Gene Expression Profiling in Wegener´s Granulomatosis

Supplementary Table 1 A

Gene
Symbol / WG vs NC / WG vs CRS / CRS vs NC
Fold Change
Cutoff / P-Value
FDR / Fold Change
Cutoff / P-Value
FDR / Fold Change
Cutoff / P-Value
FDR
CD363) / 2.92 / 0.004881 / 2.67 / 0.01372 / 1.09 / 1.254701
-1.66/1.68 / 0 / -1.7/1.7 / 0.01 / -1.68/1.69 / 70.95
DEFB13) / 4.45 / 0.000286 / 3.37 / 0.017267 / 1.32 / 1.009918
-2.57/2.61 / 0.03 / -2.65/2.63 / 0.97 / -2.61/2.64 / 60.64
DEFB4 / on / 0.000001 / on / 0.000004 / 1) / 1.220367
-3.82/4.69 / 45.19 / -4.76/4.72 / 46.68 / -3.79/4.76 / 0
FN1 / -1.78 / 0.025641 / -1.20 / 0.41699 / -1.48 / 2.414444
-1.9/1.84 / 7.02 / -1.92/1.96 / 54 / -1.95/1.9 / 20.67
IFNG3) / -14.06 / 0.028268 / -20.66 / 0.082397 / 1.47 / 1.13421
-8.51/7.92 / 1.96 / -8.52/8.92 / 1.24 / -8.91/7.74 / 75.75
IL17D3) / -2.67 / 0.027855 / -1.70 / 0.167533 / -1.57 / 1.685765
-1.73/1.71 / 0.02 / -1.75/1.77 / 7.08 / -1.78/1.73 / 10.95
IL23A / 1.16 / 0.31042 / 2.43 / 0.035723 / -2.10 / 1.321233
-2.06/2.07 / 77.05 / -2.07/2.12 / 0.73 / -2.14/2.09 / 5.48
LYZ3) / -3.42 / 0.040221 / -5.37 / 0.035611 / 1.57 / 1.021668
-1.97/1.96 / 0.05 / -2/2.06 / 0 / -2.03/1.97 / 20.99
MYD88 / 1.20 / 0.045862 / 1.24 / 0.031342 / -1.03 / 1.279825
-1.22/1.23 / 9.22 / -1.23/1.24 / 4.68 / -1.22/1.23 / 82.4
NLRC33) / -2.13 / 0.027607 / -1.70 / 0.142362 / -1.26 / 1.122808
-1.78/1.79 / 1.05 / -1.82/1.83 / 9.58 / -1.79/1.81 / 54.18
S100A7 / on / 0.000001 / on / 0.00004 / 1) / 1.988413
1) / 6.62 / 1) / 8.07 / 1) / 0
TGFB13) / -1.36 / 0.030968 / -1.42 / 0.106455 / 1.05 / 1.01658
-1.29/1.28 / 2.02 / -1.29/1.3 / 0.81 / -1.3/1.29 / 64.42
TICAM1 / -1.45 / 0.227635 / -1.67 / 0.029015 / 1.15 / 1.021668
-1.57/1.59 / 11.68 / -1.6/1.59 / 2.58 / -1.58/1.6 / 55.48
TLR43) / -2.10 / 0.001624 / -2.29 / 0.032211 / 1.09 / 1.065864
-1.54/1.53 / 0.14 / -1.55/1.6 / 0.08 / -1.58/1.53 / 71.61

Expression changes of all transcripts, which are regulated significantly in at least one of the three comparisons (WG vs NC, WG vs CRS or CRS vs NC). Fold changes are based on ratios, p-values are based on the Mann-Whitney U-test and corrected for multiple testing using the Benjamini-Hochberg correction, FDRs are based on a Westfall and Young permutation (k=10.000 permutations) while the cutoffs describe the boundaries beyond which the fold-change would result in a FDR > 5%.

1) value could not be determined (due to a on/off effect, or due to the gene not being detected); 2) gene measurement did not pass the quality control (not enough measurements); 3) considered a candidate transcript (due to its regulation when comparing WG to NC).

