Figure 1: Flowchart of data preparation, processing, and analysis in this study
Abbreviation |
Full name |
HT RNA-Seq |
high throughput RNA sequencing |
DEGs |
differentially expressed genes |
KEGG |
Kyoto Encyclopedia of Genes and Genomes |
GO |
Gene Ontology |
PPI |
protein‐protein interaction |
DGIdb |
Drug-Gene Interaction Database |
IAVs |
influenza A viruses |
CoVs |
coronaviruses |
SARS-CoV |
severe acute respiratory syndrome coronavirus |
MERS-CoV |
Middle East respiratory syndrome coronavirus |
RSV |
respiratory syncytial virus |
ISGs |
IFN-stimulated genes |
TNF-α |
tumor necrosis factor |
NK |
natural killer |
GSE |
genomic spatial event database |
adj P-value |
Adjusted P-values |
FDA |
Food and Drug Administration |
GEO |
gene expression omnibus |
GDI |
Gene-Drug Interaction |
STRING |
search tool for the retrieval of interacting genes/proteins |
IRF7 |
interferon regulatory factor 7 |
PRRs |
pattern-recognition receptors |
IFNs |
interferons |
JAK |
janus kinase |
TYK |
tyrosine kinase |
STAT |
signal transducer and activator of transcription |
PAMPs |
pathogen-associated molecular patterns |
TLR |
Toll-like receptor |
RIG-I |
retinoic acid-inducible gene I |
OAS |
2′–5′-oligoadenylate synthetases |
IFIT |
immunity is the induction of Interferon-induced protein with tetratricopeptide repeats |
IFIH1 |
Interferon-induced with helicase C domain 1 |
MAVS |
with mitochondrial antiviral signaling protein |
IFN |
interferons |
IL-6R |
IL-6 receptor |
gp130 |
glycoprotein 130 |
Gene ID |
Gene name |
logFC |
P. value |
Adj. p. value |
Degree score * |
Upregulated DEGs |
|
||||
IL6 |
Interleukin 6 |
3.008258075 |
2.73E-10 |
1.99E-07 |
29 |
IRF7 |
Interferon Regulatory Factor 7 |
1.528321986 |
1.01E-05 |
0.001419983 |
28 |
MX1 |
Interferon-induced GTP-binding protein Mx1 |
2.622073653 |
8.97E-07 |
0.000222124 |
25 |
IFIH1 |
Interferon Induced with Helicase C Domain 1 |
0.663239405 |
4.70E-06 |
0.000793441 |
25 |
OAS1 |
2'-5'-Oligoadenylate Synthetase 1 |
1.724701628 |
6.30E-11 |
5.72E-08 |
24 |
OAS2 |
2'-5'-Oligoadenylate Synthetase 2 |
1.283179817 |
8.10E-11 |
6.79E-08 |
23 |
OAS3 |
2'-5'-Oligoadenylate Synthetase 3 |
1.332988392 |
2.19E-08 |
1.01E-05 |
23 |
XAF1 |
XIAP associated factor 1 |
2.743618629 |
5.41E-08 |
2.19E-05 |
23 |
IRF9 |
Interferon Regulatory Factor 9 |
1.244703625 |
1.71E-12 |
2.48E-09 |
23 |
IFIT1 |
Interferon Induced Protein with Tetratricopeptide Repeats 1 |
0.913347803 |
0.000601272 |
0.032608456 |
23 |
IFIT3 |
Interferon Induced Protein with Tetratricopeptide Repeats 3 |
0.783392048 |
0.000315828 |
0.021512845 |
23 |
MX2 |
MX Dynamin Like GTPase 2 |
2.49141001 |
5.36E-06 |
0.000867141 |
21 |
IFI35 |
