Immunoinfiltration Analysis of Mitochondrial Damage‐Related Genes in Lung Adenocarcinoma and Construction of a Classification and Prognostic Model Integrated With WGCNA and Machine... by Jirong Zhang, Lin Lin

“…Materials & Methods Using GeneCards and The Cancer Genome Atlas (TCGA) databases, we screened differentially expressed mitochondrial damage‐related genes in LUAD. …”
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Kruppel-family zinc finger proteins as emerging epigenetic biomarkers in head and neck squamous cell carcinoma by Patrick Pearson, Kendra Smith, Nilita Sood, Elizabeth Chia, Alicia Follett, Michael B. Prystowsky, Simon Kirby, Thomas J. Belbin

“…Methods We examined prognostic significance of ZNF154 and ZNF132 expression and DNA methylation in independent patient cohort of about 500 head and neck cancer patients in the Cancer Genome Atlas (TCGA). We also overexpressed these genes in HEK-293 cells, as well as the oral cancer cell line UM-SCC-1. …”
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Online resources on gene networks containing human and animal data by E. V. Ignatieva, D. A. Afonnikov, N. A.  Kolchanov

“…Gene networks are molecular genetic systems that ensure the formation of phenotypic characteristics of organisms (molecular, biochemical, structural, morphological, behavioral, etc.) based on  information encoded in their genomes. Reconstruction of gene networks provides a methodological basis for modern systems biology. …”
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The left amygdala is genetically sexually-dimorphic: multi-omics analysis of structural MRI volumes by Yuanyuan Gui, Geyu Zhou, Shuya Cui, Hongyu Li, Hui Lu, Hongyu Zhao

“…We also constructed polygenic risk scores (PRS) to investigate sex-specific genetic correlations between left amygdala volume and mental disorders (N = 25,576~105,318) of Psychiatric Genomics Consortium and other traits of UKB (N = 347,996). …”
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Loss of protein C vs protein S results in discrepant thrombotic phenotypes by Chia-Jui Ku, Xinge Yu, Queena Y. Zhao, Steven J. Grzegorski, Jeffrey G. Daniel, Allison C. Ferguson, Jordan A. Shavit

“…Here, we generate proc (zebrafish PROC ortholog) and pros1 knockouts through genome editing in zebrafish and uncover partially discordant phenotypes. proc−/− mutants exhibited ∼70% lethality at 1 year of age, whereas pros1−/− survival was unaffected. …”
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Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing by Ting-Yu Yen, Ching Hsu, Ni-Chung Lee, Chao-Szu Wu, Hsin Wang, Kuan-Yi Lee, Chia-Ray Lin, Chun-Yi Lu, Mo-Li Tsai, Tzu-Yu Liu, Che Lin, Chien-Yu Chen, Luan-Yin Chang, Feipei Lai, Li-Min Huang

“…Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP). Results: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. …”
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Prognostic value of FCER1G expression and M2 macrophage infiltration in esophageal squamous cell carcinoma by Wei Peng, Yali Zhao, Ningning Yang, Yan Fang, Yintong Wu, Zhenzhong Feng, Qiang Wu, Xian Wang

“…Methods The expression of FCER1G and its prognostic value in ESCC was examined by The Cancer Genome Atlas and Gene Expression Omnibus databases. …”
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Mitochondrial dysfunction-driven AMPK-p53 axis activation underpins the anti-hepatocellular carcinoma effects of sulfane sulfur by Xue Zheng, Yuhua Luo, Rui Huo, Yiwen Wang, Youbang Chen, Mianrong Chen, Qi Zhao, Kexin Li, Hanyi Zhang, Xiaotong Li, Xiang Li, Hui Zhang, Zaopeng He, Li Huang, Chun-tao Yang

“…We utilized bioinformatics algorithms for clustering, function enrichment, feature screening and survival analysis on proteomic data from the Cancer Proteome Atlas (CPTAC) and transcriptomic data from the Cancer Genome Atlas (TCGA). The impact of PSCP on HCC was assessed in vitro and in vivo, focusing on the expression and activity of p53 and AMP-activated protein kinase (AMPK), as well as mitochondrial function. …”
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Absent in melanoma 2: a potent suppressor of retinal pigment epithelial-mesenchymal transition and experimental proliferative vitreoretinopathy by Yu Chen, Mingyuan Jiang, Liping Li, Shanshan Yang, Zuimeng Liu, Shiwen Lin, Wanxiao Wang, Jinyang Li, Feng Chen, Qiang Hou, Xiaoyin Ma, Ling Hou

“…Kyoto Encyclopedia of Genes and Genome analysis revealed that the PI3K-AKT signaling pathway was significantly related to RPE-EMT and that AIM2 inhibited AKT activation in RPE cells by reducing its phosphorylation. …”
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Genetic causality between insomnia and specific orthopedic conditions: Insights from a two-sample Mendelian randomization study by Mingyi Yang, Jiale Xie, Yani Su, Ke Xu, Pengfei Wen, Xianjie Wan, Hui Yu, Zhi Yang, Lin Liu, Peng Xu

