Table 1.

Genes modulated by both PML/RARα and PLZF/RARα

GenBank accession no.
PML/RARα
PLZF/RARα
Gene
Description
Fold change*
P†
Fold change*
P†
Down-regulated gene       
ELA2  M20203   Neutrophil elastase   4713.3   <.0001   3053.6   <.0001  
PRTN3  X55668   Proteinase 3 (serine proteinase, neutrophil, Wegener granulomatosis autoantigen)   1217.5   .0002   1217.5   .0002  
PAI2  M31551   Plasminogen activator inhibitor, type II   1109.8   <.0001   1109.8   <.0001  
CEBPA  U34070   CCAAT/enhancer binding protein (C/EBP), alpha   85.1   .02   85.1   .02  
GAL  M77140   Galanin   230.5   .01   314.7   .009  
PPP5  X89416   Protein phosphatase 5, catalytic subunit   373.4   .01   252.8   .07  
NFKBIE  U91616   Nuclear factor of kappa light polypeptide gene enhancer in B-cell inhibitor, epsilon   59.5   .008   47.3   .01  
PECAM1  L34657   Platelet-endothelial cell adhesion molecule (CD31 antigen)   182.5   .03   146.9   .03  
MEF2  HG4668-HT5083   Transcription factor Mef2, alt Splice 2   129.5   .05   179.7   .04  
RAB31  U59877   Ras-associated protein RAB31; Low Mr GTP-binding protein of the Rab subfamily   162.0   .001   162.0   .003  
NMB  X76534   Glycoprotein NMB; GPNMB; neuromedin B   31.7   .0003   221.7   .0003  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   6.2   .04   10.8   .03  
IFI30  J03909   Interferon-gamma-inducible protein 30; GILT   97.2   .06   21.0   .06  
ELA2  M27783   Elastase 2, neutrophil   1816.2   .001   19.9   .001  
MNDA  M81750   Myeloid cell nuclear differentiation antigen   6.1   .03   14.8   .02  
CGII  U61836   Cyclin G1 interacting protein   92.9   .007   8.6   .007  
IL-8  M28130   Human interleukin-8 gene   3.0   .02   8.7   .006  
LYZ  M21119   Lysozyme   13.9   .001   17.5   .001  
SPI1  X52056   Spleen focus-forming virus (SFFV) proviral integration oncogene spi1   8.7   .03   143.3   .03  
MCAM  M29277   Melanoma adhesion molecule   8.2   .5   9.5   .8  
CYBB  X04011   Cytochrome b-245, beta polypeptide (chronic granulomatous disease); p91-phox   98.0   .008   55.6   <.0001  
LSP1  M33552   Lymphocyte-specific protein 1 (LSP1)   260.1   .02   261.9   .02  
EPR1  L32866   Human effector cell protease receptor-1; EPR-1   117.1   .02   11.8   .03  
PRG1  X17042   Proteoglycan 1, secretory granule   35.2   <.0001   16.2   <.0001  
APP  Y00264   Amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease)   40.6   .006   91.5   .005  
IL-8  Y00787   Interleukin-8   14.5   .0005   274.7   .0001  
GLVR1  L20859   Solute carrier family 20, member 1 (SLC20A1)   4.7   .01   5.1   .01  
MCP1  HG4069-HT4339   Monocyte chemotactic protein 1   6.4   .002   8.7   .002  
ASAH  U70063   N-acylsphingosine amidohydrolase   153.6   .05   159.7   .06  
COL4A2  X05610   Collagen type IV, alpha-2; COL4A2   453.2   .0002   6.8   .0002  
RAB27A  U57094   RAB27A, member RAS oncogene family   3.1   .1   8.0   .07  
S100P  X65614   S100 calcium-binding protein P   8.8   .009   4.5   .02  
TUBA1  HG2259-HT2348   Tubulin Alpha 1, isoform 44   497.3   .005   549.3   .003  
RNASE3  X55990   Ribonuclease, RNase A family, 3 (eosinophil cationic protein)   3.5   .005   4.1   .004  
