Single-cell RNA-seq analysis reveals microenvironmental infiltration of myeloid cells and pancreatic prognostic markers in PDAC by Yanying Fan, Lili Wu, Xinyu Qiu, Han Shi, Longhang Wu, Juan Lin, Jie Lin, Tianhong Teng

“…Methods Single-cell RNA sequencing (scRNA-seq) data were downloaded from t the Tumor Immune Single-cell Hub and gene expression data were retrieved from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Gene set variation analysis (GSVA) was used to estimate the relative proportions of each cell type based on the signatures identified by scRNA-seq or previous literature. …”
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Identification of tacrolimus-related genes in familial combined hyperlipidemia and development of a diagnostic model using bioinformatics analysis by Yuan Xu, Hongfei He, Haiyang Li

“…FCHL was linked to memory B and immature B immune cells. The gene set variation analysis revealed two pathways associated with cholesterol homeostasis and the complement system that were closely associated with the potential functions of FCHL and tacrolimus-related differentially expressed genes. …”
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The key role of the NUDT3 gene in lung adenocarcinoma progression and its association with the manganese ion metabolism family by Deyong Ge, Xinyu Xu, Liyi Fang, Huihui Tao

“…Non-negative matrix factorization (NMF) and gene set variation analysis (GSVA) were applied to assess the functional enrichment and expression profiles of the manganese ion metabolism family across 14 cancers. …”
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Spatiotemporal Variation and Driving Factors of Carbon Sequestration Rate in Terrestrial Ecosystems of Ningxia, China by Yi Zhang, Chunxiao Cheng, Zhihui Wang, Hongxin Hai, Lulu Miao

“…Based on ground observation data and multimodal datasets, the optimal machine learning model (EXT) was used to invert a 30 m high-resolution vegetation and soil carbon density dataset for Ningxia from 2000 to 2023. Annual variation analysis and geographical detector methods were employed to assess the spatiotemporal distribution characteristics of the CSR from 2001 to 2023 and identify the primary influencing factors. …”
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UBE2J1 is identified as a novel plasma cell-related gene involved in the prognosis of high-grade serous ovarian cancer by Yunjie Tian, Ruoyu Dong, Yingxia Guan, Ying Wang, Wei Zhao, Jun Zhang, Shan Kang

“…The effects of immune cell markers on prognosis were analyzed via univariate Cox regression, least absolute shrinkage and selection operator (LASSO) and gene set variation analysis (GSVA) of bulk sequencing data from The Cancer Genome Atlas (TCGA)-HGSOC cohort. …”
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Single-cell profiling transcriptomic reveals cellular heterogeneity and cellular crosstalk in breast cancer lymphatic node, bone, and brain metastases by Longyu Zhu, Miaomiao Liu, Yuguang Shang, Jingge Cheng, Hongye Zhao, Jun Zhang, Dongxing Shen

“…The biological function of cell subpopulations was analyzed using gene set variation analysis. The expression of STMN1 was analyzed using immunohistochemical staining. …”
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Identification of Anoikis-Related Genes in Chronic Kidney Disease Based on Bioinformatics Analysis Combined with Experimental Validation by Liu H, Mei M, Zhong H, Lin S, Luo J, Huang S, Zhou J

“…We aimed to establish the Anoikis-related gene signature in CKD by bioinformatics analysis.Methods: We retrieved 3 datasets from the Gene Expression Omnibus (GEO) database to obtain differentially expressed genes (DEGs), followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) of them, which were intersected with Anoikis-related genes (ARGs) to derive Anoikis-related differentially expressed genes (ARDEGs). …”
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Immune regulatory genes impact the hot/cold tumor microenvironment, affecting cancer treatment and patient outcomes by Mengmeng Sang, Jia Ge, Juan Ge, Juan Ge, Gu Tang, Qiwen Wang, Jiarun Wu, Liming Mao, Liming Mao, Xiaoling Ding, Xiaorong Zhou

