Supplementary Table 2. Overview of Clustered Genes with Their Corresponding Deduced Functions

Supplementary Table 2. Overview of clustered genes with their corresponding deduced functions.

Clone ID / Clone Name / Functional Category / Cluster / 1d / 7d / 14d
BD1 / Crustin / Involved in humoral response / 1 / 2.577 / 2.121 / 2.741
IF130 / Ribosomal protein S12 / Ribosomal RNA / 1 / 1.443 / 1.894 / 1.768
IF160 / Arginase / Metabolism / 1 / 2.127 / 1.261 / 2.164
IF200 / 40s ribosomal protein S11 / Ribosomal RNA / 1 / 1.940 / 1.646 / 2.572
IF215 / Ribosomal protein S18 / Ribosomal RNA / 1 / 1.790 / 1.197 / 1.468
IF240 / Ribosomal protein , large P2 / Ribosomal RNA / 1 / 2.660 / 1.569 / 2.700
IF35 / Unknown / Unknown / 1 / 1.976 / 1.574 / 2.310
IF74 / PDGF / VEGF - like protein / Signaling and communication / 1 / 3.591 / 1.760 / 3.449
KS-2-2_F05 / Tubulointerstitial nephritis antigen-like / Transport / 1 / 3.368 / 3.400 / 5.352
LPN0401 / Unknown / Unknown / 1 / 1.418 / 1.587 / 2.311
LPN0402 / Lysosomal cofactor/neurotrophic factor prosaposin / Signaling and communication / 1 / 1.522 / 1.548 / 2.173
LPN0469 / Unknown / Unknown / 1 / 1.934 / 1.838 / 1.872
LPV0085 / Calreticulin / Transport / 1 / 1.743 / 1.834 / 1.880
LPV0170 / Rab3 GTPase activating protein / Protein binding / 1 / 1.134 / 1.317 / 3.520
LPV0172 / Unknown / Unknown / 1 / 2.634 / 1.635 / 2.315
MJ_H_1_080 / Translation initiation factor eIF4α / RNA cap binding/mRNA binding / 1 / 2.610 / 1.411 / 1.420
MJ_H_1_190 / PREDICTED: similar to RING-box protein 2 (Rbx2) (RING finger protein 7 sensitive) / Apoptosis protein binding/involved in humoral response / 1 / 2.114 / 1.357 / 1.446
MJ_H_2_185 / Ribosomal protein L26 / Ribosomal RNA / 1 / 2.145 / 1.944 / 2.650
MJ_H_3_090 / Unknown / Unknown / 1 / 1.218 / 1.116 / 1.918
MJ_H_4_053 / Unknown / Unknown / 1 / 1.998 / 1.397 / 1.329
N318 / β-thymosin / Protein binding/actin binding / 1 / 2.333 / 1.275 / 1.366
Supplementary Table 2. Continuation overview of clustered genes with their corresponding deduced functions.
Clone ID / Clone Name / Functional Category / Cluster / 1d / 7d / 14d
N357 / Unknown / Unknown / 1 / 2.668 / 1.590 / 2.257
N395 / Zinc finger protein / Miscellaneous function / 1 / 1.586 / 1.940 / 1.956
N475 / Unknown / Unknown / 1 / 1.192 / 1.450 / 2.900
PJH518f / Unknown / Unknown / 1 / 2.870 / 2.263 / 2.498
SH2008 / Unknown / Unknown / 1 / 1.311 / 1.683 / 2.196
sh971 / Clottable protein / Involved in humoral response (clotting mechanism) / 1 / 2.282 / 1.944 / 1.870
HpaN0616 / GTPase of MMR1/HSR1 type (62.3 kD) / GTPase binding/nucleotide binding / 2 / 3.895 / 1.144 / 1.338
IF279 / Unknown / Unknown / 2 / 6.374 / 1.782 / 1.728
IF298 / 60S ribosomal protein L8 / Ribosomal RNA / 2 / 2.728 / 1.437 / 1.493
IF421 / Unknown / Unknown / 2 / 3.920 / 1.546 / 0.944
IF468 / Unknown / Unknown / 2 / 3.279 / 1.950 / 1.730
IF48 / Unknown / Unknown / 2 / 3.160 / 1.460 / 1.680
KS-2-10_A04 / α2-macroglobulin homologue / Involved in humoral response / 2 / 2.540 / 1.530 / 1.544
KS-2-10_E08 / Transglutaminase / Involved in humoral response / 2 / 3.554 / 1.848 / 0.841
KS-2-6_F09 / Histone H3 / DNA binding/nucleotide binding / 2 / 2.712 / 1.720 / 1.920
KS-2-7_B01 / 34/67 kd laminin binding protein / Ribosomal RNA / 2 / 2.743 / 2.268 / 1.538
KS-2-8_E06 / Glyceraldehyde-3-phosphate dehydrogenase / Catalytic activity/oxyreductase activity / 2 / 2.463 / 1.710 / 1.100
MJ_H_1_035 / Unknown / Unknown / 2 / 3.411 / 1.848 / 0.940
MJ_H_1_044 / Unknown / Unknown / 2 / 4.240 / 1.598 / 0.843
MJ_H_1_073 / 40S ribosomal protein S24 / Ribosomal RNA / 2 / 4.780 / 2.770 / 1.640
MJ_H_1_193 / Ribosomal protein L22 / Ribosomal RNA / 2 / 6.490 / 1.982 / 2.110
Supplementary Table 2. Continuation overview of clustered genes with their corresponding deduced functions.