Interferon Induced Protein 35 |
0.986827626 |
0.0005195 |
0.030035931 |
20 |
IFI44 |
Interferon Induced Protein 44 |
0.881349811 |
9.84E-08 |
3.40E-05 |
20 |
IFI27 |
Interferon Alpha Inducible Protein 27 |
3.046637799 |
7.07E-06 |
0.001077669 |
19 |
ICAM1 |
Intercellular Adhesion Molecule 1 |
1.879758892 |
1.12E-08 |
5.66E-06 |
18 |
IFITM1 |
Interferon Induced Transmembrane Protein 1 |
1.655143451 |
1.64E-08 |
7.95E-06 |
17 |
SAMD9L |
Sterile Alpha Motif Domain Containing 9 Like |
0.634035551 |
0.00092164 |
0.04301708 |
17 |
IFITM3 |
Interferon Induced Transmembrane Protein 3 |
0.775704598 |
0.000172631 |
0.013532281 |
16 |
PARP9 |
Poly (ADP-Ribose) Polymerase Family Member 9 |
0.667454176 |
2.34E-07 |
7.27E-05 |
16 |
TNFAIP3 |
TNF Alpha Induced Protein 3 |
1.602353044 |
5.29E-15 |
2.88E-11 |
15 |
SAMHD1 |
SAM And HD Domain Containing Deoxynucleoside Triphosphate Triphosphohydrolase 1 |
0.802599368 |
1.09E-05 |
0.001504722 |
15 |
PARP12 |
Poly (ADP-Ribose) Polymerase Family Member 12 |
0.777012877 |
2.75E-07 |
8.10E-05 |
15 |
PLSCR1 |
Phospholipid Scramblase 1 |
0.862444838 |
1.01E-07 |
3.44E-05 |
14 |
GBP5 |
Guanylate Binding Protein 5 |
2.051097583 |
3.12E-05 |
0.003542176 |
13 |
NFKB2 |
Nuclear Factor Kappa B Subunit 2 |
0.955892636 |
2.00E-10 |
1.56E-07 |
12 |
EPSTI1 |
Epithelial Stromal Interaction 1 |
1.098081891 |
1.83E-05 |
0.002280005 |
12 |
CXCL2 |
C-X-C Motif Chemokine Ligand 2 |
1.421837035 |
7.19E-07 |
0.000184406 |
10 |
SOD2 |
Superoxide Dismutase 2 |
1.513765318 |
1.80E-11 |
1.84E-08 |
9 |
IL1A |
Interleukin 1 Alpha |
1.077593072 |
9.69E-06 |
0.001371078 |
9 |
SOCS3 |
Suppressor of Cytokine Signaling 3 |
1.027635624 |
2.37E-07 |
7.27E-05 |
9 |
NFKBIZ |
NFKB Inhibitor Zeta |
0.900995776 |
7.24E-10 |
4.51E-07 |
9 |
BIRC3 |
Baculoviral IAP Repeat Containing 3 |
1.638567812 |
1.85E-11 |
1.84E-08 |
6 |
IRAK2 |
Interleukin 1 Receptor Associated Kinase 2 |
1.607708143 |
7.31E-11 |
6.37E-08 |
5 |
LIF |
leukemia inhibitory factor |
1.296612746 |
7.98E-13 |
1.34E-09 |
5 |
PLAUR |
Plasminogen Activator, Urokinase Receptor |
0.691228374 |
1.13E-06 |
0.000271087 |
5 |
FOSL1 |
Fos Proto-Oncogene Like 1 |
0.59129513 |
7.53E-07 |
0.000190836 |
5 |
BCL2A1 |
Bcl-2-related protein A1 | 2.318598715 |
1.31E-08 |
6.49E-06 |
5 |
ZC3H12A |
Zinc Finger CCCH-Type Containing 12A |
1.659683733 |
4.38E-10 |
2.81E-07 |
4 |
HBEGF |
Heparin Binding EGF Like Growth Factor |
1.290525563 |
7.48E-13 |
1.34E-09 |
4 |
MAP3K8 |
Mitogen-Activated Protein Kinase Kinase Kinase 8 |
1.027745148 |
1.61E-05 |
0.002072595 |
4 |
IL32 |
Interleukin 32 |
1.227557086 |
6.49E-12 |
7.07E-09 |
2 |
LGALS9 |
Galectin 9 |
0.850730372 |
0.000686534 |
0.035629464 |
2 |
MAFF |
