Table 1.
Tumor Genes.
| Reference | Harvest time point: postinfection/other notes | Top upregulated genes | Top downregulated genes | Pathways/functional groups most affected |
|---|---|---|---|---|
| Haddad et al. (12) | 6 h | SLC5A5, HIST2H4A, AK026847, HIST1H4E, HIST1H4B | BHLHB2, CX3CL1, G0S2, SOCS1 | HMGB-1, interleukin (IL)-2, IL-6, IL8, Janus kinase/signal transducer and activator of transcription (JAK/STAT), interferon (IFN), and ERK 5 signaling |
| 24 h | SLC5A5, AK026847, HSPA6, HIST2H4A | IL8, ICAM1, SFRP1, CCL20, RSU1 | P53- and Myc-induced apoptotic processes, pancreatic adenocarcinoma signaling, and phosphoinositide 3-kinase/v-ask murine thymoma vial oncogene homolog 1 (PI3/AKT) pathways | |
| Balogh et al. (8) | 12 h | Rsad2, Cxcl11, 10869879, Ddx60, Ifnb, Ifih1, Ifnb2, 10720237, Isg15, Herc6, Usp18, Oasl2, Oasl, Oas1b, Gbp5, Gbp1, Mx1, Irgm, Ifit1, Ifit2, Ifit3, Ifi47, Cxcl9, TRAIL, Tnf, Atf3 | Tradd, Fadd, etnk2, trpc3, p2ry12, galr2, rpa3 | Toll-like receptor signaling, RIG-I-like receptor signaling, IFN signaling, IFN effector pathways, apoptosis pathways, endoplasmic reticulum stress pathways, and cell cycle regulation |
| Lee et al. (15) | 0, 24, 48, and 72 h | LEF1, PVRIG, SLFN11, LPP, CECR1, ARHGEF6, IRX3, STAMBPL1, IGFBP2, CD1D | CD151, AHNAK, TRIP6, LGALS1, MGST1, SRGN, CCND2, CCDC50, ITGB7, PDLIM1 | Phosphoprotein, mutagenesis site, regulation of programmed cell death, lysosome, regulation of apoptosis, and surface antigen |
| Lacroix et al. (11) | 72 h | EFTUD1, MMP1, PPM1F, LAMB3, TMEM200C, SIRPA, THEG, VPS18, RBM22, FOLR2, COX17, TFPI2, ACTL8 | ZIC1, FLRT3, MYC, FOXG1, MAPT, NFIA, PHLPP1, ZNF671, FZD3 | Steroid biosynthesis, ether lipid metabolism, TGF-beta signaling pathway, Wnt signaling pathway, gonadotropin releasing hormone signaling pathway, and the Jak-STAT signaling pathway |
| Reinboth et al. (29) | Early (2 h) | 114 human genes strongly correlating with viral genes | Networks: posttranslational modification, free radical scavenging, gene expression, cell death, and cellular growth and proliferation. Molecular functions: cell cycle, cellular movement, development, growth and proliferation, and cell-to-cell signaling | |
| Intermediate/late (10 h) | 84 human (early) genes strongly correlating with viral genes (intermediate/late) | Cell death, cell cycle, lipid metabolism, small molecule biochemistry, and cellular development | ||
| 48 h | Cell death, cellular growth and proliferation, protein synthesis and folding, infectious disease, genetic disorder, cell cycle, and deoxyribonucleic acid replication, recombination, and repair | |||
| Kurozumi et al. (6) | 3 days | Cxcl11, Ifnγ, Cxcl9, Ccl12_predicted, Cxcl10, Ccl4, Il1b, Ccl5, Ccr6, Cxcr3 | Spp1, Il6st | |
| Pfankuche et al. (9) | 1 day | DDX60, DLA-79, CXCR7, F13A1, LOC100685890, CCR5, TRIM22, LOC100686473, GPR34, ENPEP | SERPINB2, TPM2, SCIN, VEGFB, THBS2, COL4A1, DMD, S100P, LOC608476, GSTA3 | WebGestalt (UP): immune response-activating signal transduction activation of immune response; immune response-regulating signaling pathway; positive regulation of immune response; response to other organism; regulation of immune response; positive regulation of immune system process; regulation of immune system process; immune response; immune system process DAVID (UP): activation of innate immune response; cell migration; leukocyte proliferation; positive regulation of programmed cell death; positive regulation of leukocyte activation; regulation of leukocyte proliferation; blood coagulation |
| WebGestalt (DOWN): blood vessel morphogenesis; positive regulation of cell migration; positive regulation of cell motility; cardiovascular system development; positive regulation of cellular component movement; circulatory system development; regulation of cell adhesion; positive regulation of locomotion; localization of cell; biological adhesion DAVID (DOWN): blood vessel development; protein amino acid glycosylation; organic acid metabolic process; regulation of neurological system process; regulation of transferase activity; blood coagulation; nucleobase, nucleoside and nucleotide metabolic process; antigen receptor-mediated signaling pathway; leukocyte proliferation | ||||
| Josupeit et al. (14) | Most significantly expressed in susceptible cells | FAM49B, B4GALNT1, COL4A5, SLITRK4, SLC26A10, IFITM3, ASAP1, LAYN, NTRK2, ARHGEF25, CTGF, NXPH1, UGT8, NCAN, NAP1L3 | ||
| Most significantly expressed in resistant cells | CTHRC1, RPS4Y1, EIF1AY, DDX3Y, DPYD, PNMAL1, S100A10, TXLNG2P, TRIM38, SPP1, KDELR3, SPARCL1, MPPED2, FABP6, CCDC71L, EDNRB, TSPAN31, FAM213A | |||
| Garcia et al. (30) | 0, 2, 6, 12, 18, 24, 30, 36, and 48 h postinfection | TNFAIP8 | ||
| Tanaka et al. (16) | 0, 6, 24, and 48 h postinfection | SAMD9 | ||
| Kurozumi et al. (17) | 12 h postinfection | CYR61, Ang-2 | TSP-1 | |
| Zhang et al. (7) | 3 and 6 weeks (from the mouse chip microarray) | Ly6a, Plac8, Ly6c, Ccl8, Ifitm3, Ms4a4c, Clec4e, Ly6e, Tgtp, Ifit1, Rsad2, Ccl2, Ifi27, Ifi47, Ccl7, Dck, Ifit3, Irf7, Gas1, Gbp2, Cd69, Il18 | Elavl2, Lmcd1, Arr3, Trip4, Crmp1, Hpd, Ewsr1, Ociad2, Cox15, Hmgn3, Nfia, Cables1, Rfxank, Tusc4, Cnot3, Magi1, Mrg2, Stag1, Sca2, Pdcd2, Tub, Ndrg1, Pigl | UP: major histocompatibility class I, chemokine receptor binding, chemokine activity, and cytokine activity; down: peptidases, proteases |
| Jiang et al. (22) | 24 h | Tumor necrosis factor | ||
| Li et al. (20) | 48 h | MYCN | ||
| Ma et al. (19) | 3 days | Dm-dNK | ||
| Saito et al. (10) | 14, 18, and 22 h | CASP3, CASP7, CASP8, CASP9, CASP10, CYCS, IKK, NF-κB | ||
| Han et al. (18) | 12, 24, and 48 h | Staphylococcus enterotoxin A | ||