Article
Oncology
Huan Deng, Qingqing Hang, Dijian Shen, Yibi Zhang, Ming Chen
Summary: Our study identified 486 differentially coexpressed genes associated with LUAD, with ten hub genes closely correlated with overall survival. Through functional enrichment analysis and protein-protein interaction network establishment, we found that CHRDL1 and SPARCL1 may serve as potential therapeutic and prognostic indicators for LUAD.
CANCER CELL INTERNATIONAL
(2021)
Article
Biotechnology & Applied Microbiology
Chongyang Ma, Kai Yan, Zisong Wang, Qiuyun Zhang, Lianyin Gao, Tian Xu, Jiayang Sai, Fafeng Cheng, Yuqiong Du
Summary: The study revealed a complex relationship between hypertension and NAFLD, identifying shared genes and potential mechanisms. The genes were associated with inflammatory, metabolic, and endocrine signals, suggesting a multi-target therapeutic strategy for future clinical research.
Article
Pharmacology & Pharmacy
Xiaoyi Wei, Weixin Hou, Jiajun Liang, Peng Fang, Bo Dou, Zisong Wang, Jiayang Sai, Tian Xu, Chongyang Ma, Qiuyun Zhang, Fafeng Cheng, Xueqian Wang, Qingguo Wang
Summary: This study employed network pharmacology approach to investigate the mechanism of Sinisan in treating non-alcoholic fatty liver disease (NAFLD), identifying its ability to reduce hyperlipidemia, liver steatosis, and inflammation, while inhibiting the crucial JAK2/STAT3 signaling pathway.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Multidisciplinary Sciences
Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, Chih-Hung Jen, William J. Duddy, Gerasimos Daras, Polydefkis Hatzopoulos, David R. Westhead, Ioannis Michalopoulos
Summary: Gene coexpression analysis aims to identify sets of genes with similar expression patterns across multiple data sets, such as microarray experiments. The Arabidopsis Coexpression Tool (ACT) generates a coexpression tree from processed microarray data, revealing relationships between different genes. ACT offers a user-friendly interface for gene set enrichment analysis and is successful in identifying both ubiquitous and tissue-specific gene expressions.
Article
Biochemistry & Molecular Biology
Francisco Andujar-Vera, Maria Ferrer-Millan, Cristina Garcia-Fontana, Beatriz Garcia-Fontana, Sheila Gonzalez-Salvatierra, Raquel de la Torre, Luis Martinez-Heredia, Blanca Riquelme-Gallego, Manuel Munoz-Torres
Summary: Non-alcoholic fatty liver disease (NAFLD) and atherosclerosis (ATH) may share some molecular connections, but the underlying pathways have not been explored. This study aimed to identify common factors and potential therapeutic targets for both diseases. Differentially expressed genes (DEGs) were analyzed and common DEGs were identified. Protein-protein interaction (PPI) network analysis revealed functional modules and hub genes. Gene Ontology (GO) and pathway analysis were performed. The study found 21 genes with similar regulation in NAFLD and ATH. The hub genes ADAMTS1 and CEBPA were found to be down- and up-regulated, respectively. Functional modules related to protein modification and immune response were identified, with ADAMTS1, ADAMTS4, and CSF3 playing potential key roles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Virology
Arpita Kar, Abhisekh Samanta, Soumyadeep Mukherjee, Subhasis Barik, Avik Biswas
Summary: Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), the most common primary liver malignancy. The study of HBV-host interactions has identified various mechanisms involved in the development and progression of HBV-associated HCC. This review provides a comprehensive summary of the existing knowledge on HBV-host interplay and highlights new therapeutic strategies for HBV-induced HCC.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Qing Zhou, Yuhao Yang, Zhanxue Xu, Kai Deng, Zhenzhen Zhang, Jiawei Hao, Ni Li, Yanling Wang, Ziwen Wang, Haihang Chen, Yang Yang, Fei Xiao, Xiaohong Zhang, Song Gao, Yi-Ping Li
Summary: ATAD1 plays a crucial role in maintaining mitochondrial homeostasis and combating viral infection. HCV infection induces mitochondrial fragmentation and enhances the pro-infection effect of ATAD1 knockout. ATAD1 interacts with HCV NS5B protein and promotes its degradation, thereby exerting its antiviral function.
