Table 2.

Retinoid up-regulated genes in APL fusion protein-expressing cells

Gene
GenBank accession no.
Description
Fold change*
P†
U937     
CEBPE  U48865   CCAAT/enhancer binding protein (C/EBP), epsilon   280.6   .0005  
THBD  J02973   Thrombomodulin   515.5   .01  
ID1  HG3342-HT3519   ID1   5.6   .04  
SLC2A5  M55531   Solute carrier family 2 (facilitated glucose transporter), member 5   5.5   .0001  
SLA  D89077   Src-like adaptor   4.8   .0009  
FGR  M19722   Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog   4.3   .0009  
NCF1  M55067   Neutrophil cytosolic factor 1 (47 kDa, chronic granulomatous disease, autosomal 1)   3.5   .3  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   4.3   .0003  
CG1I  U61836   Human putative cyclin G1 interacting protein   3.6   .0004  
PIK3CG  X83368   Phosphatidylinositol 3-kinase, catalytic, gamma polypeptide   2.6   .0001  
c-mer  U08023   Mer tyrosine kinase proto-oncogene   2.4   .005  
NDRG1  D87953   N-Myc downstream-regulated gene 1   2.7   < .0001  
PIM1  M16750   pim-1 oncogene   64.1   .0008  
ALOX5AP  M63262   Arachidonate 5-lipoxygenase-activating protein   2.5   .01  
PLEK  X07743   Pleckstrin   2.2   < .0001  
U937PR9 (PML/RARα)     
CEBPA  U34070   CCAAT/enhancer binding protein (C/EBP), alpha   117.2   .02  
DIF2  S81914   Differentiation-dependent gene 2; immediate-early response 3 (IER3)   446.2   .004  
CEBPE  U48865   CCAAT/enhancer binding protein (C/EBP), epsilon   296.3   .03  
CD38  D84276   CD38 antigen (p45)   140.6   .002  
RARG  L12060   Retinoic acid receptor gamma   166.5   .03  
CD100  U60800   Leukocyte activation antigen CD 100; Semaphorin 4D (SEMA4D)   134.9   .1  
TNFAIP2  M92357   Tumor necrosis factor alpha-induced protein 2; B94   144.8   .002  
NCF1  M55067   Neutrophil cytosolic factor 1 (47 kDa)   18.0   .004  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   25.4   < .0001  
PIM1  M16750   pim-1 oncogene   385.6   .002  
ID1  HG3342-HT3519   ID1   15.6   .005  
SLC2A5  M55531   Solute carrier family 2 (facilitated glucose transporter), member 5   6.9   .0001  
SPI1  X52056   Spleen focus-forming virus (SFFV) proviral integration oncogene spi1   8.6   .0007  
SLA  D89077   Src-like adaptor protein   5.0   .001  
FGR  M19722   Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog   500.8   .005  
BIK  X89986   BCL2-interacting killer (apoptosis-inducing)   43.4   .003  
LSP1  M33552   Lymphocyte-specific protein 1 (LSP1)   118.9   .03  
NDRG1  D87953   N-Myc downstream-regulated gene 1   6.2   .002  
PRKCL1  U33053   Protein kinase C-like 1   5.3   .006  
JUND  X56681   jun D proto-oncogene   3.5   .07  
HOXA1  U37431   homeobox A1   3.4   .06  
ALOX5AP  M63262   Arachidonate 5-lipoxygenase-activating protein   4.3   .001  
IGFBP6  M62402   Insulin-like growth factor binding protein 6   4.4   .01  
RF1  L05072   Interferon regulatory factor 1   5.7   .01  
PIK3CG  X83368   Phosphatidylinositol 3-kinase, catalytic, gamma polypeptide   3.8   .04  
PSAP  J03077   Prosaposin; sphingolipid activator protein   5.2   .005  
PIG7  U77396   LPS-induced TNF-alpha factor   2.8   .02  
TNFRSF1B  M32315   Tumor necrosis factor receptor subfamily, member 1B   4.0   .001  
ELF4  U32645   E74-like factor 4 (ets domain transcription factor); Myeloid elf-1-like factor (MEF)   2.6   .0987  
TOP1  U07806   DNA topoisomerase 1   2.4   .02  
KIAA0223  D86976   Similar to C elegans protein (Z37093)   2.5   .006  
MCP1  HG4069-HT4339   Monocyte chemotactic protein 1   2.2   .06  
UP  X90858   Uridine phosphorylase   3.2   .03  
RARG  M38258   Retinoic acid receptor, gamma   13.6   .05  
IDH  U62389   Human putative cytosolic NADP-dependent isocitrate dehydrogenase   3.0   .002  
U937B412 (PLZF/RARα)     
DIF2  S81914   Differentiation-dependent gene 2   567.8   .001  
CEBPA  U34070   CCAAT/enhancer binding protein (C/EBP), alpha   127.7   .02  
CEBPE  U48865   CCAAT/enhancer binding protein (C/EBP), epsilon   262.0   .006  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   12.6   .002  
SPI1  X52056   Spleen focus-forming virus (SFFV) proviral integration oncogene spi1   224.7   .01  
SPO  U39573   Human salivary peroxidase   15.8   .05  
PIM1  M16750   pim-1 oncogene   9.1   .006  
SLC2A5  M55531   Solute carrier family 2 (facilitated glucose transporter), member 5   8.3   .0001  
ID1  HG3342-HT3519   ID1   9.0   < .0001  
NCF1  M55067   Neutrophil cytosolic factor 1 (47 kDa)   4.0   .02  
PLEK  X07743   Pleckstrin   6.5   .0003  
NDRG1  D87953   N-Myc downstream-regulated gene 1   4.9   .0003  
FGR  M19722   Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog   8.0   .02  
UP  X90858   Uridine phosphorylase   3.8   .009  
PTPN6  X62055   Protein tyrosine phosphatase, nonreceptor type 6   3.8   .005  
KIAA0223  D86976   Similar to C elegans protein (Z37093)   3.1   .0003  
ALOX5AP  M63262   Arachidonate 5-lipoxygenase-activating protein   3.0   .01  
PPARG  L40904   Peroxisome proliferator activated receptor, gamma   3.3   .05  
FLNB  M62994   Filamin, beta (actin-binding protein 276/278)   3.2   .003  
PLCB2  M95678   Phospholipase C, beta 2   4.0   .008  
LBR  L25931   Lamin B receptor   2.6   .04  
GYPC  M36284   Glycophorin C (Gerbich blood group, Ge)   2.8   .03  
TLE3  M99438   Transducin-like enhancer of split 3   78.2   .02  
IDH  U62389   Human putative cytosolic NADP-dependent isocitrate dehydrogenase   3.1   .001  
PLTP  HG3945-HT4215   Phospholipid transfer protein   2.6   .07  
SIAT4A
 		 L13972
 		 Sialyltransferase 4A (beta-galactoside alpha-2, 3-sialytransferase)
 		 2.4
 		 .05
 
