Exploring the comorbidity mechanisms between atherosclerosis and hashimoto’s thyroiditis based on microarray and single-cell sequencing analysis by Yirong Ma, Shuguang Wu, Junyu Lai, Qiang Wan, Jingxuan Hu, Yanhong Liu, Ziyi Zhou, Jianguang Wu

“…We elucidated gene functions and regulatory networks across various biological scenarios through enrichment and pathway analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Core genes were identified using Cytoscape software and further validated with external datasets. …”
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Dual role of Cathepsin S in cutaneous melanoma: insights from mendelian randomization and bioinformatics analysis by Linsa Zhou, Qiang Zhou, Qian Guo, Peng Lai, Chen Rui, Wanqing Li, Xuemei Chen, Yue Zhuo, Xiaoping Zhong, Sen Lin

“…Methods The Gene Expression Omnibus (GEO) database was used to obtain differential genes for CM and normal skin, and the Genome-Wide Association Studies (GWAS) analysis offered summary-level melanoma data for CM. …”
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AAV2 serotype demonstrates the highest transduction efficiency in porcine lung-derived cells by Won Seok Ju, Seokho Kim, Areum Choi, Jae-Yeong Lee, Haesun Lee, Jingu No, Seunghoon Lee, Keonbong Oh, Jae Gyu Yoo

“…Understanding cell type-specific preferences of AAV serotypes offer crucial insight for tailoring AAV vectors to specific tissue and optimizing genome editing strategies, with potential implications for the advancement of personalized medicine and development of treatments for human and livestock.…”
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Germline variants of the genes involved in NF-kB activation are associated with the risk of COPD and lung cancer development by Baranasic Jurica, Niazi Yasmeen, Chattopadhyay Subhayan, Rumora Lada, Ćorak Lorna, Dugac Andrea Vukić, Jakopović Marko, Samaržija Miroslav, Försti Asta, Knežević Jelena

“…We extracted summary data of variants in 1511 immune-related genes from COPD and LC genome-wide association studies (GWAS) from the UK Biobank. …”
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Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken by Jingwei Yuan, Yuanmei Wang, Yanyan Sun, Yunlei Li, Aixin Ni, Qin Li, Hanhan Yang, Xinying Xu, Yunhe Zong, Hui Ma, Jilan Chen

“…Conclusion Our study characterized the dynamic profile of genome-wide gene expression in ovary and highlighted the role of dominant expression of cell cycle pathway genes in heterosis. …”
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Global insights into MRSA bacteremia: a bibliometric analysis and future outlook by Jia-Yi Lin, Jia-Yi Lin, Jia-Kai Lai, Jia-Kai Lai, Jian-Yi Chen, Jian-Yi Chen, Jia-Yu Cai, Jia-Yu Cai, Zhan-Dong Yang, Zhan-Dong Yang, Liu-Qingqing Yang, Liu-Qingqing Yang, Liu-Qingqing Yang, Ze-Tao Zheng, Ze-Tao Zheng, Xu-Guang Guo, Xu-Guang Guo, Xu-Guang Guo

“…Future research will rely on integrating genomics, AI, and machine learning to drive personalized treatment. …”
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Analysis of the mechanism of Zangjiangzhi capsule in the treatment of hyperlipidemia based on its ingredients identified by UHPLC-Q-Exactive-Orbitrap-MS by Changting He, Yuling Zhao, Yongchun Huang, Yudong Su, Shoude Zhang

“…The targets were subjected to gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The “herb-ingredient-target” network was visualized using Cytoscape. …”
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Exploring and Verifying the Mechanism and Targets of Shenqi Pill in the Treatment of Nonalcoholic Steatohepatitis via Network Pharmacology and Experiments by Beihui He, Zheng Chen, Yunmeng Nie, Minmin Luo, Sumei Xu, Junbin Yan, Zhiyun Chen

“…Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein–protein interaction (PPI) analysis were used to search for crucial target genes and mechanisms. …”
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MKRN1 promotes colorectal cancer metastasis by activating the TGF-β signalling pathway through SNIP1 protein degradation by Yi Zhang, Qin-shan Li, Hong-lin Liu, Hong-ting Tang, Han-lin Yang, Dao-qiu Wu, Yu-ying Huang, Li-cheng Li, Li-hong Liu, Meng-xing Li