MAF BZIP Transcription Factor F |
1.129511986 |
3.07E-10 |
2.09E-07 |
2 |
XDH |
Xanthine Dehydrogenase |
0.730795237 |
9.11E-08 |
3.26E-05 |
2 |
ADRB2 |
Adrenoceptor Beta 2 |
0.682671108 |
3.30E-07 |
9.47E-05 |
2 |
DUOX2 |
Dual Oxidase 2 |
0.58104455 |
0.000532824 |
0.030643714 |
2 |
ICAM2 |
Intercellular Adhesion Molecule 2 |
2.990121945 |
0.000270681 |
0.019344408 |
1 |
ADAM8 |
ADAM Metallopeptidase Domain 8 |
1.008094337 |
4.97E-06 |
0.000820449 |
1 |
VNN3 |
Vanin 3 |
2.499860771 |
5.49E-06 |
0.00087919 |
0 |
SAA2 |
Serum Amyloid A2 |
2.405120128 |
3.90E-17 |
8.49E-13 |
0 |
RND1 |
Rho Family GTPase 1 |
1.474356937 |
3.09E-06 |
0.000590577 |
0 |
TRIML2 |
Tripartite Motif Family Like 2 |
1.448435304 |
1.18E-05 |
0.001602523 |
0 |
MYEOV |
Myeloma Overexpressed |
1.326629482 |
1.85E-06 |
0.000415158 |
0 |
C15orf48 |
Chromosome 15 Open Reading Frame 48 |
1.231469907 |
7.89E-13 |
1.34E-09 |
0 |
SLC6A14 |
Solute Carrier Family 6 Member 14 |
1.212804879 |
2.66E-12 |
3.22E-09 |
0 |
C1R |
Complement C1r |
0.838868792 |
0.000613307 |
0.032926728 |
0 |
TGM1 |
Transglutaminase 1 |
0.787494457 |
3.33E-08 |
1.45E-05 |
0 |
HSH2D |
Hematopoietic SH2 Domain Containing |
0.77207627 |
0.001150116 |
0.049128951 |
0 |
TMEM171 |
Transmembrane Protein 171 |
0.754251093 |
0.000381358 |
0.024593072 |
0 |
SPRY4 |
Sprouty RTK Signaling Antagonist 4 |
0.672842446 |
0.000586277 |
0.032108259 |
0 |
KRT23 |
Keratin 23 |
0.598854314 |
2.33E-06 |
0.000475135 |
0 |
Downregulated DEGs |
|
||||
RAB15 |
RAB15, Member RAS Oncogene Family |
-0.75807553 |
7.16E-06 |
0.00108439 |
0 |
11 top genes for presented in bold accounts the highest degree score through Cytoscape analysis
Table 1: 63 shared DEGs between IAV H3N2, RSV, and SARS-CoV-2.
Figure 1: Flowchart of data preparation, processing, and analysis in this study
Figure 2: A) The volcano plots presenting DEGs for IAV H3N2 (a), RSV (b), and SARS-CoV-2 (c). The y-axis demonstrates the log10 values of the p-values for the significance of each examined DEG, while the x-axis shows the log10 values of fold changes for each DEG. Red plots depict DEGs with logFCs =0.58 or =-0.58, and blue plots displays remained DEGs with no statistical significance. B) Venn diagram of overlapping DEGs for three viruses. C) The heatmap of 50 top DEGs (25 increased and 25 decreased) in IVA H3N2 (a), RSV (b), SARS-CoV-2 (c), and 63 common DEGs (d). Red and green colors reflected upregulation and downregulation, respectively
Figure 3: Gene Ontology (GO) enrichment analysis of the common differentially expressed genes
Figure 4: Protein-protein interactions network construction and Drug prediction with p-value <1.0e-16
Tables at a glance
Figures at a glance