Supporting information for Kobayashi et al. (April 30, 2002) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.092148299.
Table 1. Relative expression levels of differentially regulated genes
Up-regulated genes | CTL | STM |
OSM: Oncostatin M | M | H |
TNFa : tumor necrosis factor (TNF superfamily, member 2) | L | H |
VEGF: vascular endothelial growth factor | H | VH |
GRO2: cytokine GRO-b | L | VH |
GRO3: cytokine GRO-g | L | M |
SCYA3: small inducible cytokine A3 (homologous to mouse Mip-1a) | H | VH |
SCYA20: small inducible cytokine subfamily A (Exodus-1 or MIP-3a) | VL | M |
LGALS3: galectin 3 | L | VH |
SLC3A2: solute carrier family 3, member 2 | H | H |
SLC11A1: solute carrier family 11, member 1 (Nramp1) | VL | L |
SLC16A5: solute carrier family 16, member 5 | L | M |
SLC20A1: solute carrier family 20, member 1 | M | H |
SLC22A1LS: solute carrier family 22, member 1 | L | M |
SLC26A2: solute carrier family 26, member 2 | VL | L |
HSPCB: (Hsp 90) heat shock 90-kD protein 1, b | M | M |
HSPA4: (Hsp 70) heat shock 70-kD protein 4 | M | H |
PROSC: proline synthetase | L | M |
GARS: glycyl-tRNA synthetase | M | H |
NARS: asparaginyl-tRNA synthetase | M | H |
SPS2: selenophosphate synthetase 2 | M | M |
ST3GALVI: a 2,3-sialyltransferase | M | H |
GNS: glucosamine (N-acetyl)-6-sulfatase | L | M |
SSR4: signal sequence receptor | L | L |
HMOX1: heme oxygenase (decycling) 1 | M | H |
GNPI: glucosamine-6-phosphate isomerase | L | VH |
PDE2A: phosphodiesterase 2A | L | L |
AKR1B1: aldose reductase | L | L |
CXCR5 homolgue: BLR1, Burkitt lymphoma receptor 1 | VL | L |
CCR1: chemokine (C-C motif) receptor 1 | M | H |
CCRL2: chemokine (C-C motif) receptor-like 2 | M | VH |
FCAR: IgA Fc receptor (CD89) | M | M |
PTGER4: prostaglandin E receptor 4 (subtype EP4) | L | M |
PTGER2: prostaglandin E receptor 2 (subtype EP2) | L | M |
NCOR1: nuclear receptor corepressor 1 | L | M |
ADORA2A: adenosine A2a receptor | H | H |
ITPR1: inositol 1,4,5-triphosphate receptor, type 1 | L | H |
PPARD: peroxisome proliferative activated receptor, delta | L | M |
NSMAF: neutral sphingomyelinase (N-SMase) activation-associated factor (FAN) protein | H | VH |
UGCG: UDP-glucose ceramide glucosyltransferase (glucosyl ceramide synthase) | M | H |
RAGD: Rag D protein | M | H |
RAB32: Rab32 | L | H |
ARL4: ADP-ribosylation factor-like 4 | L | M |
HP1: Rho-related protein HP1 | L | M |
RASA2: RAS p21 protein activator 2 | VL | L |
IRF3: IFN regulatory factor 3 | L | M |
ILF3: IL enhancer binding factor 3, 90kD | L | M |
PPP1CA: protein phosphatase 1, catalytic subunit, a isoform | L | L |
IRAK1: IL-1 receptor-associated kinase 1 | L | H |
MAPK6: mitogen-activated protein kinase 6 | L | H |
BAIAP1: BAI1-associated protein 1 | L | M |
DUSP3: dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related) | L | H |
NR4A1: nuclear receptor subfamily 4, group A, member 1; TR3 | M | H |
NR4A2: nuclear receptor subfamily 4, group A, member 2; NUR77 homolog | H | H |
NR4A3: nuclear receptor subfamily 4, group A, member 3; NOR1 | L | H |
NR1D2: nuclear receptor subfamily 1, group D, member 2; EAR-1r | A | L |
TRAF2: TNF receptor-associated factor 2 | M | H |