“…Objective: To investigate the genetic causality for the insomnia and common orthopedic diseases, such as rheumatoid arthritis (RA), ankylosing spondylitis (AS), osteoporosis (OP), and gout (GT). Methods: The genome-wide association study (GWAS) summary data on insomnia were obtained from a published study, while the GWAS summary data on RA, AS, OP, and GT were sourced from the FinnGen consortium. …”
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High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management by Nar B. Ranabhat, John P. Fellers, Myron A. Bruce, Jessica L. Shoup Rupp

“…A phylogenetic analysis of <i>Emaravirus tritici</i> based on RNA 3A and 3B segments and whole-genome characterization of <i>Furovirus tritici</i> were also conducted. …”
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Transcriptional regulatory network analysis identifies GRN as a key regulator bridging chemotherapy and immunotherapy response in small cell lung cancer by Seungyeul Yoo, Ayushi S. Patel, Sarah Karam, Yi Zhong, Li Wang, Feng Jiang, Ranran Kong, Sharon Bikvan, Wenhui Wang, Abhilasha Sinha, Charles A. Powell, Jun Zhu, Hideo Watanabe

“…In this study, we aimed to gain insights into those leveraging a recent surge in the field of SCLC genomics. We constructed a regulatory network for SCLC and identified granulin precursor (GRN) as a hub of EP response associated genes. …”
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Differential expressed genes (DEGs) and differential alternative splicing genes (DASs) revealed the common pathologic mechanism of three bacterial pathogens to American eels (Angui... by Zihao Chen, Guanghua Sun, Songlin Guo

“…Gene Ontology (GO) enrichment analysis identified 23 common terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted 18 common pathways. …”
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InterTransViewer: a comparative description of differential gene expression profiles from different experiments by А. V. Tyapkin, V. V. Lavrekha, E. V. Ubogoeva, D. Yu. Oshchepkov, N. A. Omelyanchuk, E. V. Zemlyanskaya

“…Meta-analysis of transcriptomic data from different experiments has become increasingly prevalent due to a significantly increasing number of genome-wide experiments investigating gene expression changes under various conditions. …”
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Association of tumour mutation burden with prognosis and its clinical significance in stage III gastric cancer by Ya-Lin Han, Li Chen, Xu-Ning Wang, Mao-Lin Xu, Rui Qin, Fang-Ming Gong, Peng Sun, Hong-Yi Liu, Zhi-Peng Teng, Zhao-Xia Li, Guang-Hai Dai

“…Methods: Patients with stage III GC were divided into a high TMB and low TMB group in both a study cohort of 38 patients and the Cancer Genome Atlas (TCGA) cohort of 173 patients. In the study cohort, next-generation sequencing was used to detect mutated GC genes and obtain TMB data. …”
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High-throughput analysis of microbiomes in a meat processing facility: are food processing facilities an establishment niche for persisting bacterial communities? by Zhaohui S. Xu, Vi D. Pham, Xianqin Yang, Michael G. Gänzle

“…Isolates obtained at different sampling times or from different sampling sites that differed in fewer than 10 genome-wide single-nucleotide polymorphisms were considered the same (persistent) strains. …”
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Network pharmacology combined with experimental verification for exploring the potential mechanism of phellodendrine against depression by Lili Hu, Na Wu, Jue Wang, Donghui Cai

“…The intersection targets between PHE and MDD were obtained to identify as targets for PHE against MDD, followed by protein–protein interaction network, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Molecular docking was applied to further confirm the anti-MDD effects of PHE. …”
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Transcriptomic and behavioral studies reveal that glutamate receptors are involved in depressive-like behavior in adult olive flounder Paralichthys olivaceus by Liangfang Liu, Tangsong Feng, Mengmeng Shi, Huafeng Zou, Weiqun Lu

“…The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that ribosome, oxidative phosphorylation and glutamatergic synapse pathway were over-represented. …”
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Influence of breed and environment on leukocyte telomere length in cattle by N. S. Yudin, A. V. Igoshin, G. A. Romashov, A. A. Martynov, D. M. Larkin

“…The leukocyte telomere lengths were estimated computationally from whole-genome resequencing data. We leveraged data on leukocyte telomere length, sex, and age of 239 animals from 17 cattle breeds. …”
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The Identification and Validation of a Robust Immune-Associated Gene Signature in Cutaneous Melanoma by Le-Bin Song, Jiao-Chen Luan, Qi-Jie Zhang, Lin Chen, Hao-Yang Wang, Xue-Chen Cao, Ning-Hong Song, Yan Lu

“…Methods. 434 melanoma patients were extracted from The Cancer Genome Atlas (TCGA) database, and 1811 IAGs were downloaded from the ImmPort database in our retrospective study. …”
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