BTG1  X61123   B-cell translocation gene 1, antiproliferative   3.0   .1   67.1   .02  
ERBAL2  X12794   v-erbA—related ear-2 gene; nuclear receptor subfamily 2, group F, member 6   3.4   .003   3.2   .008  
P63  X69910   p63 transmembrane protein   3.2   .008   4.3   .006  
CTSD  M63138   Cathepsin D   3.8   .02   3.3   .03  
ZYX  X95735   Zyxin   4.1   .02   3.4   .02  
CORO1A  X89109   Coronin 1A   3.0   .006   3.6   .005  
CES1  L07765   Carboxylesterase 1 (monocyte/macrophage serine esterase 1)   5.0   .03   7.6   .03  
QSCN6  L42379   Quiescin Q6   2.4   .0007   4.4   .0003  
CHS1  U67615   Chediak-Higashi syndrome 1; lysosomal trafficking regulator (LYST)   3.1   .03   5.6   .02  
NEU1  X78687   Neuraminidase 1   3.9   .03   88.5   .04  
CTSB  HG417-HT417   Cathepsin B   3.9   .005   5.9   .009  
junB  U20734   Oncogene jun-B   2.6   .1   2.7   .09  
VAT1  U18009   Vesicle amine transport protein 1   5.1   .001   2.6   .0007  
FKBP5  U42031   FK506-binding protein 5   5.3   .01   25.0   .01  
PTPNS1  U06681   Protein tyrosine phosphatase, non-receptor type substrate 1   92.9   .007   8.6   .007  
SRPK1  U09564   Protein kinase, SR splicing factor specific, 1   4.3   .0002   3.7   .0002  
ENT1  U81375   Equilibrative nucleoside transporter 1; solute carrier family 29, member 1 (SLC29A1)   2.7   .04   2.5   .04  
NK4  M59807   Natural killer cell transcript 4   2.7   .02   2.9   .02  
TPRC  X99720   TFE3-PRCC fusion transcript; renal cell carcinoma, papillary, 1 (PRCC1)   3.5   .1   3.6   .1  
SRF  J03161   Serum response factor (c-fos serum response element-binding transcription factor)   3.2   .002   3.0   .003  
GLUL  X59834   Glutamate-ammonia ligase (glutamine synthase)   2.9   .03   2.7   .07  
PRKCA  X52479   Protein kinase C, alpha   3.2   .02   2.6   .02  
GPI  K03515   Glucose-6-phosphate isomerase   3.0   .004   2.4   .006  
Up-regulated gene       
MPO  M19507   Myeloperoxidase   1237.1   < .0001   1794.3   .0003  
PKCI-1  U51004   Putative protein kinase C inhibitor   4.3   .005   4.5   .001  
TMSB10  S54005   Thymosin, beta-10   3.9   .004   3.7   .0008  
STIP1  M86752   Stress-induced phosphoprotein, STIP1   2.4   .0006   2.4   .009  
PSME2  D45248   Proteasome (prosome, macropain) activator subunit 2 (PA28 beta)   2.9   .2   3.3   .07  
MPO  M19508   Myeloperoxidase precursor A   2.2   .03   3.9   .006  
PSMB9  X66401   Proteasome (prosome, macropain) subunit, beta type, 9   3.5   .0006   3.3   .0002  
SELPLG  U25956   Selectin P ligand   2.7   .02   2.8   .01  
SOX4  X70683   SRY (sex-determining region Y)-box 4   7.7   < .0001   8.6   .004  
AHR  L19872   Aryl hydrocarbon receptor   6.0   .06   5.0   .05  
SUCLG1  Z68204   Succinate-CoA ligase, GDP-forming, alpha subunit   3.0   .0002   2.7   .0006  
UFD2  D50916   Homolog of yeast (S cerevisiae) ufd2   3.0   .2   4.4   .03  
ANX1  X05908   Annexin I (lipocortin I)   44.5   .03   43.9   .06  
GZMA  M18737   Granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)   44.4   .03   139.6   .004  
MEF2C
 		 L08895
 		 MADS box transcription enhancer factor 2, polypeptide C (myocyte enhancer factor 2C)
 		 27.7
 		 .001
 		 36.9
 		 .04
 
GenBank accession no.
