interacting protein 10 4.4 < .001 
    201009_s_at AA812232 TXNIP (VDUP) Thioredoxin-interacting protein 10 3.0 < .001 
    221756_at AL540260 LIMK2 LIM domain kinase 2 10 4.1 < .001 
    212158_at AL577322 SDC2 Syndecan 2 10 4.0 < .001 
    204698_at U88964 ISG20 Interferon-stimulated exonuclease gene 20 kDa 10 3.7 < .001 
    33304_at NM_002201 ISG20 Interferon-stimulated exonuclease gene 20 kDa 10 3.4 < .001 
    201369_s_at U07802 ZFP36L2 (ERF2) Zinc finger protein 36, C3H type-like 2 10 3.6 < .001 
    201368_at NM_006887 ZFP36L2 (ERF2) Zinc finger protein 36, C3H type-like 2 10 2.6 < .001 
    208078_s_at NMP_030751 SNF1LK SNF1-like kinase 10 3.5 < .001 
    208763_s_at AL110191 DSIPI (TSC22D3, GILZ) Delta sleep-inducing peptide, immunoreactor 10 3.3 < .001 
    202670_at AI571419 MAP2K1 (MEK1) Mitogen-activated protein kinase kinase 1 10 3.1 < .001 
    203542_s_at NM_001206 KLF9 (BTEB1) Kruppel-like factor 9 10 3.1 < .001 
    203543_s_at AI690205 KLF9 (BTEB1) Kruppel-like factor 9 10 3.1 < .001 
    203574_at NM_005384 NFIL3 Nuclear factor, interleukin 3 regulated 10 3.0 < .001 
    209185_s_at AF073310 IRS2 Insulin receptor substrate 2 10 2.8 < .001 
    215890_at X61094 GM2A GM2 ganglioside activator 10 2.6 < .001 
    203973_s_at NM_005195 CEBPD CCAAT/enhancer-binding protein (C/EBP), delta 10 2.5 < .001 
    213792_s_at AA485908 INSR Insulin receptor 9 2.5 < .001 
    212242_at AL565074 TUBA1 Tubulin, alpha 1 (testis specific) 10 2.4 < .001 
    201041_s_at NM_004417 DUSP1 (MKP1) Dual-specificity phosphatase 1 10 2.4 < .001 
    212188_at AI718937 KCTD12 Potassium channel tetramerization domain containing 12 10 2.3 < .001 
    212192_at AA551075 KCTD12 Potassium channel tetramerization domain containing 12 9 2.3 < .001 
    218638_s_at NM_012445 SPON2 Spondin 2 10 2.3 < .001 
    207996_s_at NM_004338 C18orf1 Chromosome 18 open reading frame 1 10 2.2 < .001 
    204618_s_at NM_005254 GABPB2 GA-binding protein transcription factor, beta subunit 2 9 2.2 < .001 
    210001_s_at AB005043 SOCS1 Suppressor of cytokine signaling 1 10 2.2 < .001 
    200921_s_at NM_001731 BTG1 B-cell translocation gene 1, antiproliferative 10 2.2 < .001 
    202643_s_at AI738896 TNFAIP3 (A20) Tumor necrosis factor, alpha-induced protein 3 10 2.1 < .001 
    201037_at NM_002627 PFKP Phosphofructokinase, platelet 10 2.0 < .001 
    207945_s_at NM_001893 CSNK1D Casein kinase 1, delta 10 1.8 < .001 
    201739_at NM_005627 SGK Serum/glucocorticoid-regulated kinase 10 1.8 < .001 
    203819_s_at AU160004 IMP-3 IGF-II mRNA-binding protein 3 9 1.7 < .001 
    221563_at N36770 DUSP10 (MKP5) Dual-specificity phosphatase 10 9 1.5 < .001 
    215977_x_at X68285 GK Glycerol kinase 10 1.5 < .001 
    213310_at AI613483 EIF2C2 Eukaryotic translation initiation factor 2C, 2 10 1.4 < .001 
    215046_at AL133053 FLJ23861 EST 10 1.4 < .001 
    217356_s_at S81916 PGK1 Phosphoglycerate kinase 1 10 1.4 < .001 
    211926_s_at AI827941 MYH9 Myosin, heavy polypeptide 9, nonmuscle 10 1.3 < .001 
    218761_at NM_017610 RNF111 (ARK) Ring finger protein 111 10 1.3 < .001 
    217795_s_at W74580 THEM43 Transmembrane protein 43 10 1.3 < .001 