JUN: v-jun | L | L |
TIEG: TGFb inducible early growth response | M | H |
CRADD: CASP2 and RIPK1 domain containing adaptor with death domain (RAIDD) | L | L |
GADD45B: growth arrest and DNA-damage-inducible, beta | H | VH |
CCND2: cyclin D2 | L | L |
CNK: cytokine-inducible kinase | M | H |
CKS2: CDC28 protein kinase 2 | L | M |
ZWINTAS: ZW10 interactor anti-sense | L | M |
ABL1: v-abl Abelson murine leukemia viral oncogene | VL | L |
MAFF: v-maf | H | VH |
ETS2: v-ets avian erythroblastosis virus E26 oncogene | M | H |
EGR2: early growth response 2 (Krox-20 (Drosophila) homolog | L | M |
DDXL: nuclear RNA helicase | L | H |
ZNF165: zinc finger protein 165 | M | H |
RRN3: RNA polymerase I transcription factor RRN3 | L | H |
SFRS3: splicing factor, arginine/serine-rich 3 | L | M |
HNRPF: heterogeneous nuclear ribonucleoprotein F (HnRNP F) | L | L |
RNMT: RNA (guanine-7-) methyltransferase | L | L |
SCML2: sex comb on midleg (Drosophila)-like 2 | VL | L |
GTF2H1: general transcription factor IIH, polypeptide 1 (62-kD subunit) | L | M |
TGIF: TG-interacting factor (TALE family homeobox) | H | VH |
CD44: CD44 antigen | L | M |
CD48: CD48 antigen | M | VH |
ITGA3: integrin, a 3 (antigen CD49C, a 3 subunit of VLA-3 receptor) | M | M |
TGM3: transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase | M | H |
HEXA: beta-hexosaminidase a -chain | L | M |
GNLY: granulysin | L | M |
GZMA: granzyme A (granzyme 1) | L | L |
NEU1: sialidase 1 (lysosomal sialidase) | L | H |
ADFP: adipose differentiation-related protein | L | H |
ZP3A: zona pellucida glycoprotein 3A | L | M |
ORM1: orosomucoid , human mRNA for a 1-acid glycoprotein | M | H |
COL7A1: collagen, type VII, a 1 | VL | L |
MUC8: mucin 8 | L | L |
CGI-55: PAI-1 mRNA-binding protein | L | M |
FKBP4: FK506-binding protein 4; peptidyl-prolyl-cis trans-isomerase | L | M |
FRAP1: phosphatidylinositol kinase, FK506 binding protein 12-rapamycin-associated protein 1 | VL | L |
PKR: P1 kinase (p68 kinase) | L | M |
CCS: copper chaperone for superoxide dismutase | VL | L |
DNMT1: DNA (cytosine-5-)-methyltransferase 1 | VL | L |
PPP1R1A: protein phosphatase 1, regulatory (inhibitor) subunit 1A | L | L |
STX16: syntaxin 16 | VL | L |
VPS11: vacuolar protein sorting 11 | L | M |
KTN1: kinectin 1 (kinesin receptor) | L | L |
TPI1: triosephosphate isomerase 1 | M | H |
SERPINB9: serine/cysteine proteinase inhibitor, clade B, member 9 | L | M |
SDC1: syndecan 1 | M | H |
SNK: serum-inducible kinase | VL | L |
NCOA2: nuclear receptor coactivator 2; glucocorticoid receptor-interacting protein-1 (GRIP1) | VL | L |
TCF20: transcription factor 20 (AR1) | L | M |
CRIP2: cysteine-rich protein 2, zinc-finger LIM domain protein | L | M |
RIPK1: (RIP) receptor (TNFRSF)-interacting serine-threonine kinase | L | L |
TAF2B: TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150 kD | VL | L |
VAMP8: vesicle-associated membrane protein 8 (endobrevin) | VL | L |
SH3GLB1: SH3-domain, GRB2-like, endophilin B1: Bax-interacting factor 1 | L | M |
PSEN1: presenilin 1 (Alzheimers disease 3) | L | M |
ERCC1: excision repair cross-complementing rodent repair deficiency | A | L |
