Table 1.
Probe-sets representing 83 genes, their expression levels in the CX and in the HC at three time-points, organized according to their functional groups and SOMs. In bold are genes previously known to play a role in the pathophysiology of BM. (-) = Avg Diff change factor ≥ 1.5, and/or p > 0.05 for all pairwise comparisons.
| # | AFFY ID | REFSEQ ID | GENE | DESCR | CX mock-infected | CX early acute phase | CX Late acute phase | HC mock-infected | HC early acute phase | HC late acute phase | SOM |
| Signal transduction | |||||||||||
| 01 | AF087943_s_at | NM_021744.1 | Cd14 | monocyte differentiation antigen cd14 precursor | 73.6 | 869.4 | 610.7 | 33.6 | 805.4 | 855.8 | c7 |
| 02 | AF087944mRNA_s_at | NM_021744.1 | Cd14 | monocyte differentiation antigen cd14 precursor | - | - | - | 102.7 | 298.7 | 329.1 | c2 |
| 03 | U76206_at | NM_133577.1 | Gpr105 | probable g protein-coupled receptor (vtr 15–20) | - | - | - | 79.0 | 132.6 | 199.4 | c3 |
| 04 | M18330_at | NM_133307.1 | Prkcd | protein kinase c, delta type (npkc-delta) | 68.2 | 135.8 | 259.9 | - | - | - | c19 |
| 05 | M18330_g_at | NM_133307.1 | Prkcd | protein kinase c, delta type (npkc-delta) | 137.1 | 224.4 | 445.2 | - | - | - | c19 |
| 06 | U38376_s_at | NM_133551.1 | Pla2g4a | phospholipase a2 | - | - | - | 341.1 | 637.3 | 992.7 | c3 |
| 07 | AB000778_s_at | NM_030992.1 | Pld1 | phospholipase d1 | 79.9 | 86.6 | 222.3 | 0.0 | 0.0 | 0.0 | c19 |
| 08 | U38812_s_at | XM_216233.1 | Itpr1 | inositol 1,4,5-triphosphate receptor type 1 | 5.03 | 14.47 | 125.6 | - | - | - | c19 |
| 09 | rc_AA859981_at | NM_172224.1 | Impa2 | myo-inositol monophosphatase 2 | 13.47 | 27.81 | 90.51 | - | - | - | c19 |
| 10 | U55192_at | NM_019311.1 | Inpp5d | inositol ployphosphate 5' phosphatase (ship) | 201.68 | 155.16 | 430.00 | 98.29 | 84.22 | 358.8 | c14 |
| 11 | rc_AA946044_s_at | NM_030857.1 | Lyn | lyn tyrosine-protein kinase | 34.15 | 84.15 | 172.62 | 22.02 | 68.72 | 192.35 | c15 |
| 12 | L14782_s_at | NM_030857.1 | Lyn | lyn tyrosine-protein kinase | 40.01 | 124.89 | 240.08 | 52.11 | 102.81 | 389.1 | c15 |
| 13 | S74141_s_at | NM_013185.1 | Hck | tyrosine-protein kinase hck (p56-hck) | 149.61 | 316.45 | 483.81 | -22.42 | 409.21 | 690.65 | c11 |
| 14 | rc_AA892404_at | Btk | bruton's tyrosine kinase (btk) | - | - | - | 134.22 | 46.21 | -33.89 | c20 | |
| 15 | M74488cds_s_at | NM_012727.1 | Camk4 | calcium/calmodulin-dependent protein kinase type iv catalytic chain (CaM kinase-Gr) | - | - | - | 85.79 | 48.6 | 33.04 | c20 |
| 16 | U77038_g_at | NM_053908.1 | Ptph6 | protein-tyrosine phosphatase 1c (ptp-1c) | 159.7 | 304.7 | 851.4 | 73.8 | 224.9 | 901.7 | c15 |
| 17 | U77038_at | NM_053908.1 | Ptph6 | protein-tyrosine phosphatase 1c (ptp-1c) | -55.5 | 16.4 | 165.0 | -4.6 | 8.2 | 226.5 | c15 |
