Table 2.

List of Initial Set of Genes Analyzed on NanoString

Entrez gene symbol	Entrez gene name	IFN probe set ID	Fold change	CANDLE probe set ID	Fold change	Genes removed
Upregulated genesa
>2 × increased in CANDLE
AIM2	Absent in melanoma 2			206513_at	5.77	x
APOL1	Apolipoprotein L, 1			209546_s_at	2.26	x
APOL6	Apolipoprotein L, 6	219716_at	3.44	241869_at	5.02
BCL2L1	BCL2-like 1	206665_s_at	2.25	215037_s_at	3.80
BIRC5	Baculoviral IAP repeat-containing 5	202094_at	−2.66	202095_s_at	3.70	x
C1QB	Complement component 1, q subcomponent, B chain			202953_at	2.16	x
CASP1	Caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)			1552703_s_at	2.96	x
CCNA1	Cyclin A1			205899_at	7.71	x
CCNA2	Cyclin A2	203418_at	2.85	203418_at	2.19	x
CCRL2	Chemokine (C-C motif) receptor-like 2			211434_s_at	2.36	x
CD274	CD274 molecule	223834_at	6.70	227458_at	3.81
CD80	CD80 molecule			1554519_at	2.05	x
CLTCL1	Clathrin, heavy chain-like 1			205944_s_at	2.80	x
CXCL10	Chemokine (C-X-C motif) ligand 10	204533_at	12.92	204533_at	4.03
DDX58	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	218943_s_at	4.65	242961_x_at	6.53
DDX60	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	218986_s_at	2.00	218986_s_at	4.60
EIF2AK2	Eukaryotic translation initiation factor 2-alpha kinase 2	204211_x_at	2.53	204211_x_at	2.72
FCGR1A	Fc fragment of IgG, high-affinity Ia, receptor (CD64)	216951_at	2.13	216951_at	5.22
FCGR1B	Fc fragment of IgG, high-affinity Ib, receptor (CD64)			214511_x_at	4.34	x
GBP1	Guanylate-binding protein 1, interferon-inducible	202269_x_at	4.85	231578_at	4.45
GBP2	Guanylate-binding protein 2, interferon-inducible			242907_at	2.01	x
H6PD	Hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)			226160_at	2.28	x
HERC5	Hect domain and RLD 5	219863_at	5.56	219863_at	6.50
HERC6	Hect domain and RLD 6	219352_at	2.23	219352_at	4.63
IFI27	Interferon alpha-inducible protein 27	202411_at	2.28	202411_at	72.76
IFI35	Interferon-induced protein 35	209417_s_at	3.51	209417_s_at	2.80
IFI44	Interferon-induced protein 44	214059_at	4.01	214059_at	9.41
IFI44L	Interferon-induced protein 44-like	204439_at	2.94	204439_at	13.36
IFI6	Interferon alpha-inducible protein 6	204415_at	6.22	204415_at	3.94
IFIH1	Interferon induced with helicase C domain 1	216020_at	4.41	1555464_at	3.52
IFIT1	Interferon-induced protein with tetratricopeptide repeats 1	203153_at	5.85	203153_at	8.68
IFIT2	Interferon-induced protein with tetratricopeptide repeats 2	217502_at	31.77	217502_at	2.52
IFIT3	Interferon-induced protein with tetratricopeptide repeats 3	204747_at	11.11	204747_at	7.16
IFIT5	Interferon-induced protein with tetratricopeptide repeats 5	203595_s_at	2.96	203596_s_at	3.63
IGLL1/IGLL5	Immunoglobulin lambda-like polypeptide 1			217235_x_at	2.15	x
IL10	Interleukin 10			207433_at	2.18	x
IL15	Interleukin 15			205992_s_at	2.52	x
IL18R1	Interleukin 18 receptor 1			206618_at	2.67	x
IL1RN	Interleukin 1 receptor antagonist	212657_s_at	2.45	216243_s_at	2.43
IRF7	Interferon regulatory factor 7	208436_s_at	2.19	208436_s_at	3.09
ISG15	ISG15 ubiquitin-like modifier	205483_s_at	7.20	205483_s_at	7.05
LAMP3	Lysosomal-associated membrane protein 3	205569_at	4.99	205569_at	4.24
LGALS3BP	Lectin, galactoside-binding, soluble, 3-binding protein			200923_at	5.39	x
LY6E	Lymphocyte antigen 6 complex, locus E	202145_at	3.08	202145_at	6.19
MMP1	Matrix metallopeptidase 1 (interstitial collagenase)			204475_at	4.25	x
MMP9	Matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)	203936_s_at	3.27	203936_s_at	3.53	x
MTMR3	Myotubularin-related protein 3			202198_s_at	2.33	x
MUC1	Mucin 1, cell surface-associated			213693_s_at	2.84	x