    201859_at NM_002727 PRG1 Proteoglycan 1 10 1.3 < .001 
    218528_s_at NM_022781 RNF38 Ring finger protein 38 10 1.3 < .001 
Down-regulated genes 
    205749_at NM_000499 CYP1A1 Cytochrome P450, family 1, subfamily A, polypeptide 1 10 −2.0 < .001 
    209969_s_at BC002704 STAT1 Signal transducer and activator of transcription 1 10 −2.0 < .001 
    219066_at NM_021823 MDS018 EST 10 −2.0 < .001 
    205013_s_at NM_000675 ADORA2A Adenosine A2a receptor 10 −2.0 < .001 
    205006_s_at NM_004808 NMT2 N-myristoyltransferase 2 10 −1.7 < .001 
    203612_at NM_004053 BYSL Bystin-like 10 −1.7 < .001 
    219665_at NM_024815 NUDT18 Nudix-type motif 18 10 −1.7 < .001 
    221933_at AI338338 NLGN4X Neuroligin 4, X-linked 9 −1.7 < .001 
    204070_at NM_004585 RARRES3 Retinoic acid receptor responder (tazarotene induced) 3 10 −1.7 < .001 
    211430_s_at M87789 IGHG1 Immunoglobulin heavy constant gamma 1 10 −1.4 < .001 
    218046_s_at NM_016065 MRPS16 Mitochondrial ribosomal protein S16 10 −1.4 < .001 
    219344_at NM_018344 SLC29A3 (ENT3) Solute carrier family 29, member 3 10 −1.4 < .001 
    203814_s_at NM_000904 NQO2 NAD(P)H dehydrogenase, quinone 2 10 −1.4 < .001 
Probe IDAccession no.Gene name*DescriptionNo. of patient samples†Fold change‡P
Up-regulated genes 
    204560_at NM_004117 FKBP5 FK506-binding protein 5 10 35.4 < .001 
    205883_at NM_006006 ZBTB16 (PLZF) Zinc finger and BTB domain containing 16 10 8.8 < .001 
    201008_s_at AI439556 TXNIP (VDUP) Thioredoxin-interacting protein 10 4.4 < .001 
    201009_s_at AA812232 TXNIP (VDUP) Thioredoxin-interacting protein 10 3.0 < .001 
    221756_at AL540260 LIMK2 LIM domain kinase 2 10 4.1 < .001 
    212158_at AL577322 SDC2 Syndecan 2 10 4.0 < .001 
    204698_at U88964 ISG20 Interferon-stimulated exonuclease gene 20 kDa 10 3.7 < .001 
    33304_at NM_002201 ISG20 Interferon-stimulated exonuclease gene 20 kDa 10 3.4 < .001 
    201369_s_at U07802 ZFP36L2 (ERF2) Zinc finger protein 36, C3H type-like 2 10 3.6 < .001 
    201368_at NM_006887 ZFP36L2 (ERF2) Zinc finger protein 36, C3H type-like 2 10 2.6 < .001 
    208078_s_at NMP_030751 SNF1LK SNF1-like kinase 10 3.5 < .001 
    208763_s_at AL110191 DSIPI (TSC22D3, GILZ) Delta sleep-inducing peptide, immunoreactor 10 3.3 < .001 
    202670_at AI571419 MAP2K1 (MEK1) Mitogen-activated protein kinase kinase 1 10 3.1 < .001 
    203542_s_at NM_001206 KLF9 (BTEB1) Kruppel-like factor 9 10 3.1 < .001 
    203543_s_at AI690205 KLF9 (BTEB1) Kruppel-like factor 9 10 3.1 < .001 
    203574_at NM_005384 NFIL3 Nuclear factor, interleukin 3 regulated 10 3.0 < .001 
    209185_s_at AF073310 IRS2 Insulin receptor substrate 2 10 2.8 < .001 
    215890_at X61094 GM2A GM2 ganglioside activator 10 2.6 < .001 
    203973_s_at NM_005195 CEBPD CCAAT/enhancer-binding protein (C/EBP), delta 10 2.5 < .001 
    213792_s_at AA485908 INSR Insulin receptor 9 2.5 < .001 
    212242_at AL565074 TUBA1 Tubulin, alpha 1 (testis specific) 10 2.4 < .001 
    201041_s_at NM_004417 DUSP1 (MKP1) Dual-specificity phosphatase 1 10 2.4 < .001 
    212188_at AI718937 KCTD12 Potassium channel tetramerization domain containing 12 10 2.3 < .001 