Article
Biochemical Research Methods
Md Rabiul Auwul, Md Rezanur Rahman, Esra Gov, Md Shahjaman, Mohammad Ali Moni
Summary: This study identified key gene modules and hub targets involved in COVID-19 by analyzing transcriptomic data of SARS-CoV-2 infected PBMCs, revealing genes related to immune and inflammatory responses. Moreover, drug-gene interaction analysis suggested potential repurposed drugs for COVID-19 treatment.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Athina I. Amanatidou, George V. Dedoussis
Summary: Non-alcoholic fatty liver disease (NAFLD) is a complex disease that requires identification and study of new candidate proteins. This study analyzed the interaction network of human proteins associated with NAFLD to identify novel associations with other proteins involved in the disease. The computational analysis detected 77 candidate proteins with high network scores, and clustering analysis identified densely connected regions with biological significance. Additionally, gene expression analysis was conducted to validate some of the research findings, aiming to provide insights for addressing the pathogenesis and progression of NAFLD.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Microbiology
Yu Hao, Jinke Yang, Bo Yang, Ting Zhang, Xijuan Shi, Xing Yang, Dajun Zhang, Dengshuai Zhao, Wenqian Yan, Lingling Chen, Xiangtao Liu, Haixue Zheng, Keshan Zhang
Summary: This study reveals the interaction network of ASFV D1133L protein in porcine kidney cells and identifies host proteins involved in various cellular processes. Furthermore, the study confirms the interaction of D1133L with VIM, TRIM21, and TUFM, and shows that overexpression of VIM or TRIM21 promotes ASFV replication while overexpression of TUFM inhibits ASFV replication.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Soudeh Ghafouri-Fard, Arash Safarzadeh, Mohammad Taheri, Elena Jamali
Summary: A co-expression network of differentially expressed genes (DEGs) related to colorectal cancer (CRC) and their target genes was constructed using the weighted gene co-expression network analysis (WGCNA) algorithm. GO and KEGG pathway analysis revealed that these genes were mainly involved in the regulation of hormone levels, extracellular matrix organization, and extracellular structure organization. The study also identified DKC1, PA2G4, LYAR and NOLC1 as the key hub genes of CRC.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Shiv Kumar, Rohit Verma, Sandhini Saha, Ashish Kumar Agrahari, Shivangi Shukla, Oinam Ningthemmani Singh, Umang Berry, Tushar Kanti Maiti, Shailendra Asthana, C. T. Ranjith-Kumar, Milan Surjit
Summary: Multiple processes exist in a cell to ensure continuous production of essential proteins through different translation processes. Viruses have evolved strategies to use the host translation machinery for their protein synthesis. This study identifies the RNA-protein interactome of the HEV IRESl element and demonstrates the roles of ribosomal protein RPL5 and RNA helicase A (DHX9) in mediating HEV IRESl activity, establishing it as a bona fide internal translation initiation site.
MICROBIOLOGY SPECTRUM
(2023)
Article
Gastroenterology & Hepatology
Fangwan Yang, Yujuan Liu, Baimei Zeng, Jun Chu, Han Hu, Yanqing Yang, Huan Chen, Caiyun Tian, Ying Li, Shide Lin
Summary: The Lok index has strong predictive accuracy for progression to ACLF in patients with acute exacerbation and severe exacerbation of chronic HBV infection, requiring different thresholds of liver fibrosis based on severity of liver injury.
HEPATOLOGY INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Simon Gosset, Annie Glatigny, Melina Gallopin, Zhou Yi, Marion Sale, Marie-Helene Mucchielli-Giorgi
Summary: Protein-protein interactions are crucial for cell processes and analyzing PPI networks can provide insights into protein functions. APPINetwork is a user-friendly open-source package for building and analyzing PPI networks from any species.
Article
Genetics & Heredity
Jinxing Hu, Shan Zhou, Weiying Guo
Summary: In this study, a coexpression network related to thyroid eye disease (TED) was constructed using bioinformatic approaches, and key genes, transcription factors (TFs), microRNAs (miRs), and drugs were predicted. These results are important for the treatment and diagnosis of TED and may stimulate molecular research on TED.