PML/RARα
PLZF/RARα
Gene
Description
Fold change*
P†
Fold change*
P†
Down-regulated gene       
ELA2  M20203   Neutrophil elastase   4713.3   <.0001   3053.6   <.0001  
PRTN3  X55668   Proteinase 3 (serine proteinase, neutrophil, Wegener granulomatosis autoantigen)   1217.5   .0002   1217.5   .0002  
PAI2  M31551   Plasminogen activator inhibitor, type II   1109.8   <.0001   1109.8   <.0001  
CEBPA  U34070   CCAAT/enhancer binding protein (C/EBP), alpha   85.1   .02   85.1   .02  
GAL  M77140   Galanin   230.5   .01   314.7   .009  
PPP5  X89416   Protein phosphatase 5, catalytic subunit   373.4   .01   252.8   .07  
NFKBIE  U91616   Nuclear factor of kappa light polypeptide gene enhancer in B-cell inhibitor, epsilon   59.5   .008   47.3   .01  
PECAM1  L34657   Platelet-endothelial cell adhesion molecule (CD31 antigen)   182.5   .03   146.9   .03  
MEF2  HG4668-HT5083   Transcription factor Mef2, alt Splice 2   129.5   .05   179.7   .04  
RAB31  U59877   Ras-associated protein RAB31; Low Mr GTP-binding protein of the Rab subfamily   162.0   .001   162.0   .003  
NMB  X76534   Glycoprotein NMB; GPNMB; neuromedin B   31.7   .0003   221.7   .0003  
NFIL6  HG3494-HT3688   Nuclear factor, NF-IL6 (C/EBP beta)   6.2   .04   10.8   .03  
IFI30  J03909   Interferon-gamma-inducible protein 30; GILT   97.2   .06   21.0   .06  
ELA2  M27783   Elastase 2, neutrophil   1816.2   .001   19.9   .001  
MNDA  M81750   Myeloid cell nuclear differentiation antigen   6.1   .03   14.8   .02  
CGII  U61836   Cyclin G1 interacting protein   92.9   .007   8.6   .007  
IL-8  M28130   Human interleukin-8 gene   3.0   .02   8.7   .006  
LYZ  M21119   Lysozyme   13.9   .001   17.5   .001  
SPI1  X52056   Spleen focus-forming virus (SFFV) proviral integration oncogene spi1   8.7   .03   143.3   .03  
MCAM  M29277   Melanoma adhesion molecule   8.2   .5   9.5   .8  
CYBB  X04011   Cytochrome b-245, beta polypeptide (chronic granulomatous disease); p91-phox   98.0   .008   55.6   <.0001  
LSP1  M33552   Lymphocyte-specific protein 1 (LSP1)   260.1   .02   261.9   .02  
EPR1  L32866   Human effector cell protease receptor-1; EPR-1   117.1   .02   11.8   .03  
PRG1  X17042   Proteoglycan 1, secretory granule   35.2   <.0001   16.2   <.0001  
APP  Y00264   Amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease)   40.6   .006   91.5   .005  
IL-8  Y00787   Interleukin-8   14.5   .0005   274.7   .0001  
GLVR1  L20859   Solute carrier family 20, member 1 (SLC20A1)   4.7   .01   5.1   .01  
MCP1  HG4069-HT4339   Monocyte chemotactic protein 1   6.4   .002   8.7   .002  
ASAH  U70063   N-acylsphingosine amidohydrolase   153.6   .05   159.7   .06  
COL4A2  X05610   Collagen type IV, alpha-2; COL4A2   453.2   .0002   6.8   .0002  
RAB27A  U57094   RAB27A, member RAS oncogene family   3.1   .1   8.0   .07  
S100P  X65614   S100 calcium-binding protein P   8.8   .009   4.5   .02  
TUBA1  HG2259-HT2348   Tubulin Alpha 1, isoform 44   497.3   .005   549.3   .003  
RNASE3  X55990   Ribonuclease, RNase A family, 3 (eosinophil cationic protein)   3.5   .005   4.1   .004  
BTG1  X61123   B-cell translocation gene 1, antiproliferative   3.0   .1   67.1   .02  