SLC4A1AP: solute carrier family 4, member 1 | M | M |
PSMD13: proteasome (prosome, macropain) 26S subunit | VL | L |
BAT8: HLA-B associated transcript 8 | VL | L |
MPIF-1: MIP-3 precursor (SCYA23) | VL | L |
ABCB9: ATP-binding cassette, sub-family B (MDR/TAP), member 9 | L | M |
KIF3C: kinesin family of microtubule-associated motor proteins | L | L |
MEF2C: MADS box transcription enhancer factor 2 | VL | L |
KPNA3: karyopherin a 3 (importin a 4) | VL | M |
CTSL: Cathepsin L | L | M |
RAD1: RAD1 (Schizosaccharomyces pombe) homolog | L | M |
FUS: fusion, Tls/Chop oncogene derived from malignant liposarcoma | H | VH |
HM74: putative chemokine receptor | VH | VH |
SGSH: N-sulfoglucosamine sulfohydrolase (sulfamidase) | M | H |
GADD34: growth arrest and DNA-damage-inducible 34 | H | VH |
PLAU: plasminogen activator, urokinase | H | VH |
LARGE: like-glycosyltransferase | L | L |
HSPA9B: heat shock 70-kD protein 9B (mortalin-2) | VL | L |
SCYA4: small inducible cytokine A4 (homologous to mouse Mip-1b) | VH | VH |
MTCP1: mature T-cell proliferation 1 | VL | L |
GLA: galactosidase, a | H | VH |
CCNT1: cyclin T1 | L | M |
C8FW phosphoprotein: phosphoprotein regulated by mitogenic pathways | H | H |
YY1: YY1 transcription factor | VL | L |
GLUD1: glutamate dehydrogenase 1 (EC 1.4.1.3.) | L | L |
TYRO3: TYRO3 protein tyrosine kinase (Sky) | VL | L |
PDE2A: phosphodiesterase 2A | L | L |
CSE1L: (CAS) chromosome segregation 1 (yeast homolog)-like | A | VL |
GNA13: guanine nucleotide binding protein (G protein), a 13 | H | H |
GCB: glucocerebrosidase | M | H |
VATD: vacuolar proton pump delta polypeptide | L | H |
SH3BP2: SH3-domain binding protein 2 | VL | L |
TP53BP2: tumor protein p53-binding protein, 2; Bcl2, p53 binding protein | VL | L |
LILRA2: leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2 | L | M |
RENBP: renin-binding protein | VL | L |
SNAP23: synaptosomal-associated protein, 23 kD | VL | L |
ATF6: activating transcription factor 6 | L | L |
TEGT: testis enhanced gene transcript (BAX inhibitor 1) (BI-1) | M | H |
CREG: cellular repressor of E1A-stimulated genes | L | H |
SPIB: Spi-B transcription factor (Spi-1/PU.1 related) | L | L |
EIF2S3: eukaryotic translation initiation factor 2, subunit 3 (gamma, 52 kD) | L | M |
CR1: complement component (3b/4b) receptor 1 (CD35) | L | L |
CEACAM1: (CD66a) | L | M |
CTNS: cystinosis, nephropathic; lysosomal membrane protein cystinosin | L | M |
FCGR2A: receptor for Fc fragment of IgG, low affinity IIa, (CD32) | H | H |
GK: glycerol kinase | L | M |
ZNF288: zinc finger protein 288 | L | L |
TRIP8: thyroid hormone receptor interactor 8 | M | H |
AKR1A1: aldo-keto reductase family 1, member A1 (aldehyde reductase) | M | H |
PSCDBP: pleckstrin homology, Sec7 and coiled/coil domains, binding protein | M | H |
MAN1A1: mannosidase, a , class 1A, member 1 | L | L |
MFNG: manic fringe (Drosophila) homolog | M | M |
TNFRSF8: tumor necrosis factor receptor superfamily, member 8 | A | L |
Phret 1 homolog: hypothetical protein FLJ20783 | L | M |
IFIT2 IFN-induced protein with tetratricopeptide repeats 2 | M | H |
RBMX: RNA binding motif protein, X chromosome: | L | L |