Supplementary Table 1 B

Gene
Symbol / WG vs NC / WG vs CRS / CRS vs NC
Fold Change / P-Value / Fold Change / P-Value / Fold Change / P-Value
CAMP / -1.02 / 1.021277 / -2.30 / 0.649966 / 2.24 / 1.070704
CARD8 / 1.13 / 0.926151 / 1.00 / 0.553923 / 1.12 / 1.411793
CARD9 / -1.37 / 0.395114 / -1.25 / 0.480362 / -1.09 / 1.022222
CD14 / 1.19 / 0.642477 / -1.02 / 0.75425 / 1.21 / 2.449074
DEFA52) / 1) / 1 / 1) / 1 / 1) / 1
DEFB103B2) / 1) / 0.963441 / 1) / 1 / 1) / 1
F2RL1 / 1.09 / 0.792474 / 1.14 / 0.683452 / -1.04 / 1.168741
IL1B / -1.16 / 0.969675 / -1.56 / 0.668628 / 1.34 / 1.179097
IL32 / -1.58 / 0.405279 / -1.54 / 0.363319 / -1.03 / 1.024463
IL4 / - / 1 / 1) / 1 / 1) / 1
IL8 / 1.32 / 0.82502 / 1.02 / 0.79002 / 1.29 / 1.057862
MEFV / -1.18 / 0.699808 / 1.67 / 0.665974 / -1.97 / 1.451105
NLRC4 / -1.37 / 0.761711 / on / 0.522714 / off / 1.598635
NLRC5 / off / 0.889857 / off / 0.80064 / 1.20 / 1.05608
NLRP1 / -1.51 / 0.213394 / 1.01 / 0.669865 / -1.53 / 1.122808
NLRP3 / -1.29 / 0.775128 / -1.46 / 0.697957 / 1.13 / 1.178552
NLRX1 / -1.77 / 0.267325 / -1.63 / 0.725827 / -1.08 / 1.190666
NOD1 / -1.32 / 0.066606 / -1.38 / 0.100836 / 1.04 / 1.10453
NOD2 / -1.51 / 0.223005 / -1.74 / 0.505001 / 1.15 / 1.189159
PGLYRP1 / on / 0.880161 / -2.64 / 0.428797 / on / 1.814924
PGLYRP22) / 1) / 0.220607 / 1) / 0.095295 / 1) / 0.997975
PRTN32) / 1) / 0.752351 / 1) / 0.687135 / 1) / 1
RIPK1 / -1.22 / 0.229791 / -1.15 / 0.445544 / -1.06 / 1.209533
RIPK2 / -1.28 / 0.684022 / -1.14 / 0.698311 / -1.12 / 1.032452
RNASE7 / on / 0.399725 / on / 0.657455 / 1) / 1.147006
SFTPA1B / 1) / 0.015905 / 1) / 0.078259 / 1) / 1.060683
TLR1 / 1.08 / 0.86408 / 1.08 / 0.995009 / -1.00 / 1.013623
TLR2 / 1.02 / 0.688348 / 1.09 / 0.682141 / -1.07 / 1.035869
TLR3 / -1.24 / 0.307091 / -1.12 / 0.698311 / -1.11 / 0.959684
TLR6 / -1.16 / 0.716512 / 1.10 / 0.654605 / -1.28 / 1.10453
TLR7 / -1.48 / 0.199486 / -1.37 / 0.691091 / -1.08 / 1
TLR9 / -1.79 / 0.875452 / -1.36 / 0.908279 / -1.32 / 1
TNF / -1.65 / 0.857346 / -2.04 / 0.445544 / 1.24 / 1
TNFRSF1A / -1.23 / 1 / -1.35 / 1 / 1.10 / 1
TOLLIP / 1.08 / 1 / -1.07 / 1 / 1.16 / 1

Expression changes of all transcripts, which are not significantly regulated. Fold changes are based on ratios, p-values are based on the Mann-Whitney U-test and corrected for multiple testing using the Benjamini-Hochberg correction.

