Endogenous Retrovirus Elements Are Co-Expressed with IFN Stimulation Genes in the JAK–STAT Pathway
Abstract
:1. Introduction
2. Materials and Method
2.1. RNA-Seq Data Acquisition
2.2. Reads Mapping and Counting
2.3. Differential Expression Analysis
2.4. GO and KEGG-Enrichment Analyses
2.5. Construction of Protein–Protein Interaction (PPI) Networks
3. Results
3.1. IFNAR Knockout Validation
3.2. RNA-Seq Datasets Analysis
3.3. Screening and Classification of DEHERVs
3.4. Identification and Functional Enrichment of DEGs
3.5. Identification of DEHERV-G Pairs in Each Dataset
3.6. Functional Enrichment Analysis of DEHERV-G Pair Genes and Protein–Protein Interaction (PPI) Network Construction
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ERVs | endogenous retroviruses |
REs | retrotransposon |
TEs | transposable elements |
LTRs | long terminal repeats |
dsRNA | double-stranded RNA |
TLR3 | toll-like receptor 3 |
RIG-I | retinoic-acid-inducible gene I |
MDA5 | melanoma differentiation-associated gene 5 |
IFNAR | type I interferon receptor |
JAK | Janus-activated kinase |
STAT2 | signal transducer and activator of transcription 2 |
IRF9 | IFN regulatory factor 9 |
ISG | IFN-stimulated gene |
ISGF3 | IFN-stimulated gene factor 3 |
ISRE | interferon-stimulated regulatory element |
GAS | IFN-γ-activated site |
IRF1 | interferon regulatory factor 1 |
KO | knockout |
DAVID | Database for Annotation, Visualization, and Integrated Discovery |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
PPI | Protein–protein interaction |
DE | differentially expressed |
STRING | Search Tool for the Retrieval of Interacting Genes |
PCA | principal component analysis |
BP(s) | biological process(es) |
CC | cell component |
MF | molecular function |
TFBSs | transcription factors binding sites |
AP | activator protein |
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Wang, Y.; Liu, M.; Guo, X.; Zhang, B.; Li, H.; Liu, Y.; Han, J.; Jia, L.; Li, L. Endogenous Retrovirus Elements Are Co-Expressed with IFN Stimulation Genes in the JAK–STAT Pathway. Viruses 2023, 15, 60. https://doi.org/10.3390/v15010060
Wang Y, Liu M, Guo X, Zhang B, Li H, Liu Y, Han J, Jia L, Li L. Endogenous Retrovirus Elements Are Co-Expressed with IFN Stimulation Genes in the JAK–STAT Pathway. Viruses. 2023; 15(1):60. https://doi.org/10.3390/v15010060
Chicago/Turabian StyleWang, Yanglan, Mengying Liu, Xing Guo, Bohan Zhang, Hanping Li, Yongjian Liu, Jingwan Han, Lei Jia, and Lin Li. 2023. "Endogenous Retrovirus Elements Are Co-Expressed with IFN Stimulation Genes in the JAK–STAT Pathway" Viruses 15, no. 1: 60. https://doi.org/10.3390/v15010060