    212192_at AA551075 KCTD12 Potassium channel tetramerization domain containing 12 9 2.3 < .001 
    218638_s_at NM_012445 SPON2 Spondin 2 10 2.3 < .001 
    207996_s_at NM_004338 C18orf1 Chromosome 18 open reading frame 1 10 2.2 < .001 
    204618_s_at NM_005254 GABPB2 GA-binding protein transcription factor, beta subunit 2 9 2.2 < .001 
    210001_s_at AB005043 SOCS1 Suppressor of cytokine signaling 1 10 2.2 < .001 
    200921_s_at NM_001731 BTG1 B-cell translocation gene 1, antiproliferative 10 2.2 < .001 
    202643_s_at AI738896 TNFAIP3 (A20) Tumor necrosis factor, alpha-induced protein 3 10 2.1 < .001 
    201037_at NM_002627 PFKP Phosphofructokinase, platelet 10 2.0 < .001 
    207945_s_at NM_001893 CSNK1D Casein kinase 1, delta 10 1.8 < .001 
    201739_at NM_005627 SGK Serum/glucocorticoid-regulated kinase 10 1.8 < .001 
    203819_s_at AU160004 IMP-3 IGF-II mRNA-binding protein 3 9 1.7 < .001 
    221563_at N36770 DUSP10 (MKP5) Dual-specificity phosphatase 10 9 1.5 < .001 
    215977_x_at X68285 GK Glycerol kinase 10 1.5 < .001 
    213310_at AI613483 EIF2C2 Eukaryotic translation initiation factor 2C, 2 10 1.4 < .001 
    215046_at AL133053 FLJ23861 EST 10 1.4 < .001 
    217356_s_at S81916 PGK1 Phosphoglycerate kinase 1 10 1.4 < .001 
    211926_s_at AI827941 MYH9 Myosin, heavy polypeptide 9, nonmuscle 10 1.3 < .001 
    218761_at NM_017610 RNF111 (ARK) Ring finger protein 111 10 1.3 < .001 
    217795_s_at W74580 THEM43 Transmembrane protein 43 10 1.3 < .001 
    201859_at NM_002727 PRG1 Proteoglycan 1 10 1.3 < .001 
    218528_s_at NM_022781 RNF38 Ring finger protein 38 10 1.3 < .001 
Down-regulated genes 
    205749_at NM_000499 CYP1A1 Cytochrome P450, family 1, subfamily A, polypeptide 1 10 −2.0 < .001 
    209969_s_at BC002704 STAT1 Signal transducer and activator of transcription 1 10 −2.0 < .001 
    219066_at NM_021823 MDS018 EST 10 −2.0 < .001 
    205013_s_at NM_000675 ADORA2A Adenosine A2a receptor 10 −2.0 < .001 
    205006_s_at NM_004808 NMT2 N-myristoyltransferase 2 10 −1.7 < .001 
    203612_at NM_004053 BYSL Bystin-like 10 −1.7 < .001 
    219665_at NM_024815 NUDT18 Nudix-type motif 18 10 −1.7 < .001 
    221933_at AI338338 NLGN4X Neuroligin 4, X-linked 9 −1.7 < .001 
    204070_at NM_004585 RARRES3 Retinoic acid receptor responder (tazarotene induced) 3 10 −1.7 < .001 
    211430_s_at M87789 IGHG1 Immunoglobulin heavy constant gamma 1 10 −1.4 < .001 
    218046_s_at NM_016065 MRPS16 Mitochondrial ribosomal protein S16 10 −1.4 < .001 
    219344_at NM_018344 SLC29A3 (ENT3) Solute carrier family 29, member 3 10 −1.4 < .001 
    203814_s_at NM_000904 NQO2 NAD(P)H dehydrogenase, quinone 2 10 −1.4 < .001 

After 8 hours of prednisolone exposure, 57 probe sets (51 unique genes and 2 ESTs) were differentially expressed at P < .001 and FDR < 10%. Aliases between brackets.

*

Human genome nomenclature.

†

Number of up-regulated patient samples for up-regulated genes and number of down-regulated patient samples for down-regulated gene.

‡

The median fold change reflects the change in expression of genes after 8 hours of prednisolone exposure compared with culture medium exposed control cells.

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