Gene
GenBank accession no.
Description
Fold change*
P†
U937     
CEBPE  U48865   CCAAT/enhancer binding protein (C/EBP), epsilon   280.6   .0005  
THBD  J02973   Thrombomodulin   515.5   .01  
ID1  HG3342-HT3519   ID1   5.6   .04  
SLC2A5  M55531   Solute carrier family 2 (facilitated glucose transporter), member 5   5.5   .0001  
SLA  D89077   Src-like adaptor   4.8   .0009  
FGR  M19722   Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog   4.3   .0009  
NCF1  M55067   Neutrophil cytosolic factor 1 (47 kDa, chronic granulomatous disease, autosomal 1)   3.5   .3  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   4.3   .0003  
CG1I  U61836   Human putative cyclin G1 interacting protein   3.6   .0004  
PIK3CG  X83368   Phosphatidylinositol 3-kinase, catalytic, gamma polypeptide   2.6   .0001  
c-mer  U08023   Mer tyrosine kinase proto-oncogene   2.4   .005  
NDRG1  D87953   N-Myc downstream-regulated gene 1   2.7   < .0001  
PIM1  M16750   pim-1 oncogene   64.1   .0008  
ALOX5AP  M63262   Arachidonate 5-lipoxygenase-activating protein   2.5   .01  
PLEK  X07743   Pleckstrin   2.2   < .0001  
U937PR9 (PML/RARα)     
CEBPA  U34070   CCAAT/enhancer binding protein (C/EBP), alpha   117.2   .02  
DIF2  S81914   Differentiation-dependent gene 2; immediate-early response 3 (IER3)   446.2   .004  
CEBPE  U48865   CCAAT/enhancer binding protein (C/EBP), epsilon   296.3   .03  
CD38  D84276   CD38 antigen (p45)   140.6   .002  
RARG  L12060   Retinoic acid receptor gamma   166.5   .03  
CD100  U60800   Leukocyte activation antigen CD 100; Semaphorin 4D (SEMA4D)   134.9   .1  
TNFAIP2  M92357   Tumor necrosis factor alpha-induced protein 2; B94   144.8   .002  
NCF1  M55067   Neutrophil cytosolic factor 1 (47 kDa)   18.0   .004  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   25.4   < .0001  
PIM1  M16750   pim-1 oncogene   385.6   .002  
ID1  HG3342-HT3519   ID1   15.6   .005  
SLC2A5  M55531   Solute carrier family 2 (facilitated glucose transporter), member 5   6.9   .0001  
SPI1  X52056   Spleen focus-forming virus (SFFV) proviral integration oncogene spi1   8.6   .0007  
SLA  D89077   Src-like adaptor protein   5.0   .001  
FGR  M19722   Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog   500.8   .005  
BIK  X89986   BCL2-interacting killer (apoptosis-inducing)   43.4   .003  
LSP1  M33552   Lymphocyte-specific protein 1 (LSP1)   118.9   .03  
NDRG1  D87953   N-Myc downstream-regulated gene 1   6.2   .002  
PRKCL1  U33053   Protein kinase C-like 1   5.3   .006  
JUND  X56681   jun D proto-oncogene   3.5   .07  
HOXA1  U37431   homeobox A1   3.4   .06  
ALOX5AP  M63262   Arachidonate 5-lipoxygenase-activating protein   4.3   .001  
IGFBP6  M62402   Insulin-like growth factor binding protein 6   4.4   .01  
RF1  L05072   Interferon regulatory factor 1   5.7   .01  
PIK3CG  X83368   Phosphatidylinositol 3-kinase, catalytic, gamma polypeptide   3.8   .04  
