Table 2.
Categories of human and viral genes displaying altered transcription profiles during SARS-CoV infection of Vero cells
| GenBank accession | Fold change in transcription |
|||
|---|---|---|---|---|
| no. | Gene | Acuity | MIDAS | Real-time RT-PCR |
| Cell cycle and development | ||||
| NM_004417 | Dual specificity phosphatase 1 (DUSP1) | 19.15 | 11.12 | 42.67 (0.012) |
| NM_000136 | Fanconi anemia, complementation group C (FANCC) | 7.41 | 4.64 | |
| NM_012206 | Hepatitis A virus cellular receptor 1 (HAVCR1) | –11.11 | –11.18 | –10.27 (0.030) |
| NM_000598 | Insulin-like growth factor binding protein 3 (IGFBP3) | –6.67 | –8.72 | –16.62 (0.001) |
| NM_005901 | MAD, mothers against decapentaplegic homolog 2 (Drosophila) (MADH2) | 5.71 | 4.65 | 1.60 (0.009) |
| NM_000582 | Secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) (SPP1) | –3.05 | –5.88 | |
| Cellular metabolism | ||||
| NM_001912 | Cathepsin L (CTSL), transcript variant 1 | –2.54 | –4.36 | –4.96 (0.017) |
| NM_000127 | Exostoses (multiple) 1 (EXT1) | –2.86 | –4.13 | |
| NM_002410 | Mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase (MGAT5) | 11.18 | 7.28 | |
| Cytoskeleton-associated proteins | ||||
| NM_018477 | Actin-related protein 10 homolog (Saccharomyces cerevisiae) (ACTR10) | –6.41 | –8.62 | |
| NM_003388 | Cytoplasmic linker 2 (CYLN2) | –3.33 | –4.50 | |
| NM_015282 | Cytoplasmic linker associated protein 1 (CLASP1) | –6.02 | –7.17 | |
| NM_021103 | Thymosin, beta 10 (TMSB10) | –2.63 | –4.09 | |
| NM_021109 | Thymosin, beta 4, X-linked (TMSB4X) | –4.44 | –5.92 | |
| DNA repair | ||||
| AY275681 | MutS homolog 3 (Escherichia coli) (MSH3) | 7.63 | 6.87 | |
| Heat shock and stress response | ||||
| NM_006145 | DnaJ (Hsp40) homolog, subfamily B, member 1 (DNAJB1) | 11.02 | 8.56 | |
| NM_006644 | Heat shock 105/110 kDa protein 1 (HSPH1) | 15.61 | 9.40 | |
| NM_005345 | Heat shock 70 kDa protein 1A (HSPA1A) | 14.37 | 7.11 | 54.19 (0.002) |
| NM_005348 | Heat shock 90-kDa protein 1, alpha (HSPCA) | 7.00 | 4.06 | 7.09 (0.014) |
| mRNA processing factors | ||||
| NM_004593 | Splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila) (SFRS10) | 4.38 | 5.09 | |
| Protein modulators | ||||
| NM_004071 | CDC-like kinase 1 (CLK1) | 13.13 | 8.09 | 58.49 (0.005) |
| NM_007067 | MYST histone acetyltransferase 2 (MYST2) | –4.22 | –4.07 | |
| NM_005742 | Protein disulfide isomerase-related protein (P5) | –5.95 | –5.80 | |
| NM_002714 | Protein phosphatase 1, regulatory subunit 10 (PPP1R10) | 8.98 | 8.60 | |
| NM_003255 | Tissue inhibitor of metalloproteinase 2 (TIMP2) | –8.00 | –9.69 | –4.77 (0.012) |
| Signal transduction | ||||
| NM_004039 | Annexin A2 (ANXA2) | –3.05 | –4.39 | –4.04 (0.009) |
| NM_000634 | Interleukin 8 receptor, alpha (IL8RA) | 4.44 | 4.47 | 26.91 (0.002) |
| NM_006860 | RAB, member of RAS oncogene family-like 4 (RABL4) | 9.91 | 8.99 | |
| NM_006908 | Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP-binding protein Rac1) (RAC1) | –4.35 | –4.43 | –3.15 (0.020) |
| NM_001040 | Sex hormone-binding globulin (SHBG) | 5.80 | 5.77 | |
| NM_003473 | Signal transducing adaptor molecule 1 (STAM1) | 6.56 | 4.29 | 13.74 (0.023) |
| Trafficking and protein degradation | ||||
| NM_014713 | Lysosomal-associated protein transmembrane 4 alpha (LAPTM4A) | –4.59 | –5.10 | |
| NM_006432 | Niemann-Pick disease, type C2 (NPC2) | –7.81 | –8.93 | –35.38 (0.013) |
