Article
Genetics & Heredity
Lin Chen, Yong Wang, Juan Huang, Binbin Hu, Wei Huang
Summary: This study identified four hub genes (SLC18A2, L1CAM, S100A12, and CXCR4) and seven immune cell types (neutrophils, T follicular helper cells, myeloid-derived suppressor cells, type 1 helper cells, immature B cells, immature dendritic cells, and CD56 bright natural killer cells) associated with the pathogenesis of PD. The combined model of the four genes showed a high accuracy in differentiating PD patients from healthy controls.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Piaopiao Li, Yingxia Li, Lei Ma
Summary: This study investigated the biological roles and mechanisms of chimeric genes in pigs using weighted co-expression network analysis. The results showed that most protein domains of chimeric genes were derived from fused pre-genes and were involved in negative regulation of cell proliferation and protein localization to centrosomes. Additionally, chimeric genes were related to the growth factor-beta superfamily and played a key role in regulating T cell pathways.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2021)
Article
Biology
Zuhier Awan, Nuha Alrayes, Zeenath Khan, Majid Almansouri, Abdul Ibrahim Hussain Bima, Haifa Almukadi, Hussam Ibrahim Kutbi, Preetha Jayasheela Shetty, Noor Ahmad Shaik, Babajan Banaganapalli
Summary: This study identified potential genetic biomarkers for familial hypercholesterolemia (FH) by studying the global gene expression profile of blood cells. Dysregulated expression of genes related to lipid homeostasis, immune responses, and cell adhesion molecules was found in FH patients. The involvement of dysregulated thyroid hormone and ErbB signaling pathways, as well as the enrichment of specific genes, were observed. The key hub genes JAK3, PLCG2, and ZEB2 were identified to contribute to inflammation and immune response related phenotypes. These findings provide insights into the immune dysregulation underlying atherosclerosis among FH patients and may contribute to the development of genomic medicine for cardiovascular diseases.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemical Research Methods
Jun Wang, Ziying Yang, Carlotta Domeniconi, Xiangliang Zhang, Guoxian Yu
Summary: CDPathway is a novel approach that can identify cooperative driver pathways by quantifying driver weights and constructing heterogeneous networks, which effectively identify candidate driver genes and reconstruct pathway interaction networks.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Luling He, Andrea Palos-Jasso, Yao Yi, Manman Qin, Liang Qiu, Xiaofeng Yang, Yifeng Zhang, Jun Yu
Summary: This study used bioinformatic analysis to identify metabolic pathways and immune-related pathways involved in the progression of atherosclerosis. Key genes and modules associated with immune and muscle system function were also identified. This research improves our understanding of the molecular mechanisms underlying atherosclerosis and provides potential biomarkers and drug targets for its management.
Article
Agronomy
Hongli Dong, Lei Yang, Yilin Liu, Guifu Tian, Huan Tang, Shuangshuang Xin, Yixin Cui, Qing Xiong, Huafang Wan, Zhi Liu, Christian Jung, Wei Qian
Summary: This study constructed a gene coexpression network in the early developmental stage of rapeseed seeds and identified gene modules related to seed weight regulation. A key gene, SCPL19, was found through candidate gene association analysis and functionally investigated using Arabidopsis. The study expands our understanding of the molecular mechanism for seed weight regulation in rapeseed.
Article
Genetics & Heredity
Jian Zhou, Dazhi Zou, Rongjun Wan, Jie Liu, Qiong Zhou, Zhen Zhou, Wanchun Wang, Cheng Tao, Tang Liu
Summary: This study investigates the molecular mechanisms and hub genes associated with osteoarthritis (OA) using bioinformatics analysis. Differential gene expression analysis and GO/KEGG pathway analysis were performed on OA synovial tissue samples. Various upregulated and downregulated genes were identified, with upregulated genes involved in immune response and cell adhesion, and downregulated genes enriched in response to mechanical stimuli and the MAPK signaling pathway. Several intersection genes and hub genes were also identified. These findings provide insights into the molecular mechanisms of OA and may contribute to the development of biomarkers and drug targets.
