Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication
Purpose: The current outbreak of monkeypox (MPX) has created colossal concerns. However, immense research gaps have been noted in our understanding of the replication process, machinery, and genomic landscape during host cell infection. To fill this gap, differentially expressed genes (DEGs) were co...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | Journal of Infection and Public Health |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1876034123000254 |
| _version_ | 1797903502172749824 |
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| author | Chiranjib Chakraborty Manojit Bhattacharya Kuldeep Dhama Sang-Soo Lee |
| author_facet | Chiranjib Chakraborty Manojit Bhattacharya Kuldeep Dhama Sang-Soo Lee |
| author_sort | Chiranjib Chakraborty |
| collection | DOAJ |
| description | Purpose: The current outbreak of monkeypox (MPX) has created colossal concerns. However, immense research gaps have been noted in our understanding of the replication process, machinery, and genomic landscape during host cell infection. To fill this gap, differentially expressed genes (DEGs) were comprehensively analyzed during viral replication in host (MK2) cells. Methods: We used a microarray GEO dataset which was divided into three groups: control, MPXV-infected MK2 cells at 3 h, and MPXV-infected MK2 cells at 7 h. Using the dataset, DEG analysis, PPI network analysis, co-expression, and pathway analysis were conducted using bioinformatics, systems biology, and statistical approaches. Results: We identified 250 DEGs and 24 top-ranked genes. During the DEG analysis, we identified eight up-regulated genes (LOC695323, TMEM107, LOC695427, HIST1H2AD, LOC705469, PMAIP1, HIST1H2BJ, and HIST1H3D) and 16 down-regulated genes (HOXA9, BAMBI, LMO4, PAX6, AJUBA, CREBRF, CD24, JADE1, SLC7A11, EID2, SOX4, B4GALT5, PPARGC1A, BUB3, SOS2, and CDK19). We also developed PPI networks and performed co-expression analyses using the top-ranked genes. Furthermore, five genes were listed for co-expression pattern analysis. Conclusions: This study will help in better understanding the replication process, machinery, and genomic landscape of the virus. This will further aid the discovery and development of therapeutics against viruses. |
| first_indexed | 2024-04-10T09:34:01Z |
| format | Article |
| id | doaj.art-3266cbcb5b23464baf77367f3212b43d |
| institution | Directory Open Access Journal |
| issn | 1876-0341 |
| language | English |
| last_indexed | 2024-04-10T09:34:01Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Infection and Public Health |
| spelling | doaj.art-3266cbcb5b23464baf77367f3212b43d2023-02-18T04:16:41ZengElsevierJournal of Infection and Public Health1876-03412023-03-01163399409Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replicationChiranjib Chakraborty0Manojit Bhattacharya1Kuldeep Dhama2Sang-Soo Lee3Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India; Corresponding authors.Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, IndiaDivision of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, IndiaInstitute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon 24252, Gangwon-Do, Republic of Korea; Corresponding authors.Purpose: The current outbreak of monkeypox (MPX) has created colossal concerns. However, immense research gaps have been noted in our understanding of the replication process, machinery, and genomic landscape during host cell infection. To fill this gap, differentially expressed genes (DEGs) were comprehensively analyzed during viral replication in host (MK2) cells. Methods: We used a microarray GEO dataset which was divided into three groups: control, MPXV-infected MK2 cells at 3 h, and MPXV-infected MK2 cells at 7 h. Using the dataset, DEG analysis, PPI network analysis, co-expression, and pathway analysis were conducted using bioinformatics, systems biology, and statistical approaches. Results: We identified 250 DEGs and 24 top-ranked genes. During the DEG analysis, we identified eight up-regulated genes (LOC695323, TMEM107, LOC695427, HIST1H2AD, LOC705469, PMAIP1, HIST1H2BJ, and HIST1H3D) and 16 down-regulated genes (HOXA9, BAMBI, LMO4, PAX6, AJUBA, CREBRF, CD24, JADE1, SLC7A11, EID2, SOX4, B4GALT5, PPARGC1A, BUB3, SOS2, and CDK19). We also developed PPI networks and performed co-expression analyses using the top-ranked genes. Furthermore, five genes were listed for co-expression pattern analysis. Conclusions: This study will help in better understanding the replication process, machinery, and genomic landscape of the virus. This will further aid the discovery and development of therapeutics against viruses.http://www.sciencedirect.com/science/article/pii/S1876034123000254Monkeypox virusReplicationMK2 cellsDEGPPI networkCo-expression |
| spellingShingle | Chiranjib Chakraborty Manojit Bhattacharya Kuldeep Dhama Sang-Soo Lee Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication Journal of Infection and Public Health Monkeypox virus Replication MK2 cells DEG PPI network Co-expression |
| title | Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication |
| title_full | Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication |
| title_fullStr | Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication |
| title_full_unstemmed | Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication |
| title_short | Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication |
| title_sort | evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox infected mk2 cells a bioinformatics and systems biology approach to understanding the genomic pattern of viral replication |
| topic | Monkeypox virus Replication MK2 cells DEG PPI network Co-expression |
| url | http://www.sciencedirect.com/science/article/pii/S1876034123000254 |
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