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Network analysis provides deep insight into real complex systems. Revealing the link between topological and functional role of network elements can be crucial to understand the mechanisms underlying the system. Here we propose a Cytoscape plugin (GIANT) to perform network clustering and characterize nodes at the light of a modified Guimerà-Amaral cartography. This approach results into a vivid picture of the a topological/functional relationship at both local and global level. The plugin has been already approved and uploaded on the Cytoscape APP store.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183485 | PMC |
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105001 | PLOS |
Medicine (Baltimore)
September 2025
Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China.
Type 2 diabetes mellitus (T2DM) and cardiogenic stroke (CS) are harmful to human health. Previous studies have shown a correlation between T2DM and CS, but the causal relationships and pathogenic mechanisms between T2DM and CS remain unclear. We downloaded T2DM and CS datasets from a genome-wide Association Study and performed Mendelian randomization (MR) analysis using the TwoSampleMR package in R software.
View Article and Find Full Text PDFReprod Sci
September 2025
The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, China.
Background: Cervical cancer (CC) is the fourth most frequently diagnosed cancer and the fourth leading cause of cancer-related deaths in women worldwide, however, the treatment options for advanced CC are limited. Therefore, there is an urgent need in the clinic for reliable prognostic models to guide clinical decision-making.
Methods: We conducted differential gene expression analysis on cervical cancer samples and normal samples to obtain differentially expressed genes (DEGs).
Int J Gen Med
August 2025
Department of Emergency, Hebei Provincial Hospital of TCM, Shijiazhuang, Hebei Province, People's Republic of China.
Background: Yinghuang Decoction is an herbal formula that is used for the treatment of sepsis. This study used network pharmacology and molecular docking methods to explore the potential mechanism of Yinghuang Decoction against sepsis.
Methods: The active ingredients, target genes, and sepsis-related differentially expressed genes (DEGs) were acquired from the public database.
Sci Rep
August 2025
Department of Emergency Trauma Center, Henan University of Chinese Medicine Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China.
Tendon injury is a common and challenging clinical problem, and its healing process involves complex cellular and biological factors. Therefore, this study aims to reveal the mechanism of tendon healing and provide theoretical basis for clinical treatment. We first selected GSE26051 dataset from the GEO database and used R language to obtain 721 DEGs (459 up-regulated and 262 down-regulated).
View Article and Find Full Text PDFPathogens
August 2025
Division of Research Capacity Development, South African Medical Research Council (SAMRC), Tygerberg, Cape Town 7505, South Africa.
The immunological interactions between soil-transmitted helminths (STHs) and herpes simplex virus type 2 (HSV-2), particularly in the context of co-infection, are poorly understood. Next-generation sequencing (NGS) offers a powerful approach to explore these complex immune responses and uncover potential therapeutic targets. This study leveraged NGS and bioinformatic tools to investigate transcriptional changes and immunological pathways in female genital tract (FGT) tissues of BALB/c mice acutely infected with (), HSV-2, or co-infected.
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