“…Kyoto Encyclopedia of Genes and Genomes and Hallmark pathway enrichment were evaluated through gene set variation analysis. Additionally, hub genes that regulate the tumor microenvironment were identified, and their expression patterns were analyzed using single-cell RNA sequencing. …”
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Hubungan Sanitasi Lingkungan Rumah dengan Kejadian Askariasis dan Trikuriasis pada Siswa SD N 29 Purus Padang by Hildya Kusmi, Nuzulia Irawati, Husnil Kadri

“…Research instruments were stool examination and questionnaire. Bi variate analysis was chi-square test. The results showed that the worm infection rate in student of Elementary School 29 Purus Padang<br />was 38 %, consist of Ascaris lumbricoides infection (33%), Trichuris trichiura infection (9.1%) and infection of both species (3.6%). …”
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Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability by Amira M. Mahfouz, Walaa A. Eraqi, Hala Nour El Din El Hifnawi, Alaa El Din Shawky, Reham Samir, Mohamed A. Ramadan

“…Conclusions For the detection of single-nucleotide polymorphisms (SNPs) and the identification of all variants (SNPs, insertions, and deletions) in our isolates, the Variation Analysis Service tool available in the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) was used. …”
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Cuproptosis-Related Signature Predicts the Prognosis, Tumor Microenvironment, and Drug Sensitivity of Hepatocellular Carcinoma by Xiangjun Qi, Jiayun Guo, Guoming Chen, Caishan Fang, Leihao Hu, Jing Li, Chi Zhang

“…The survival characteristics of the molecular subtype and the signature were analyzed. The Gene Set Variation Analysis was performed for functional annotation. …”
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New bitongling regulates gut microbiota to predict angiogenesis in rheumatoid arthritis via the gut-joint axis: a deep neural network approach by Yin Guan, Xiaoqian Zhao, Yun Lu, Yue Zhang, Yan Lu, Yue Wang

“…Five characteristic microbial taxa, including f_Mycoplasmataceae, s_Metamycoplasma_sualvi, and g_Prevotellaceae_Ga6A1_group, were identified and associated with NBTL’s modulation of the VEGF pathway. Gene set variation analysis (GSVA) revealed significant downregulation of the VEGF signaling pathway following NBTL treatment. …”
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Efferocytosis-related gene IL33 predicts prognosis and immune response and mediates proliferation and migration in vitro and in vivo of breast cancer by Xiao He, Xianjie Cheng, Zhun Zhang, Lanhui Chen, Changjun Xie, Mengjie Tang

“…The enrichment of metabolic pathways within the detected clusters was evaluated using gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA). …”
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Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients by Shi-Xia Liao, Lan-Ying Zhang, Ling-Mei Shi, Huai-Yu Hu, Yan-Hui Gu, Ting-Hua Wang, Yao Ouyang, Peng-Peng Sun

“…Functional enrichment analyses, including Gene Ontology (GO), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA), were performed. Weighted gene co-expression network analysis (WGCNA) and immune infiltration analysis were conducted. …”
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The role of FTO in m6A RNA methylation and immune regulation in Staphylococcus aureus infection-related osteomyelitis by Sijing Liu, Sijing Liu, Sijing Liu, Kai Li, Changhai Long, Mingwu Lao, Biao Ma, Changquan Liu, Haoyuan He, Chunjiang Wang, Wangzhu Chen, Bin Yu

“…Further, unsupervised clustering analysis, gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA) were employed to assess immune cell infiltration. …”
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Spatiotemporal Variation of Water Use Efficiency and Its Responses to Climate Change in the Yellow River Basin from 1982 to 2018 by Jie Li, Fen Qin, Yingping Wang, Xiuyan Zhao, Mengxiao Yu, Songjia Chen, Jun Jiang, Linhua Wang, Junhua Yan

“…This research was conducted based on Gross Primary Productivity (GPP), Evapotranspiration (ET), meteorological station data, and land use/cover data, and the methods of Ensemble Empirical Mode Decomposition (EEMD), trend variation analysis, the Mann–Kendall Significant Test (M-K test), and Partial Correlation Analysis (PCA) methods. …”
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