| 18 | L19180_at | NM_019140.1 | Ptprd | receptor-linked protein tyrosine phosphatase(ptp-p1) | - | - | - | 1106.6 | 524.8 | 243.7 | c20 |
| 19 | M10072mRNA_s_at | NM_138507.1 | Ptprc | leukocyte common antigen variant 4 (cd45) | -22.25 | 28.57 | 132.68 | -17.53 | 14.35 | 167.07 | c15 |
| Innate immunity | |||||||||||
| 20 | L00981mRNA#2_at | NM_012675.1 | Tnf | tumor necrosis factor precursor (tnf-alpha) | - | - | - | -64.6 | 87.3 | 93.3 | c2 |
| 21 | AJ222813_s_at | NM_019165.1 | Il18 | interleukin-18 precursor | 30.8 | 133.6 | 207.2 | 21.1 | 80.1 | 289.7 | c11 |
| 22 | U77777_s_at | NM_019165.1 | Il18 | interleukin-18 precursor | 67.3 | 148.4 | 292.6 | 38.9 | 119.0 | 321.0 | c15 |
| 23 | rc_AA892553_at | NM_032612.1 | Stat1 | signal transducer and activator of transcription 1 | -90.9 | 295.2 | 654.8 | -66.5 | 234.4 | 676.0 | c11 |
| 24 | AF028784cds#1_s_at | NM_017009.1 | Gfap | glial fibrillary acidic protein | 534.9 | 3993.1 | 3184.2 | 923.9 | 4524.2 | 4733.2 | c7 |
| 25 | U04808_at | NM_133534.1 | Rbs11 | cx3c chemokine receptor 1 (CX3CR1) | 74.79 | 61.15 | 164.92 | 58.37 | 39.06 | 108.2 | c14 |
| 26 | U10894_s_at | NM_017196.1 | Aif1 | alograft inflammatory factor-1 (aif-1) | 174.02 | 223.69 | 781.79 | 168.54 | 210.13 | 784.71 | c14 |
| 27 | U17919_s_at | NM_017196.1 | Aif1 | alograft inflammatory factor-1 (aif-1) | 687.06 | 805.9 | 2154.2 | 620.75 | 733.07 | 2182.67 | c14 |
| 28 | X71127_at | NM_019262.1 | C1qb | complement c1q subcomponent, b chain precursor | 1158.3 | 1939.1 | 4410.7 | 981.7 | 1652.3 | 4279.6 | c15 |
| 29 | X71127_g_at | NM_019262.1 | C1qb | complement c1q subcomponent, b chain precursor | 134.4 | 507.1 | 1025.3 | 176.6 | 418.8 | 975.5 | c15 |
| 30 | X52477_at | NM_016994.1 | complement c3 precursor | -93.1 | 493.2 | 751 | 81.4 | 367.5 | 568 | c11 | |
| 31 | M29866_g_at | NM_016994.1 | complement c3 precursor | -76.3 | 465.2 | 953.3 | 20.8 | 439.3 | 993.2 | c11 | |
| 32 | U42719_at | XM_215318.1 | c4 complement protein mRNA | 8 | 120.2 | 255.7 | 63.7 | 86.7 | 320.2 | c15 | |
| 33 | rc_AI639117_s_at | XM_215326.1 | alternative-complement pathway C3/C5 convertase | -519.8 | 818.2 | 1142.1 | -382.7 | 1188.8 | 4030.51 | c10 | |
| 34 | rc_AA900582_at | NM_012488.1 | A2m | alpha-2-macroglobulin precursor | - | - | - | 285.4 | 599.5 | 846.0 | c3 |
| 35 | M23566exon_s_at | NM_012488.1 | A2m | alpha-2-macroglobulin precursor | -1469.4 | -5.3 | 527.7 | -609.4 | 307.7 | 2352.1 | c11 |
| Adaptive immunity | |||||||||||
| 36 | M31038_at | NM_012645.1 | RT1Aw2 | class i histocompatibility antigen, non-rt1.a alpha-1 chain precursor | -103.5 | 24.5 | 114.8 | - | - | - | c19 |
| 37 | M24324_f_at | NM_012645.1 | RT1Aw2 | class i histocompatibility antigen, non-rt1.a alpha-1 chain precursor | 767.5 | 2015.0 | 3287.2 | 809.0 | 2211.3 | 4525.7 | c11 |