FRONTIERS IN GENETICS
(2022)
Article
Cardiac & Cardiovascular Systems
Weikang Bian, Zhicheng Wang, Xiaobo Li, Xiao-Xin Jiang, Hongsong Zhang, Zhizhong Liu, Dai-Min Zhang
Summary: In this study, weighted gene coexpression network analysis (WGCNA) was used to identify the key module and hub genes for heart failure (HF). Differential gene expression analysis, coexpression network construction, functional enrichment analysis, and protein-protein interaction network construction were conducted to identify potential hub genes. The results may provide potential biomarkers for the diagnosis of HF and enhance our understanding of the molecular mechanisms underlying HF.
Article
Microbiology
Teresa R. O'Meara, Matthew J. O'Meara
Summary: The study focused on building a comprehensive and unbiased co-expression network for Candida albicans, known as CalCEN, using data from RNA sequencing runs. This network was successfully used to predict gene function and identified a novel cell cycle regulator, CCJ1. The tool provides a valuable resource for future analyses of gene function in C. albicans.
Article
Horticulture
Puspa Raj Poudel, Akifumi Azuma, Shozo Kobayashi, Kazuya Koyama, Nami Goto-Yamamoto
Summary: The study identified target genes of VvMYBAs in grapevines by analyzing gene expression in red and white grape varieties. The results showed that VvMYBAs regulate the expression of multiple genes involved in anthocyanin biosynthesis, with some genes specifically induced by VvMYBAs and others induced by both VvMYBAs and other transcription factors. Additionally, it was found that VvMYBA proteins directly interact with certain key genes in the anthocyanin biosynthesis pathway.
SCIENTIA HORTICULTURAE
(2021)
Article
Pediatrics
Wangkai Liu, Yihua Su, Sitao Li, Haitian Chen, Yumei Liu, Xiaoyu Li, Wei Shen, Xinqi Zhong, Fan Wu, Qiong Meng, Xiaoyun Jiang
Summary: This study identified a significantly downregulated coexpression module related to the bronchopulmonary dysplasia (BPD) phenotype, enriched in genes associated with human T-cell leukemia virus infection and the mitogen-activated protein kinase pathway. The decreased expression of hub genes FOS, BTG2, JUN, and EGR1 in infants with BPD could serve as biomarkers for early diagnosis of BPD.
PEDIATRIC PULMONOLOGY
(2021)
Article
Developmental Biology
S. Marla, S. Mortlock, S. Houshdaran, J. Fung, B. McKinnon, S. J. Holdsworth-Carson, J. E. Girling, P. A. W. Rogers, L. C. Giudice, G. W. Montgomery
Summary: The study found that genetic regulation of genes in the ESR1 region is associated with endometriosis risk, with gene expression influenced more significantly by hormone concentrations and receptor expression. Due to limited sample size and cellular heterogeneity, the study also noted that detecting genetic effects on gene expression may be challenging.
MOLECULAR HUMAN REPRODUCTION
(2021)
Article
Biochemistry & Molecular Biology
Megan Crow, Hamsini Suresh, John Lee, Jesse Gillis
Summary: Differences in gene regulation play a critical role in cell specialization and diversification, and the differential regulation of ancient gene programs contributes to transcriptional cell identity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Ming Yang, Benjamin R. Harrison, Daniel E. L. Promislow
Summary: This study focuses on gene coexpression in diverse cell types of the fruit fly using single-cell RNA sequencing data. The researchers discovered a set of highly coordinated genes that form a core cellular network, which accounts for only a minority of essential functions.
G3-GENES GENOMES GENETICS
(2022)
Article
Chemistry, Multidisciplinary
George I. Lambrou, Kleanthis Vichos, Dimitrios Koutsouris, Apostolos Zaravinos
Summary: Urinary bladder cancer (UBC) is the second most common urogenital solid tumor, with several new candidate prognostic markers identified. This study aimed to detect global gene co-expression profiles among a high number of UBC tumors, resulting in the identification of novel candidate markers and potential drugs for the disease.
APPLIED SCIENCES-BASEL
(2021)