MX1	Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)	202086_at	4.19	202086_at	5.53
NF1	Neurofibromin 1	204323_x_at	2.31	216115_at	3.00
OAS1	2′-5′-Oligoadenylate synthetase 1, 40/46 kDa	202869_at	2.12	205552_s_at	8.06
OAS2	2′-5′-Oligoadenylate synthetase 2, 69/71 kDa	204972_at	2.22	228607_at	4.26
OAS3	2′-5′-Oligoadenylate synthetase 3, 100 kDa	218400_at	2.66	218400_at	9.20
OASL	2′-5′-Oligoadenylate synthetase-like	205660_at	6.72	210797_s_at	5.44
PLSCR1	Phospholipid scramblase 1	202430_s_at	2.51	202446_s_at	3.65
PML	Promyelocytic leukemia	206503_x_at	2.57	211012_s_at	3.07
PRDX2	Peroxiredoxin 2			211658_at	2.05	x
RBX1	Ring-box 1, E3 ubiquitin protein ligase			218117_at	2.64	x
RSAD2	Radical S-adenosyl methionine domain-containing 2	213797_at	4.39	213797_at	12.91
RTP4	Receptor (chemosensory) transporter protein 4	219684_at	3.20	219684_at	5.05
SAMD9	Sterile alpha motif domain-containing 9	219691_at	3.00	219691_at	3.00
SEPT4	Septin 4			210657_s_at	7.52	x
SOCS1	Suppressor of cytokine signaling 1	210001_s_at	5.65	210001_s_at	2.13
STAT1	Signal transducer and activator of transcription 1, 91 kDa	AFFX-HUMISGF3A/M97935_5_at	2.07	AFFX-HUMISGF3A/M97935_MA_at	3.25
STAT2	Signal transducer and activator of transcription 2, 113 kDa	205170_at	2.45	205170_at	2.18
TAP2	Transporter 2, ATP-binding cassette, subfamily B (MDR/TAP)			208428_at	3.89	x
TDRD7	Tudor domain-containing 7	213361_at	2.73	213361_at	2.05
USP18	Ubiquitin-specific peptidase 18	219211_at	12.11	219211_at	13.86
USP6NL	USP6N terminal-like			238164_at	4.61	x
ZC3HAV1	Zinc finger CCCH-type, antiviral 1	213051_at	2.14	220104_at	2.33
>2 × increased in IFN probe set, but not increased in CANDLE
ATF3	Activating transcription factor 3	202672_s_at	9.33
BST2	Bone marrow stromal cell antigen 2	201641_at	2.25
CCL2	Chemokine (C-C motif) ligand 2	216598_s_at	45.74			x
DEFB1	Defensin beta 1	210397_at	3.98			x
FAS	Fas (TNF receptor superfamily, member 6)	215719_x_at	2.75
HSH2D	Hematopoietic SH2 domain-containing	1552623_at	3.68			x
IDO1	Indoleamine 2,3-dioxygenase 1	210029_at	2.39
IL1B	Interleukin 1, beta	205067_at	3.58
IRF1	Interferon regulatory factor 1	202531_at	2.16
IRF2	Interferon regulatory factor 2	203275_at	2.25			x
ITGB3	Integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	204626_s_at	2.03
KLF6	Kruppel-like factor 6	208960_s_at	2.72
MDM2	Mdm2 p53-binding protein homolog (mouse)	211832_s_at	2.28
MX2	Myxovirus (influenza virus) resistance 2 (mouse)	204994_at	2.13
PELI1	Pellino E3 ubiquitin protein ligase 1	218319_at	2.21
PRKCD	Protein kinase C delta	202545_at	2.16			x
PRKD2	Protein kinase D2	209282_at	2.28
PTAFR	Platelet-activating factor receptor	206278_at	3.22
PTGES	Prostaglandin E synthase	210367_s_at	2.58
SOD2	Superoxide dismutase 2, mitochondrial	215078_at	2.41
SP100	SP100 nuclear antigen	202864_s_at	2.22
SP110	SP110 nuclear body protein	208392_x_at	3.47
SPI1	Spi-1 proto-oncogene	205312_at	2.54
TLR4	Toll-like receptor 4	221060_s_at	2.10
TNFRSF1A	TNF receptor superfamily member 1A	207643_s_at	2.05
TNFSF10	TNF superfamily member 10	202687_s_at	2.39
TNFSF13B	TNF superfamily member 13b	223502_s_at	2.47
TREX1	Three prime repair exonuclease 1	205875_s_at	3.56
TRIM14	Tripartite motif-containing 14	203147_s_at	2.45
TYMP	Thymidine phosphorylase	217497_at	4.08
Downregulated genesb
>2 × decreased in CANDLE
ADORA2B	Adenosine A2b receptor			205891_at	−2.55	x
ALOX15	Arachidonate 15-lipoxygenase			207328_at	−4.15
AUTS2	Autism susceptibility candidate 2			212599_at	−3.65	x
CAMK4	Calcium/calmodulin-dependent protein kinase IV			241871_at	−3.27	x
CCL5	Chemokine (C-C motif) ligand 5			204655_at	−2.11
CCR5	Chemokine (C-C motif) receptor 5			206991_s_at	−2.39	x
CD2	CD2 molecule			205831_at	−2.74	x