Clone ID / Clone Name / Functional Category / Cluster / 1d / 7d / 14d
MJ_H_1_197 / Ribonuclear protein / Ribosomal RNA / 2 / 6.759 / 1.975 / 2.190
MJ_H_1_212 / CDH1-D / Lactose hydrolysis/catalytic activity / 2 / 5.562 / 1.566 / 1.486
MJ_H_1_219 / Unknown / Unknown / 2 / 3.400 / 1.439 / 1.115
MJ_H_2_091 / Erythrocyte binding protein 4 / Mitochondrial protein / 2 / 5.713 / 1.679 / 2.514
MJ_H_3_133 / Unknown / Unknown / 2 / 4.974 / 1.545 / 0.821
MJ_H_3_162 / Unknown / Unknown / 2 / 3.450 / 1.472 / 1.370
MJ_H_3_172 / Unknown / Unknown / 2 / 2.974 / 1.579 / 1.172
MJ_H_3_230 / Unknown / Unknown / 2 / 3.442 / 2.480 / 0.985
MJ_H_3_253 / Unknown / Unknown / 2 / 3.687 / 1.464 / 0.712
N227 / Acidic ribosomal protein P1 / Ribosomal RNA / 2 / 4.289 / 1.635 / 1.147
N298 / Unknown / Unknown / 2 / 4.860 / 1.445 / 0.781
PJA620r / Unknown / Unknown / 2 / 2.333 / 1.980 / 0.950
PJH535f / Unknown / Unknown / 2 / 3.122 / 1.758 / 1.330
PJI14r / Integral membrance protein 2A / Cellular component / 2 / 6.184 / 1.522 / 1.622
PJV603f / Antimicrobial peptide PEN2-4 / Involved in humoral response / 2 / 6.951 / 2.290 / 1.254
sh2007 / Actin, cytoplasmic A3 / External Structure/Mobility / 2 / 3.661 / 1.394 / 1.442
SH2013 / Unknown / Unknown / 2 / 2.100 / 1.978 / 1.343
sh970 / 11.5 kDa antibacterial protein / Involved in humoral response / 2 / 4.572 / 1.616 / 2.262
HpaN0029 / Chitinase / Chitinase activity/catalytic activity / 3 / 8.710 / 1.385 / 0.550
IF284 / Unknown / Unknown / 3 / 6.668 / 1.194 / 0.830
IF314 / Unknown / Unknown / 3 / 4.370 / 0.870 / 0.590
IF456 / Unknown / Unknown / 3 / 5.569 / 1.288 / 0.517
IF488 / Unknown / Unknown / 3 / 5.387 / 1.100 / 0.814
IF496 / Ribosomal protein P2 / Ribosomal RNA / 3 / 7.982 / 1.250 / 1.161
Supplementary Table 2. Overview of clustered genes with their corresponding deduced functions.
Clone ID / Clone Name / Functional Category / Cluster / 1d / 7d / 14d
KS-2-2_F06 / Cytochrome b / Transport/ electron Transport / 3 / 4.531 / 1.436 / 0.581
LPV0269 / Unknown / Unknown / 3 / 3.896 / 1.749 / 0.515
LPV0461 / Unknown / Unknown / 3 / 4.297 / 2.250 / 0.523
MJ_H_1_039 / Cleavage and polyadenylation specificity factor / mRNA cleavage factor complex / 3 / 3.113 / 0.917 / 0.850
MJ_H_1_077 / Ribosomal protein L18A / Ribosomal RNA / 3 / 6.496 / 2.700 / 0.573
MJ_H_1_081 / Unknown / Unknown / 3 / 4.734 / 1.283 / 1.170
MJ_H_1_111 / Unknown / Unknown / 3 / 4.867 / 0.790 / 0.670
MJ_H_1_191 / Unknown / Unknown / 3 / 2.864 / 1.370 / 0.700
MJ_H_1_196 / ATP synthase subunit 6 / ATPase activity, coupled to transmembrane movement of substances/catalytic activity / 3 / 5.432 / 1.439 / 0.376
MJ_H_1_205 / Unknown / Unknown / 3 / 3.483 / 0.975 / 0.826
MJ_H_1_242 / Translation initiation factor 2 / GTPase binding/nucleotide binding / 3 / 3.927 / 1.276 / 0.371
MJ_H_1_266 / Unknown / Unknown / 3 / 5.670 / 1.182 / 0.531
MJ_H_2_078 / Unknown / Unknown / 3 / 6.884 / 1.567 / 0.598
MJ_H_2_264 / 60s ribosomal protein L13 / Ribosomal RNA / 3 / 4.152 / 1.241 / 0.557
MJ_H_2_292 / Ribosomal protein L37 / Ribosomal RNA / 3 / 5.158 / 1.349 / 0.570
MJ_H_3_194 / Unknown / Unknown / 3 / 3.483 / 0.742 / 0.579
MJ_H_3_223 / Unknown / Unknown / 3 / 3.156 / 0.877 / 0.724
MJ_H_3_240 / Unknown / Unknown / 3 / 3.680 / 0.892 / 0.743
PJA811r / Unknown / Unknown / 3 / 6.274 / 1.840 / 0.580
PJV413f / Kazal-type proteinase inhibitor type 2 / Involved in humoral response (ProPO cascade) / 3 / 2.643 / 0.896 / 0.637
Supplementary Table 2. Overview of clustered genes with their corresponding deduced functions.