| NM_003900 | Sequestosome 1 (SQSTM1) | 6.20 | 4.90 | |
| Transcription and transcriptional regulators | ||||
| NM_000937 | Polymerase (RNA) II (DNA directed) polypeptide A, 220 kDa (POLR2A) | 9.24 | 6.18 | |
| NM_181552 | Cut-like 1, CCAAT displacement protein (Drosophila) (CUTL1) | –2.51 | –4.54 | |
| L17131 | High-mobility group protein (HMG-I(Y)) gene | –38.46 | –13.70 | |
| NM_002158 | Human T-cell leukemia virus enhancer factor (HTLF) | 7.02 | 5.74 | |
| NM_001730 | Kruppel-like factor 5 (intestinal) (KLF5) | 7.04 | 4.74 | 44.94 (0.001) |
| NM_005594 | Nascent-polypeptide-associated complex alpha polypeptide (NACA) | –10.75 | –10.75 | |
| NM_020529 | Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (NFKBIA) | 11.50 | 5.88 | 61.18 (0.008) |
| NM_003457 | Zinc finger protein 207 (ZNF207) | –4.44 | –4.48 | |
| Translation | ||||
| NM_013417 | Isoleucine-tRNA synthetase (IARS) | –8.13 | –6.91 | |
| NM_033251 | Ribosomal protein L13 (RPL13) | –5.05 | –7.16 | |
| NM_000979 | Ribosomal protein L18 (RPL18) | –4.35 | –5.92 | |
| NM_000980 | Ribosomal protein L18a (RPL18A) | –7.94 | –7.61 | |
| NM_000990 | Ribosomal protein L27a (RPL27A) | –4.59 | –5.25 | |
| NM_000967 | Ribosomal protein L3 (RPL3) | –2.96 | –5.23 | |
| NM_033643 | Ribosomal protein L36 (RPL36) | –8.55 | –13.75 | |
| NM_001014 | Ribosomal protein S10 (RPS10) | –3.51 | –4.56 | |
| NM_001018 | Ribosomal protein S15 (RPS15) | –4.23 | –5.38 | |
| NM_022551 | Ribosomal protein S18 (RPS18) | –8.47 | –8.59 | |
| NM_001022 | Ribosomal protein S19 (RPS19) | –7.81 | –7.90 | |
| NM_002952 | Ribosomal protein S2 (RPS2) | –3.28 | –4.76 | |
| NM_001005 | Ribosomal protein S3 (RPS3) | –2.39 | –4.28 | |
| NM_001402 | Translation elongation factor 1 alpha 1 (EEF1A1) | –4.17 | –5.77 | |
| NM_001404 | Translation elongation factor 1 gamma (EEF1G) | –3.60 | –4.13 | –4.13 (0.004) |
| NM_017646 | tRNA isopentenyltransferase 1 (TRIT1) | –3.80 | –4.38 | |
| Hypothetical proteins | ||||
| BC047078 | Hypothetical protein LOC283507 | 4.13 | 8.49 | |
| NM_024511 | Hypothetical protein MGC4701 | 5.54 | 5.03 | |
| BC040148 | Hypothetical protein MGC49942 | –3.48 | –4.46 | |
| D63478 | KIAA0144 gene | –4.74 | –4.80 | |
| Expressed sequence tags | ||||
| AK123640 | cDNA FLJ41646 fis, clone FEBRA2024019 | 5.74 | 4.41 | |
| AA968926 | Op38b10.s1 | 10.41 | 10.75 | |
| AI379149 | Tc66a01.x1 | –4.33 | –5.40 | |
| R60834 | Yh04d12.r1 | 7.72 | 7.50 | |
| N94144 | Za25b09.r1 | 7.21 | 7.41 | |
| W91949 | Zh47e08.r1 | 6.36 | 6.86 | |
| AA677283 | Zj61d05.s1 | –4.88 | –4.76 | |
| AA476783 | Zw94h11.s1 | 2.88 | 6.93 | |
| Additional genes | ||||
| U44953 | DENN mRNA | N.A. | N.A. | 3.75 (0.017) |
| NM_018147 | Fas apoptotic inhibitory molecule (FAIM) | N.A. | N.A. | –5.46 (0.013) |
| AF070674 | Inhibitor of apoptosis protein-1 (hIAP1) | N.A. | N.A. | 3.54 (0.010) |
| NM_002462 | Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) (Mx1) | N.A. | N.A. | 59.51 (0.004) |
| AY268070 | SARS coronavirus RNA-directed RNA polymerase | N.A. | N.A. | 9.42 × 104 (0.009) |
The microarray data were analyzed using both Acuity and MIDAS software. For the real-time RT-PCR data, the values in brackets indicate the P-values at the 95% confidence level. The test of significance was performed based on the differences between duplicate values as well as between data for infected versus uninfected samples. N.A., not applicable.