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 (Alzheimer’s 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.