1) value could not be determined (due to a on/off effect, or due to the gene not being detected); 2) gene measurement did not pass the quality control (not enough measurements)

Supplementary Table 2

Gene symbol / alias / description / ABI assay
ACTB / beta-Actin / housekeeping gene / Hs99999903_m1
GAPDH / housekeeping gene / Hs99999905_m1
18S / housekeeping gene / Hs99999901_s1
MYD88 / adaptor molecule / Hs00182082_m1
RIPK1 / RIP, RIP1 / adaptor molecule / Hs00169407_m1
RIPK2 / CARDIAK, RICK / adaptor molecule / Hs00169419_m1
TICAM1 / TRIF / adaptor molecule / Hs00706140_s1
TOLLIP / adaptor molecule / Hs01553188_m1
CAMP / LL37, CRAMP / antimicrobial peptide / Hs00189038_m1
DEFA5 / alpha-Defensin 5 / antimicrobial peptide / Hs00360716_m1
DEFB1 / HBD1, beta-Defensin 1 / antimicrobial peptide / Hs00608345_m1
DEFB103A,B / HBD3, beta-Defensin 3 / antimicrobial peptide / Hs00218678_m1
DEFB4 / HBD2, beta-Defensin 2 / antimicrobial peptide / Hs00823638_m1
LYZ / Lysozyme / antimicrobial peptide / Hs00426231_m1
RNASE7 / antimicrobial peptide / Hs0022963_s1
S100A7 / Psoriasin, PSOR1 / antimicrobial peptide / Hs00161488_m1
SFTPA1B / SP-A, SPA1, COLLECTIN4 / antimicrobial peptide / Hs00831305_s1
IFNG / Interferon-gamma / cytokine / Hs00174143_m1
IL17D / cytokine / Hs00370528_m1
IL1B / IL-1-beta / cytokine / Hs00174097_m1
IL23A / IL23-alpha, p19 / cytokine / Hs00372324_m1
IL32 / cytokine / Hs00170403_m1
IL4 / cytokine / Hs00174122_m1
IL8 / cytokine / Hs00174103_m1
TGFB1 / TGF-beta, TGFB / cytokine / Hs00171257_m1
TNF / TNF-alpha, TNFA, Cachectin / cytokine / Hs00174128_m1
TNFRSF1A / TNFR1, TNFR55, TNF receptor 1 / cytokine receptor / Hs01042313_m1
FN1 / Fibronectin, FN, LETS / extracellular matrix protein / Hs01549940_m1
CARD8 / TUCAN, CARDINAL / NOD-like receptor / Hs00209095_m1
CARD9 / NOD-like receptor / Hs00364485_m1
MEFV / Pyrin / NOD-like receptor / Hs00165145_m1
NLRC3 / CLR16.2, NOD3 / NOD-like receptor / Hs01054716_m1
NLRC4 / CARD12, IPAF, CLAN / NOD-like receptor / Hs00368367_m1
NLRC5 / NOD27 / NOD-like receptor / Hs00260008_m1
NLRP1 / NALP1, DEFCAP, CARD7 / NOD-like receptor / Hs00248187_m1
NLRP3 / CIAS1, CRYOPYRIN, NALP3, PYPAF1 / NOD-like receptor / Hs00366465_m1
NLRX1 / NOD9 / NOD-like receptor / Hs00226360_m1
NOD1 / CARD4 / NOD-like receptor / Hs00196075_m1
NOD2 / CARD15 / NOD-like receptor / Hs00223394_m1
PGLYRP1 / PGRPS / peptidoglycan recognition receptor / Hs00175475_m1
PGLYRP2 / PGRPL / peptidoglycan recognition receptor / Hs00994650_m1
F2RL1 / PAR2, GPR11 / protease-activated receptor / Hs00608346_m1
PRTN3 / PR3, AGP7 / proteinase 3 / Hs00160521_m1
CD36 / FAT,GP4 / Thrombospondin receptor / Hs00169627_m1
TLR1 / Toll - like receptor 1 / Toll-like receptor / Hs00413978_m1
TLR2 / Toll - like receptor 2 / Toll-like receptor / Hs00610101_m1
TLR3 / Toll - like receptor 3 / Toll-like receptor / Hs01551078_m1
TLR4 / Toll - like receptor 4 / Toll-like receptor / Hs00152939_m1
TLR6 / Toll - like receptor 6 / Toll-like receptor / Hs00271977_s1
TLR7 / Toll - like receptor 7 / Toll-like receptor / Hs00152971_m1
TLR9 / Toll - like receptor 9 / Toll-like receptor / Hs00152973_m1
CD14 / Toll-like receptor complex / Hs00169122_g1

List of genes analyzed within this study. The last column refers to the gene expression assays (Applied Biosystems, Foster City, CA) that were used for Low Density real-time PCR analysis. Highlighted clusters indicate distinct functional groups of genes.

1