| 38 | M31018_f_at | XM_228021.1 | rt1 class i histocompatibility antigen, aa alpha chain precursor | 401.5 | 2335.9 | 5023.4 | 416.4 | 2893.1 | 7012.5 | c15 | |
| 39 | M64795_f_at | XM_228021.1 | h-2 class i histocompatibility antigen, d-37 alpha chain precursor | -186.5 | -8.3 | 345.6 | -133.0 | -15.2 | 584.4 | c15 | |
| 40 | L40362_f_at | XM_227984.1 | h-2 class i histocompatibility antigen, d-k alpha chain precursor | 189.5 | 1022.8 | 2404.2 | 124.3 | 1025.7 | 3378.6 | c15 | |
| 41 | X13044_g_at | NM_013069.1 | Cd74 | h-2 class ii histocompatibility antigen, gamma chain | -58.7 | 273.0 | 2479.2 | -79.8 | 335.3 | 2427.6 | c15 |
| 42 | X13044_at | NM_013069.1 | Cd74 | h-2 class ii histocompatibility antigen, gamma chain | 3.5 | 219.0 | 1232.5 | 2.2 | 187.1 | 1139.5 | c15 |
| 43 | X14254cds_at | NM_013069.1 | Cd74 | h-2 class ii histocompatibility antigen, gamma chain | -68.3 | 14.9 | 238.6 | -39.3 | -10.1 | 230.2 | c15 |
| 44 | X14254cds_g_at | NM_013069.1 | Cd74 | h-2 class ii histocompatibility antigen, gamma chain | -247.3 | -84.2 | 643.7 | -200.6 | -108.2 | 572.6 | c15 |
| 45 | X56596_at | XM_228006.1 | RT1.B-BETA(1) | rt1 class ii histocompatibility antigen, b-1 beta chain precursor (rt1.b-beta(1)). | 49.9 | 141.0 | 400.2 | 39.7 | 138.8 | 408.3 | c15 |
| 46 | X53054_at | XM_215333.1 | rt1 class ii histocompatibility antigen, d-1 beta chain precursor. | -54.0 | -7.4 | 77.3 | -24.2 | -15.9 | 96.1 | c15 | |
| Extracellular matrix/vasculature | |||||||||||
| 47 | M12112mRNA#3_s_at | NM_007428.2 | Agt | angiotensinogen | - | - | - | 227.7 | 75.3 | 87.6 | c20 |
| 48 | J04035_at | XM_237869.1 | Trela | elastin precursor (tropoelastin) | - | - | - | 254.9 | 51.9 | -64.5 | c20 |
| 49 | X02601_at | NM_133523.1 | Mmp3 | stromelysin-1 precursor (MMP3) | - | - | - | 30.5 | 76.1 | 67.1 | c2 |
| 50 | rc_AI169327_at | NM_053819.1 | Timp1 | metalloproteinase inhibitor 1 precursor (TIMP1) | 352.2 | 1573.0 | 1312.1 | 357.2 | 1475.4 | 1913.9 | c7 |
| 51 | rc_AI169327_g_at | NM_053819.1 | Timp1 | metalloproteinase inhibitor 1 precursor (TIMP1) | 9.8 | 2099.0 | 1779.3 | 50.6 | 2171.3 | 3101.5 | c7 |
| Cytoskeleton | |||||||||||
| 52 | rc_AA859305_s_at | NM_173111.1 | tropomyosin 3 | 60.7 | 143.4 | 184.4 | - | - | - | c19 | |
| 53 | X62952_at | NM_031140.1 | Vim | vimentin | 1415.3 | 3269.2 | 4141.0 | 1032.8 | 3165.7 | 6517.2 | c11 |
| 54 | rc_AA892333_at | XM_147357.1 | Tuba6 | tubulin alpha-6 chain. | -58.1 | 1246.0 | 1762.2 | 34.0 | 989.2 | 2595.5 | c11 |
| 55 | X73524_at | NM_022531.1 | Des | desmin | 113.1 | 108.6 | 32.2 | - | - | - | c12 |
| 56 | rc_AA852046_s_at | XM_238547.1 | gamma-smooth muscle isoactin promoter and exon 1 | 7.6 | 65.22 | 82.99 | - | - | - | c19 | |
| Redox homeostasis | |||||||||||