CD40LG	CD40 ligand			207892_at	−4.33	x
CIITA	Class II, major histocompatibility complex, transactivator			205101_at	−2.26
CXCL1	Chemokine (C-X-C motif) ligand 1 (melanoma growth-stimulating activity, alpha)			204470_at	−2.40
CXCR3	Chemokine (C-X-C motif) receptor 3			207681_at	−2.03
DPP4	Dipeptidyl-peptidase 4			203717_at	−2.28	x
EEF1A1	Eukaryotic translation elongation factor 1 alpha 1			227708_at	−2.27	x
GATA3	GATA-binding protein 3			209604_s_at	−3.17	x
HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1			212999_x_at	−3.53	x
IL23A	Interleukin 23, alpha subunit p19			240102_at	−3.08	x
IL24	Interleukin 24			206569_at	−2.13
IL32	Interleukin 32			203828_s_at	−2.31
IL8	Interleukin 8	202859_x_at	−2.40	202859_x_at	−5.24
KLRK1	Killer cell lectin-like receptor subfamily K, member 1			1555691_a_at	−2.61	x
MARCKSL1	MARCKS-like 1			200644_at	−2.58	x
NCR3	Natural cytotoxicity-triggering receptor 3			211583_x_at	−3.11	x
PIGR	Polymeric immunoglobulin receptor			226147_s_at	−2.03	x
PTGS2	Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	1554997_a_at	2.82	1554997_a_at	−4.94	x
TBX21	T-box 21			220684_at	−2.14	x
>2 × decreased in IFN probe set, but not increased in CANDLE
CCDC75	Coiled-coil domain-containing 75	228495_at	−2.30
CXCL2	Chemokine (C-X-C motif) ligand 2	209774_x_at	−2.88
ELAVL1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)	244660_at	−5.24			x
ICOSLG	Inducible T cell costimulator ligand	213450_s_at	−2.36			x
ITGAV	Integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)	202351_at	−2.17			x
PARVG	Parvin, gamma	244229_at	−2.20
TLR3	Toll-like receptor 3	206271_at	−2.04
Added later for initial NanoString IRG listc
C1QC	Complement component 1, q subcomponent, C chain					x
CEACAM1	Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)					x
CYSLTR2	Cysteinyl leukotriene receptor 2					x
IGFBP4	Insulin-like growth factor-binding protein 4					x
IRF3	Interferon regulatory factor 3					x
IFN and IFNR genesd
IFNA1	Interferon, alpha 1	208375_at				x
IFNA10	Interferon alpha 10	208261_x_at				x
IFNA16	Interferon alpha 16	208448_x_at				x
IFNA2	Interferon alpha 2	211338_at
IFNA21	Interferon, alpha 21	211145_x_at				x
IFNA5	Interferon alpha 5	214569_at				x
IFNA6	Interferon alpha 6	208548_at				x
IFNA7	Interferon, alpha 7	208259_x_at				x
IFNA8	Interferon alpha 8	207932_at				x
IFNAR1	Interferon alpha and beta receptor subunit 1	204191_at
IFNAR2	Interferon (alpha, beta, and omega) receptor 2	204785_x_at
IFNB1	Interferon, beta 1, fibroblast	208173_at
IFNG	Interferon, gamma	210354_at
IFNGR1	Interferon gamma receptor 1	202727_s_at
IFNGR2	Interferon gamma receptor 2	201642_at
Housekeeping genese
ALAS1	Delta-aminolevulinate synthase 1
G6PD	Glucose-6-phosphate dehydrogenase					x
HPRT1	Hypoxanthine phosphoribosyltransferase 1
POLR2A	RNA polymerase II subunit A					x
TBP	TATA box-binding protein
TUBB	Tubulin beta class I

^aIncreased expression versus HCs potential IFN target genes.

^bDecreased expression versus HCs IFN target genes.

^cAdded afterwards.

^dIFN or IFNR gene added.

^eHousekeeping gene.

This list of genes is based on previous microarray data from an IFN-alpha-treated hepatitis patient and 1 CANDLE patient at multiple time points with microarray probe set ID and fold change comprising the initial 152 candidate gene list and 6 housekeeping genes. Genes have been grouped alphabetically within each category as described. In the right-most column, x indicates genes removed from initial candidate list to get to target gene list 2, which has 92 IRS genes and 4 housekeeping genes.

IFN, interferon; IRG, IFN response gene; IRS, IFN-regulated gene signature.