PLAB: prostate differentiation factor | L | M |
EGR3: early growth response 3 | H | VH |
CKS2: CDC28 protein kinase 2 | L | H |
SMPD1: sphingomyelin phosphodiesterase 1, acid lysosomal (acid sphingomyelinase) | L | M |
SMPD2: sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase) | L | M |
MCM2: minichromosome maintenance deficient (Saccharomyces cerevisiae) 2 (mitotin) | L | M |
MCM6: minichromosome maintenance deficient (mis5, S. pombe) 6 | L | H |
MAP-1: modulator of apoptosis 1 | L | M |
PPAP2B: phosphatidic acid phosphatase type 2B | L | VH |
DUSP10: dual specificity phosphatase 10 | L | M |
DYRK3: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3 | A | L |
BRF2: butyrate response factor 2 (EGF-response factor 2) | M | VH |
TRAF1: TNF receptor-associated factor 1 | M | H |
MAD: MAX dimerization protein | M | H |
MGA: Max-interacting protein | VL | L |
RAD1: RAD1 (S. pombe) homolog | VL | M |
UQCRC2: ubiquinol-cytochrome c reductase core protein II | L | H |
TSSC3: tumor suppressing subtransferable candidate 3 | M | H |
GPNMB: glycoprotein (transmembrane) nmb | A | L |
SCML2: sex comb on midleg (Drosophila)-like 2 | VL | L |
PAK2: p21 (CDKN1A)-activated kinase 2 | M | H |
FOSB: FBJ murine osteosarcoma viral oncogene homolog B | H | VH |
USF2: upstream transcription factor 2, c-fos interacting | L | H |
DSS1: deleted in split-hand/split-foot 1 region | L | L |
MAP4K4: mitogen-activated protein kinase kinase kinase kinase 4 | L | L |
NFKB2: nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) | H | H |
TLR2: toll-like receptor 2 | H | VH |
BTG3: BTG family, member 3; member of the Tob/BTG1 family of antiproliferative proteins | VL | L |
MADH1: MAD (mothers against decapentaplegic, Drosophila) homolog 1 | M | H |
TNFRSF14: tumor necrosis factor receptor superfamily, member 14 | H | VH |
FIP2: tumor necrosis factor a -inducible cellular protein containing leucine zipper domains | VL | L |
BAX: BCL2-associated X protein | L | M |
TRAF3: TNF receptor-associated factor 3 | M | H |
Down-regulated genes |
|
|
UBCH10: ubiquitin carrier protein E2-C | L | VL |
STX10: syntaxin 10 | H | L |
TBCC: tubulin-specific chaperone c | H | M |
CA4: carbonic anhydrase IV | H | M |
GPX3: plasma glutathione peroxidase 3 | H | L |
HRB2: HIV-1 rev binding protein 2 | L | VL |
TLR1: toll-like receptor 1 | H | H |
FOLR3: folate receptor 3 (gamma) | M | VL |
ROCK2: rho kinase | L | VL |
PTK9L: protein tyrosine kinase 9-like (A6-related protein) | H | M |
PIK3CG: phosphoinositide-3-kinase, catalytic, gamma polypeptide | L | VL |
SIPA1: signal-induced proliferation-associated gene 1 | H | H |
RASA1: RAS p21 protein activator (GTPase activating protein) 1 | L | L |
CEP2: Cdc42 effector protein 2 | H | M |
DEDD: death effector domain-containing | M | L |
CASP3: caspase 3 | L | L |
BCL2L1: BCL2-like 1, BCL-XL | L | VL |
BLZF1: basic leucine zipper nuclear factor 1 (JEM-1) | L | VL |
ZNF200: zinc finger protein 200 | H | M |
PCDHA13: protocadherin a 13 | L | VL |
THBD: thrombomodulin | H | L |
CNTN2: contactin 2, axonal (axonin-1) | M | L |
MAP3K4: (MTK1) mitogen-activated protein kinase kinase kinase | VL | A |
TACI: Transmembrane activator and CAML interactor | M | L |