PSAP  J03077   Prosaposin; sphingolipid activator protein   5.2   .005  
PIG7  U77396   LPS-induced TNF-alpha factor   2.8   .02  
TNFRSF1B  M32315   Tumor necrosis factor receptor subfamily, member 1B   4.0   .001  
ELF4  U32645   E74-like factor 4 (ets domain transcription factor); Myeloid elf-1-like factor (MEF)   2.6   .0987  
TOP1  U07806   DNA topoisomerase 1   2.4   .02  
KIAA0223  D86976   Similar to C elegans protein (Z37093)   2.5   .006  
MCP1  HG4069-HT4339   Monocyte chemotactic protein 1   2.2   .06  
UP  X90858   Uridine phosphorylase   3.2   .03  
RARG  M38258   Retinoic acid receptor, gamma   13.6   .05  
IDH  U62389   Human putative cytosolic NADP-dependent isocitrate dehydrogenase   3.0   .002  
U937B412 (PLZF/RARα)     
DIF2  S81914   Differentiation-dependent gene 2   567.8   .001  
CEBPA  U34070   CCAAT/enhancer binding protein (C/EBP), alpha   127.7   .02  
CEBPE  U48865   CCAAT/enhancer binding protein (C/EBP), epsilon   262.0   .006  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   12.6   .002  
SPI1  X52056   Spleen focus-forming virus (SFFV) proviral integration oncogene spi1   224.7   .01  
SPO  U39573   Human salivary peroxidase   15.8   .05  
PIM1  M16750   pim-1 oncogene   9.1   .006  
SLC2A5  M55531   Solute carrier family 2 (facilitated glucose transporter), member 5   8.3   .0001  
ID1  HG3342-HT3519   ID1   9.0   < .0001  
NCF1  M55067   Neutrophil cytosolic factor 1 (47 kDa)   4.0   .02  
PLEK  X07743   Pleckstrin   6.5   .0003  
NDRG1  D87953   N-Myc downstream-regulated gene 1   4.9   .0003  
FGR  M19722   Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog   8.0   .02  
UP  X90858   Uridine phosphorylase   3.8   .009  
PTPN6  X62055   Protein tyrosine phosphatase, nonreceptor type 6   3.8   .005  
KIAA0223  D86976   Similar to C elegans protein (Z37093)   3.1   .0003  
ALOX5AP  M63262   Arachidonate 5-lipoxygenase-activating protein   3.0   .01  
PPARG  L40904   Peroxisome proliferator activated receptor, gamma   3.3   .05  
FLNB  M62994   Filamin, beta (actin-binding protein 276/278)   3.2   .003  
PLCB2  M95678   Phospholipase C, beta 2   4.0   .008  
LBR  L25931   Lamin B receptor   2.6   .04  
GYPC  M36284   Glycophorin C (Gerbich blood group, Ge)   2.8   .03  
TLE3  M99438   Transducin-like enhancer of split 3   78.2   .02  
IDH  U62389   Human putative cytosolic NADP-dependent isocitrate dehydrogenase   3.1   .001  
PLTP  HG3945-HT4215   Phospholipid transfer protein   2.6   .07  
SIAT4A
 		 L13972
 		 Sialyltransferase 4A (beta-galactoside alpha-2, 3-sialytransferase)
 		 2.4
 		 .05
 
*

Probability of a false positive on individual genes using Student t test is reported as P value.

†

Mean fold changes were calculated using a simple division of raw expression values between experimental sample and control.

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