| 57 | U18729_at | NM_024160.1 | Cyba | nadph oxidase light chain subunit p22phox | -40.6 | 20.3 | 202.5 | -109.7 | 5.4 | 255.8 | c15 |
| 58 | rc_AI172247_at | NM_017154.1 | Xdh | xanthine dehydrogenase | -33.5 | 248.0 | 420.6 | 9.1 | 281.3 | 529.0 | c11 |
| 59 | J02722cds_at | NM_012580.1 | Hmox1 | heme oxygenase 1 | -3.4 | 258.0 | 389.9 | -32.4 | 385.8 | 1074.1 | c11 |
| 60 | rc_AI179610_at | NM_010442.1 | Hmox1 | heme oxygenase | 94.5 | 733.2 | 797.4 | 96.5 | 778.6 | 1995.6 | c10 |
| 61 | S81433_at | S81433.1 | heme oxygenase-2 | -154.9 | -95.2 | 187.4 | - | - | - | c19 | |
| 62 | X07365_s_at | NM_030826.2 | Gpx1 | glutathione peroxidase 1 | 1243.0 | 1709.8 | 3171.5 | 1286.8 | 1683.8 | 4025.0 | c15 |
| 63 | X12367cds_s_at | NM_030826.2 | Gpx1 | glutathione peroxidase 1 | 310.7 | 359.2 | 814.5 | 278.8 | 314.5 | 924.1 | c14 |
| 64 | J03752_at | NM_134349.1 | Mgst1 | microsomal glutathione s-transferase 1 | 40.8 | 36.5 | 110.9 | 43.5 | 39.2 | 428.1 | c14 |
| 65 | AF056031_at | NM_021593.1 | Kmo | kynurenine 3-hydroxylase | 58.4 | 80.5 | 153.2 | 56.2 | 64.2 | 209.3 | c15 |
| Cell death/survival | |||||||||||
| 66 | C07012_f_at | NM_139096.1 | Ppicap | cyclophilin c | - | - | - | 283.5 | 750.3 | 1145.2 | c3 |
| 67 | rc_AA891591_at | NM_031356.1 | Pdcd8 | apoptosis-inducing factor (Aif) | - | - | - | 49.8 | 96.7 | 132.5 | c3 |
| 68 | X76453_at | NM_017060.1 | Hrasls3 | h-rev 107 | - | - | - | 120.1 | 213.4 | 405.7 | c3 |
| 69 | rc_AI231213_g_at | XM_237691.1 | metastasis suppressor homolog (Kai1) | - | - | - | 89.7 | 142.7 | 302.4 | c3 | |
| 70 | L12138_at | NM_019179.1 | Tyms | thymidylate synthase (tsase) | 8.5 | 6.8 | 53.4 | - | - | - | c19 |
| 71 | U89282_at | NM_022591.1 | Tep1 | telomerase protein component 1 (tlp1) | -92.4 | -58.0 | 66.0 | - | - | - | c19 |
| 72 | U14647_at | NM_012762.2 | Casp1 | caspase-1 | 56.8 | 282.8 | 442.9 | 53.0 | 253.6 | 479.3 | c11 |
| 73 | S79676_s_at | NM_012762.2 | Casp1 | caspase-1 | - | - | - | 153.5 | 361.4 | 508.0 | c3 |
| 74 | J05122_at | NM_012515.1 | Bzrp | peripheral-type benzodiazepine receptor | 116.0 | 468.5 | 964.8 | 121.8 | 424.7 | 1241.2 | c15 |
| 75 | J02962_at | NM_031832.1 | Lgals3 | galectin-3 | 23.7 | 282.9 | 470.9 | 10.9 | 266.4 | 751.6 | c11 |
| 76 | L21711_s_at | NM_012976.1 | Lgals5 | galectin-5 | 175.3 | 1620.0 | 2164.8 | 240.5 | 1713.2 | 3658.9 | c11 |
| 77 | U72741_g_at | NM_010708.1 | Lgals9 | galectin-9 | 723.4 | 2339.9 | 2827.1 | 605.9 | 2388.0 | 4132.9 | c11 |
| 78 | U72741_at | NM_010708.1 | Lgals9 | galectin-9 | 90.4 | 447.0 | 388.1 | 74.3 | 400.3 | 566.9 | c7 |
| 79 | rc_AI104781_at | NM_017260.1 | Alox5ap | 5-lipoxygenase activating protein (FLAP) | 45.53 | 116.35 | 176.86 | 35.42 | 81.00 | 131.91 | c11 |
| 80 | AB000199_at | NM_139329.1 | Cca2 | cca2 | -10.36 | 18.14 | 101.83 | - | - | - | c19 |