PMS2L8: postmeiotic segregation increased 2-like 8 | L | VL |
RAC1: ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) | L | VL |
FLOT2: flotillin 2 | H | M |
TFF-I interacting peptide: mucin-associated molecule | M | L |
CACNB4: calcium channel, voltage-dependent, beta 4 subunit | VL | A |
CCNG2: cyclin G2: Cyclin G2 | H | M |
CLK2: CDC-like kinase 2 | VL | VL |
CLK3: CDC-like kinase 3 | M | L |
CDKN1B: cyclin-dependent kinase inhibitor 1B (p27, Kip1) | H | M |
NR3C1: nuclear receptor subfamily 3, group C, member 1 | M | L |
PPM1A: protein phosphatase 1A (formerly 2C) | M | L |
MINK: misshapen/NIK-related kinase | L | VL |
PP15: nuclear transport factor 2 (placental protein 15) or NFT2 | L | VL |
GPLD1: (PLD1) glycosylphosphatidylinositol specific phospholipase D1 | L | VL |
PDGFB: platelet-derived growth factor beta polypeptide | L | VL |
LSM4: U6 snRNA-associated Sm-like protein | L | VL |
VPS45B: vacuolar protein sorting 45B | VL | A |
CASP2: caspase 2 | L | VL |
SORL1: sortillin receptor | VH | H |
PTP4A1: protein tyrosine phosphatase type IVA, member 1 | M | L |
CD14: CD14 antigen | VH | H |
PIG7: LPS-induced TNF- a factor | VH | H |
ARHA: RhoA | VH | H |
HLA-F: major histocompatibility complex, class I, F | VH | H |
TAF2A: TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250 kD | M | L |
ADH5: alcohol dehydrogenase | L | VL |
LY117: lymphocyte antigen 117 (B144) | H | M |
TYROBP: TYRO protein tyrosine kinase binding protein | VH | H |
IFITM1: IFN-induced transmembrane protein 1 | H | M |
LENG4: leukocyte receptor cluster (LRC) member 4 | H | M |
ARSA: arylsulfatase A | M | L |
GYPE: glycophorin E | L | VL |
FRAG1: FGF receptor-activating protein 1 | L | VL |
TBP: TATA box binding protein | L | VL |
TGFBR2: transforming growth factor, beta receptor II (70-80 kD) | H | M |
IL1A: IL 1, a ; IL 1 a (IL-1 a) | L | VL |
MBD4: methyl-CpG binding domain protein 4 | H | M |
TRN-SR: transportin-SR | L | VL |
ZNF238: zinc finger protein 238 | H | M |
IL17B: IL 17 b | L | VL |
MDS019: (MCM2, CDC47) | L | VL |
DGSI: DiGeorge syndrome critical region gene DGSI | L | VL |
CCT6A: chaperonin containing TCP1, subunit 6A (zeta 1) | VL | VL |
SLC7A11: solute carrier family 7,member 11 | L | VL |
DDX1: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1 | VL | VL |
MRC OX-2 antigen (CD200) | L | VL |
ITGA1: (VLA-1) integrin, a 1 | L | VL |
RPP20: POP7 | VL | VL |
LDLR: low density lipoprotein receptor | L | VL |
MBL2: mannose-binding lectin (protein C) 2 | VL | VL |
PRKCABP: protein kinase C, a binding protein | M | L |
PMS2L9: postmeiotic segregation increased 2-like 9 | L | VL |
MAN1A2: mannosidase, a , class 1A, member 2 | VL | VL |
ABL: c-abl | M | L |
API5L1: API5-like 1 | VL | VL |
QSCN6: quiescin Q6 | M | L |
MAP4K1: mitogen-activated protein kinase kinase kinase kinase 1 | L | VL |
MAP2K4: mitogen-activated protein kinase kinase 4 | L | VL |
MINK: Misshapen/NIK-related kinase | L | VL |
EPOR: erythropoietin receptor | M | L |
TGFBI: transforming growth factor, beta-induced, 68 kD | L | VL |
SKIL: SKI-like oncoprotein | L | VL |
XPC: xeroderma pigmentosum, complementation group C | H | M |
