ArticleFrontiers in immunology2022
A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2.
Article in Frontiers in immunology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 16 citations in OpenAlex.
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- The Roles of TOPK in Tumorigenesis and Development: Structure, Mechanisms, Pathways, and Therapeutic Implications.International journal of biological sciences · 2026Review
- Network-based approach identifies key genes associated with tumor heterogeneity in HPV positive and negative head and neck cancer patients.Scientific reports · 2025Article
- Immune transcriptomic analysis on COVID-19 patients with varying clinical presentations identifies severity markers.Scientific reports · 2025Article
- Protocol for identifying key genes using network-based approach as an alternative to differential expression analysis.STAR protocols · 2024Article
- Identification and evaluation of candidate COVID-19 critical genes and medicinal drugs related to plasma cells.BMC infectious diseases · 2024Article
- SARS-CoV-2 nucleocapsid protein promotes self-deacetylation by inducing HDAC6 to facilitate viral replication.Virology journal · 2024Article
- Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.iScience · 2024Article
- Systems-wide view of host-pathogen interactions across COVID-19 severities using integrated omics analysis.iScience · 2024Article
- Exploration of the potential common pathogenic mechanisms in COVID-19 and silicosis by using bioinformatics and system biology.Functional & integrative genomics · 2023Article
- Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing.Scientific reports · 2023Article
- Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform.iScience · 2023Article
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4 authors at 3 institutions in 2 countries.
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Abstract
Most transcriptomic studies of SARS-CoV-2 infection have focused on differentially expressed genes, which do not necessarily reveal the genes mediating the transcriptomic changes. In contrast, exploiting curated biological network, our PathExt tool identifies central genes from the differentially active paths mediating global transcriptomic response. Here we apply PathExt to multiple cell line infection models of SARS-CoV-2 and other viruses, as well as to COVID-19 patient-derived PBMCs. The central genes mediating SARS-CoV-2 response in cell lines were uniquely enriched for ATP metabolic process, G1/S transition, leukocyte activation and migration. In contrast, PBMC response reveals dysregulated cell-cycle processes. In PBMC, the most frequently central genes are associated with COVID-19 severity. Importantly, relative to differential genes, PathExt-identified genes show greater concordance with several benchmark anti-COVID-19 target gene sets. We propose six novel anti-SARS-CoV-2 targets ADCY2, ADSL, OCRL, TIAM1, PBK, and BUB1, and potential drugs targeting these genes, such as Bemcentinib, Phthalocyanine, and Conivaptan.
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