| 81 | rc_AA998164_s_at | NM_171991.1 | Ccnb1 | cyclin b1 | 61.05 | 38.71 | 110.33 | 41.28 | 45.38 | 107.2 | c14 |
| 82 | D16308_at | XM_216276.1 | cyclin d2 | - | - | - | 222.21 | 34.01 | 31.73 | c20 | |
| 83 | AF036548_at | NM_054008.1 | Rgc32 | rgc-32 | - | - | - | 116.07 | 9.22 | 9.5 | c20 |
| Growth control/neuroplasticity | |||||||||||
| 84 | A09811cds_s_at | NM_013122.1 | Igfbp2 | insulin-like growth factor binding protein 2 precursor | 218.1 | 744.1 | 1292.1 | - | - | - | c19 |
| 85 | X52498cds_at | NM_021578.1 | Tgfb1 | transforming growth factor beta 1 precursor | 59.3 | 199.0 | 324.5 | 115.2 | 106.2 | 327.1 | c15 |
| 86 | AF089825_at | NM_031815.1 | Inhbe | activin beta-e chain | 146.2 | 151.4 | 40.9 | - | - | - | c12 |
| 87 | S79820_at | NM_172563.1 | Hlf | hepatic leukemia factor | - | - | - | 207.0 | 88.9 | 16.3 | c20 |
| 88 | E03082cds_s_at | NM_031073.1 | Ntf3 | neurotrophin-3 precursor (nt-3) | 68.6 | 103.4 | 11.3 | - | - | - | c12 |
| 89 | X62322_g_at | NM_017113.1 | Grn | granulins precursor | 543.09 | 1259.51 | 1686.5 | 544.37 | 1010.75 | 1952.91 | c11 |
| 90 | X06916_at | NM_012618.1 | S100a4 | nerve growth factor induced protein 42a | 211.43 | 616.49 | 558.56 | 133.32 | 566.98 | 1346.52 | c10 |
| Neurotransmission | |||||||||||
| 91 | AF020757_s_at | NM_053656.2 | P2rx2 | p2x purinoreceptor 2 | - | - | - | 54.41 | 28.99 | 20.25 | c20 |
| 92 | D63665_at | NM_057124.1 | P2ry6 | p2y purinoreceptor 6 | 84.30 | 312.05 | 447.53 | 44.77 | 213.71 | 493.88 | c11 |
| 93 | D00833_g_at | NM_013133.1 | Glra1 | glycine receptor alpha-1 precursor | - | - | - | 57.99 | 42.25 | 16.72 | c20 |
| Ionic homeostasis | |||||||||||
| 94 | U75916_at | NM_011597.1 | Tjp2 | zonula occludens 2 | - | - | - | 236.4 | 633.7 | 576.1 | c2 |
| Lipid metabolism | |||||||||||
| 95 | AA850219_at | NM_012823.1 | Anx3 | lipocortin-iii | - | - | - | 30.8 | 61.5 | 101.9 | c3 |
| Miscellaneous | |||||||||||
| 96 | M86389cds_s_at | NM_031970.1 | Hspb1 | heat shock 27 kda protein (hsp27) | -264.3 | 112.6 | 72.1 | -157.6 | 75.5 | 173 | c7 |
| 97 | U13177_at | NM_031237.1 | Ube2d3 | ubiquitin-conjugating enzyme E2D 3 | 414.3 | 220.7 | 87.2 | - | - | - | c12 |
| 98 | D10729_s_at | NM_080767.1 | Psmb8 | proteasome subunit beta type 8 precursor | 51.9 | 216.6 | 449.7 | 74.1 | 246.4 | 579.4 | c15 |
| 99 | D10757_at | NM_012708.1 | Psmb9 | proteasome subunit beta type 9 precursor | 30 | 35.3 | 96.6 | 4 | 76.4 | 131.9 | c15 |
| 100 | D10757_g_at | NM_012708.1 | Psmb9 | proteasome subunit beta type 9 precursor | 148.7 | 820.5 | 1059.9 | 120 | 806.5 | 1644.2 | c11 |
| 101 | D45249_g_at | NM_017264.1 | Psme1 | proteasome activator complex subunit 1 | - | - | - | 2145.6 | 4508.6 | 7335.3 | c3 |
| 102 | D45250_s_at | NM_017257.1 | Psme2 | proteasome activator complex subunit 2 | 405.4 | 988.1 | 1494.7 | 439.3 | 1047.9 | 1876 | c11 |