ERBAL2  X12794   v-erbA—related ear-2 gene; nuclear receptor subfamily 2, group F, member 6   3.4   .003   3.2   .008  
P63  X69910   p63 transmembrane protein   3.2   .008   4.3   .006  
CTSD  M63138   Cathepsin D   3.8   .02   3.3   .03  
ZYX  X95735   Zyxin   4.1   .02   3.4   .02  
CORO1A  X89109   Coronin 1A   3.0   .006   3.6   .005  
CES1  L07765   Carboxylesterase 1 (monocyte/macrophage serine esterase 1)   5.0   .03   7.6   .03  
QSCN6  L42379   Quiescin Q6   2.4   .0007   4.4   .0003  
CHS1  U67615   Chediak-Higashi syndrome 1; lysosomal trafficking regulator (LYST)   3.1   .03   5.6   .02  
NEU1  X78687   Neuraminidase 1   3.9   .03   88.5   .04  
CTSB  HG417-HT417   Cathepsin B   3.9   .005   5.9   .009  
junB  U20734   Oncogene jun-B   2.6   .1   2.7   .09  
VAT1  U18009   Vesicle amine transport protein 1   5.1   .001   2.6   .0007  
FKBP5  U42031   FK506-binding protein 5   5.3   .01   25.0   .01  
PTPNS1  U06681   Protein tyrosine phosphatase, non-receptor type substrate 1   92.9   .007   8.6   .007  
SRPK1  U09564   Protein kinase, SR splicing factor specific, 1   4.3   .0002   3.7   .0002  
ENT1  U81375   Equilibrative nucleoside transporter 1; solute carrier family 29, member 1 (SLC29A1)   2.7   .04   2.5   .04  
NK4  M59807   Natural killer cell transcript 4   2.7   .02   2.9   .02  
TPRC  X99720   TFE3-PRCC fusion transcript; renal cell carcinoma, papillary, 1 (PRCC1)   3.5   .1   3.6   .1  
SRF  J03161   Serum response factor (c-fos serum response element-binding transcription factor)   3.2   .002   3.0   .003  
GLUL  X59834   Glutamate-ammonia ligase (glutamine synthase)   2.9   .03   2.7   .07  
PRKCA  X52479   Protein kinase C, alpha   3.2   .02   2.6   .02  
GPI  K03515   Glucose-6-phosphate isomerase   3.0   .004   2.4   .006  
Up-regulated gene       
MPO  M19507   Myeloperoxidase   1237.1   < .0001   1794.3   .0003  
PKCI-1  U51004   Putative protein kinase C inhibitor   4.3   .005   4.5   .001  
TMSB10  S54005   Thymosin, beta-10   3.9   .004   3.7   .0008  
STIP1  M86752   Stress-induced phosphoprotein, STIP1   2.4   .0006   2.4   .009  
PSME2  D45248   Proteasome (prosome, macropain) activator subunit 2 (PA28 beta)   2.9   .2   3.3   .07  
MPO  M19508   Myeloperoxidase precursor A   2.2   .03   3.9   .006  
PSMB9  X66401   Proteasome (prosome, macropain) subunit, beta type, 9   3.5   .0006   3.3   .0002  
SELPLG  U25956   Selectin P ligand   2.7   .02   2.8   .01  
SOX4  X70683   SRY (sex-determining region Y)-box 4   7.7   < .0001   8.6   .004  
AHR  L19872   Aryl hydrocarbon receptor   6.0   .06   5.0   .05  
SUCLG1  Z68204   Succinate-CoA ligase, GDP-forming, alpha subunit   3.0   .0002   2.7   .0006  
UFD2  D50916   Homolog of yeast (S cerevisiae) ufd2   3.0   .2   4.4   .03  
ANX1  X05908   Annexin I (lipocortin I)   44.5   .03   43.9   .06  
GZMA  M18737   Granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)   44.4   .03   139.6   .004  
MEF2C
 		 L08895
 		 MADS box transcription enhancer factor 2, polypeptide C (myocyte enhancer factor 2C)
 		 27.7
 		 .001
 		 36.9
 		 .04
 
*

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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