Article
Biochemistry & Molecular Biology
Cheng Luo, Bin Huang, Yukun Wu, Yadong Xu, Wei Ou, Junxing Chen, Lingwu Chen
Summary: This study identified key genes related to lymph node metastasis in bladder cancer, constructed a prognostic signature, and explored the biological functions and pathways of these genes through the analysis of the TCGA database. The findings provide new insights into therapeutic targets for bladder cancer.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Forestry
Zhenghai Mo, Xiaozhuang Jiang, Yan Zhang, Min Zhai, Longjiao Hu, Jiping Xuan
Summary: Weighted gene co-expression network analysis was used to identify key pathways and genes related to successful grafting in pecan. Oxidative detoxification and hormone signaling were found to be important in grafting success.
Article
Plant Sciences
Tingchun Li, Yiting Wang, Qing Dong, Fang Wang, Fanna Kong, Guihu Liu, Yanli Lei, Huaying Yang, Yingbing Zhou, Cheng Li
Summary: This study identified the module and hub genes related to anthocyanins biosynthesis in maize seeds. The cyan module, containing 183 genes, showed the highest correlation with the anthocyanins trait. The yeast one-hybrid assays confirmed that the transcription factor Lc gene directly regulates the biosynthesis of anthocyanins in the pericarp.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Yun Dai, Xiao Sun, Chenggang Wang, Fei Li, Shifan Zhang, Hui Zhang, Guoliang Li, Lingyun Yuan, Guohu Chen, Rifei Sun, Shujiang Zhang
Summary: This study investigates the gene expression differences between two Chinese cabbage accessions with different bolting behaviors during vernalization. Through transcriptome analysis and WGCNA, it was found that specific pathways such as shoot system morphogenesis and signaling pathways play a role in promoting early bolting, while pathways related to chitin, ABA, and ethylene signaling are involved in late bolting. Hub genes like MTHFR2, CPRD49, AAP8, and specific genes related to flower development were also identified. These findings provide valuable insights for breeders in optimizing Chinese cabbage production.
Article
Cell Biology
Yang Liu, Lanlan Chen, Xiangbo Meng, Shujun Ye, Lianjun Ma
Summary: This study identified hub genes associated with colorectal adenocarcinoma and constructed a 3-gene signature to predict the prognosis of patients. The findings provide valuable insights into the molecular mechanisms and potential prognosis factors of colorectal adenocarcinoma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang
Summary: This study identified hub genes with diagnostic and therapeutic potential in gastric cancer through weighted gene co-expression network analysis and logistic regression, and successfully validated their discriminative ability in an independent testing set using artificial neural network algorithm.
Article
Biotechnology & Applied Microbiology
Kang Tang, Lin Li, Bowen Zhang, Wei Zhang, Ningbo Zeng, Hao Zhang, Dengwang Liu, Zinan Luo
Summary: Two peanut cultivars, large-seed and small-seed, showed different molecular mechanisms under different calcium treatments. The large-seed cultivar focused more on plant defensive responses and antioxidant activities, while the small-seed cultivar mainly focused on maintaining membrane features for normal photosynthesis and signal transduction.
Article
Oncology
Xiaoqing Shen, Zhujuan Yang, Songwei Feng, Yi Li
Summary: This study used bioinformatics methods to identify hub genes and immune cell infiltration patterns associated with uterine leiomyosarcoma (ULMS). The results showed higher infiltration of five types of cells in ULMS tissues compared to normal tissues, while two types of cells showed lower infiltration. Additionally, five hub genes were identified, which were found to be associated with specific immune cell types.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2021)
Article
Nutrition & Dietetics
Fu-Jun Liao, Peng-Fei Zheng, Yao-Zong Guan, Hong-Wei Pan, Wei Li
Summary: This study identified the royal blue module associated with total cholesterol, triglycerides, and non-HDL-C, and revealed SQLE and SCD as key molecules related to hypercholesterolaemia and hypertriglyceridaemia. Gene Ontology and KEGG enrichment analyses indicated that genes in the royal blue module are involved in carbon metabolism, steroid biosynthesis, fatty acid metabolism, and biosynthesis pathways of unsaturated fatty acids.
NUTRITION & METABOLISM
(2021)
Article
Genetics & Heredity
Zhengze Shen, Shengwei Liu, Jie Liu, Jingdong Liu, Caoyuan Yao
Summary: This study aimed to predict hub genes affecting LUAD recurrence using weighted gene co-expression network analysis. Through analysis of microarray samples, a protein-protein interaction network was established, and eight hub genes closely related to LUAD recurrence were identified. Transcription factors regulating these hub genes were predicted, and drugs for treating these genes were explored.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Xinfeng Wang, Akhilesh K. Bajpai, Qingqing Gu, David G. Ashbrook, Athena Starlard-Davenport, Lu Lu
Summary: In this study, a cross-species integrative approach was used to identify genes strongly associated with acute myeloid leukemia (AML). Through the integration of protein-protein interactions, transcription factors, gene function, genetic regulation, and coding sequence variants, key hub genes in AML were identified. The findings highlight the importance of this cross-species approach in identifying multiple key candidate genes in AML.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Li Peng, Wei Ma, Qing Xie, Baihua Chen
Summary: The study identified novel key genes associated with the formation of diabetic retinopathy (DR) through bioinformatics analysis, focusing on mitochondrial function, fatty acid oxidation, and oxidative stress. Experimental validation confirmed the importance of SLC25A33 and NDUFS1 in the pathogenesis of DR.
Article
Dentistry, Oral Surgery & Medicine
Denghui Zhang, Chen Zheng, Tianer Zhu, Fan Yang, Yiqun Zhou
Summary: This study identified key genes related to pulpitis using microarray data analysis and the weighted gene co-expression network analysis (WGCNA) method. Hub genes in the module most associated with pulpitis were screened out and validated using RT-qPCR. Pulp capping using iRoot BP plus was shown to reverse the expression levels of some hub genes.
Article
Microbiology
Zongling Liu, Xiufang Li, Jie Li, Haiyun Zhao, Xingli Deng, Yizu Su, Ru Li, Baoshan Chen
Summary: In this study, the key genes involved in S. scitamineum infection were investigated using RNA sequencing and weighted gene co-expression network analysis. Two co-expressed gene modules associated with S. scitamineum infection were identified. Further analysis revealed genes and proteins related to pathogen virulence and small secreted cysteine-rich proteins (SCRPs) that may play important roles in infection. A S. scitamineum infection model was proposed based on the findings, deepening the understanding of early events in S. scitamineum infection.
Article
Genetics & Heredity
Guoqing Li, Jun Zhang, Dechen Liu, Qiong Wei, Hui Wang, Yingqi Lv, Zheng Ye, Gaifang Liu, Ling Li
Summary: This study aimed to identify novel biomarkers and mechanisms for diabetic nephropathy (DN) disease progression through weighted gene co-expression network analysis. Four potential RNA regulatory pathways were proposed, and IL6, CXCL8, MMP9, and ATF3 were identified as markers for early diagnosis of DN. Insights into the disease development mechanisms in DN at the transcriptome level were provided.
FRONTIERS IN GENETICS
(2021)