Clone ID / Clone Name / Functional Category / Cluster / 1d / 7d / 14d
PJV851f / Calcium-sensitive chloride channel 2 / Transepithelial transport/ cell volume regulation / 3 / 3.864 / 1.414 / 0.554
sh2063 / 40S ribosomal protein S3a / Ribosomal RNA / 3 / 4.433 / 1.480 / 1.630
sh719 / 60S ribosomal protein L19 / Ribosomal RNA / 3 / 2.731 / 0.825 / 0.538
sh729 / Cytochrome C oxidase subunit III / mitochondiral protein/transport / 3 / 3.219 / 1.149 / 0.413
sh871 / Putative large subunit ribosomal protein rpL 44 / Ribosomal RNA / 3 / 2.770 / 0.983 / 0.744
HpaN0305 / Ribosomal protein S21 / Ribosomal RNA / 4 / 1.320 / 0.937 / 0.671
IF139 / Unknown / Unknown / 4 / 0.948 / 0.550 / 0.617
IF4 / Cytochrome B / Mitochondrial protein / 4 / 1.570 / 0.925 / 0.641
IF413 / Unknown / Unknown / 4 / 0.915 / 0.659 / 0.670
IF436 / Unknown / Unknown / 4 / 0.862 / 0.778 / 0.483
LPN0299 / Ribosomal protein S3A / Ribosomal RNA / 4 / 1.560 / 1.830 / 0.417
LPV0076 / Cytochrome C oxidase subunit I / Mitochondiral protein/transport / 4 / 0.834 / 0.761 / 0.358
LPV0092 / Unknown / Unknown / 4 / 0.932 / 0.884 / 0.590
LPV0510 / Unknown / Unknown / 4 / 0.867 / 0.699 / 0.717
MJ_H_1_097 / Unknown / Unknown / 4 / 0.991 / 0.756 / 0.624
MJ_H_1_100 / Chaperonin / ATP binding/nucleotide binding / 4 / 0.819 / 0.740 / 0.527
MJ_H_1_102 / Ribosomal protein S2 / Ribosomal RNA / 4 / 1.420 / 0.872 / 0.667
MJ_H_1_110 / Unknown / Unknown / 4 / 1.690 / 0.743 / 0.730
MJ_H_1_112 / Unknown / Unknown / 4 / 0.967 / 0.836 / 0.670
MJ_H_1_180 / Unknown / Unknown / 4 / 1.270 / 0.770 / 0.697
MJ_H_2_279 / Unknown / Unknown / 4 / 0.869 / 1.600 / 0.429
MJ_H_3_192 / Unknown / Unknown / 4 / 1.400 / 0.870 / 0.583
MJ_H_3_203 / Unknown / Unknown / 4 / 1.730 / 0.884 / 0.593
Supplementary Table 2. Overview of clustered genes with their corresponding deduced functions.
Clone ID / Clone Name / Functional Category / Cluster / 1d / 7d / 14d
MJ_H_3_260 / Unknown / Unknown / 4 / 1.320 / 0.725 / 0.656
N194 / Histone H1 / Cell division/DNA synthesis, repair, replication / 4 / 0.740 / 0.889 / 0.543
N433 / Unknown / Unknown / 4 / 1.135 / 0.810 / 0.585

Supplementary Table 2. Comparison between quantitative real-time PCR and microarray results for representative genes.

LYSOZYME
Day 1 / Day 7 / Day 14
PG stimulated samples (ave. copy number) / 8.37 ± 7.79x105 / 1.56 ± 0.63x106 / 2.51 ± 2.50x106
Control samples (ave. copy number) / 3.40 ± 3.21x105 / 7.75 ± 5.71x105 / 2.44 ± 1.03x106
Fold increase in copy number / 2.460 / 2.013 / 1.029
Microarray result / 3.623 / 1.349 / 0.878
TRANSGLUTAMINASE
Day 1 / Day 7 / Day 14
PG stimulated samples (ave. copy number) / 7.23 ± 1.99x105 / 5.47 ± 2.49x105 / 7.35 ± 3.02x105
Control samples (ave. copy number) / 2.56 ± 0.34x105 / 3.01 ± 2.88x105 / 6.27 ± 4.63x105
Fold increase in copy number / 2.823 / 1.820 / 1.172
Microarray result / 3.554 / 1.848 / 0.841