ERCC5: excision repair cross-complementing rodent repair deficiency | M | L |
PSMD13: proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 | VL | VL |
MEF2C: MADS box transcription enhancer factor 2, polypeptide C | L | VL |
TP53BPL: tumor protein p53-binding protein | M | L |
BCL11A: B-cell CLL/lymphoma 11A (zinc finger protein) | VL | A |
TUCAN: tumor up-regulated CARD-containing antagonist of caspase nine | M | L |
CASP8: caspase 8 | L | VL |
CASP9: caspase 9 | VL | VL |
POLB: polymerase (DNA directed), beta | M | L |
CDKN2D: cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) | H | M |
STK17A: serine/threonine kinase 17a (apoptosis-inducing) | L | VL |
STK17B: serine/threonine kinase 17b (apoptosis-inducing) | H | M |
TP53BPL: tumor protein p53-binding protein | M | L |
GADD45G: growth arrest and DNA-damage-inducible, gamma | L | VL |
TNFSF10: TNF (ligand) superfamily, member 10 | H | M |
TRADD: TNFRSF1A-associated via death domain | M | L |
DEFCAP: death effector filament-forming Ced-4-like apoptosis protein | H | M |
TGFB1: transforming growth factor, beta 1 | L | VL |
TIAF1: TGFB1-induced antiapoptotic factor 1 | L | VL |
MAP2K1: mitogen-activated protein kinase kinase 1 | L | VL |
MAPK14: mitogen-activated protein kinase 14 | H | M |
MAPK9: mitogen-activated protein kinase 9 | L | VL |
MKNK1: MAP kinase-interacting serine/threonine kinase 1 | M | L |
JIK: STE20-like kinase:JNK/SAPK inhibitory kinase | L | VL |
MADHIP: MAD homolog interacting protein | M | L |
MLX: MAX-like bHLHZIP protein | L | VL |
MXI1: MAX-interacting protein 1 | H | M |
MAP4K2: mitogen-activating protein kinase kinase kinase kinase 2 | L | VL |
FOXO1A: forkhead box O1A | M | L |
HOXA1: homeobox A1 | L | VL |
HHEX: hematopoietically expressed homeobox | M | L |
NFATC3: nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 3 | M | L |
CDC2L5: cell division cycle 2-like 5 (cholinesterase-related cell division controller) | L | VL |
CLASP1: CLIP-associating protein 1 | M | L |
PRKDC: protein kinase, DNA-activated, catalytic polypeptide | M | L |
FOS: v-fos FBJ murine osteosarcoma viral oncogene homolog | H | M |
DATF1: death-associated transcription factor 1 | L | VL |
ING1: inhibitor of growth family, member 1 | L | VL |
TLE4: transducin-like enhancer of split 4, homolog of Drosophila E (sp1) | L | VL |
Relative levels of differentially expressed genes. Genes identified as differentially expressed were categorized by average difference intensity (ADI) values. A, genes called absent by Affymetrix software; VL, very low expression = ADI <50; L, low expression = ADI 50-200; M, moderate expression = ADI 200-500; H, high expression = ADI 500-1500; VH, very high expression = ADI >1500. The gene expression levels in the time-matched control (CTL) or polymorphonuclear leukocytes (PMNs) activated after phagocytosis (STM) were assigned based on the average ADI of the 3 stimuli for shared genes at a given time or based on the expression level for genes regulated by specific receptors as indicated in Figs. 3 and 4. Data analysis was performed with GENESPRING software (Silicon Genetics, Redwood City, CA) as described in Materials and Methods.