“…Methods MKRN1 expression in CRC was analysed using the Cancer Cell Line Encyclopaedia and the Cancer Genome Atlas (TCGA) databases. Rectal tumour tissues were frozen to explore the MKRN1 expression in CRC and its clinical significance. …”
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Comparative analysis of the primary structure and production of recombinant poly(ADP-ribose)polymerase 1 of long-lived Heterocephalus glaber by K. N. Naumenko, A. R. Nurislamov, K. D. Nazarov, V. S. Fishman, A. A. Popov, I. O. Petruseva, A. N. Evdokimov, O. I. Lavrik

“…DNA repair is a most important cellular process that helps maintain the integrity of the genome and is currently considered by researchers as one of the factors determining the maximum lifespan. …”
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Exploring the associations of gut microbiota with inflammatory and the early hematoma expansion in intracerebral hemorrhage: from change to potential therapeutic objectives by Haixiao Jiang, Wei Zeng, Fei Zhu, Xiaoli Zhang, Demao Cao, Aijun Peng, Hongsheng Wang

“…Analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) exposed disturbances in essential physiological pathways, especially those related to inflammation (such as the Toll-like receptor signaling pathway), in the HE group.ConclusionsOur exploration indicated that individuals with emICH, especially those with HE, demonstrate notably different host-microbe interactions when compared to healthy individuals. …”
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The role of long non-coding RNA LINC00839 in oral squamous cell carcinoma based on bioinformatics and experimental research by Ashkan Kalantary-Charvadeh, Saman Morovat, Somayeh Aslani, Nasrin Ziamajidi, Amirnader Emami Razavi, Roghayeh Abbasalipourkabir

“…Abstract This study explores the role of LINC00839 and its potential interaction with the miR-195-5p/cyclin E1 (CCNE1) axis in oral squamous cell carcinoma (OSCC). Using The Cancer Genome Atlas, we analyzed lncRNA, miRNA, and mRNA sequencing data for OSCC. …”
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Transcriptomic and metabolomic-based revelation of the effect of fresh corn extract on meat quality of Jingyuan chicken by Jinli Tian, Yanxu Wu, Wei Zhao, Guojun Zhang, Hu Zhang, Lin Xue, Lijuan Yang, Tong Zhang, Yaling Gu, Juan Zhang

“…Kyoto Encyclopedia of Genes and Genomes (GSEA-KEGG) analysis identified sphingolipid_metabolism and multiple genes affecting IMF deposition including SPHK1, CERS1, CERS6, GLB1L, SGMS2, UGT8, and UGCG. …”
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Study on the multidrug resistance and transmission factors of Staphylococcus aureus at the ‘animal–environment–human’ interface in the broiler feeding cycle by Fangyuan Hu, Fangyuan Hu, Yaopeng Liu, Yaopeng Liu, Lin Wang, Juan Wang, Na Liu, Yan Li, Xiaoxiao Duan, Junwei Wang, Mingzhe Lu, Junhui Liu, Zhina Qu, Keguang Han

“…Based on the concept of “One Health,” this study analyzed the multidrug resistance and transmission factors of S. aureus isolated from the “animal–environment–human” interface during one feeding cycle of commercial broilers in China by using antimicrobial susceptibility testing and whole genome sequencing (WGS) technologies. The results showed that in stage 1, the isolation rate of S. aureus was 1.32% (6/453), that of workers was 25.0% (4/16), and that of environmental samples was 0.69% (2/287), and the multidrug resistance rate was 83.33%. …”
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Gastric Cancer Cell Lines Have Different MYC-Regulated Expression Patterns but Share a Common Core of Altered Genes by Jersey Heitor da S. Maués, Helem Ferreira Ribeiro, Giovanny R. Pinto, Luana de Oliveira Lopes, Letícia M. Lamarão, Carla Mariana F. Pessoa, Caroline de Fátima Aquino Moreira-Nunes, Raimundo Miranda de Carvalho, Paulo P. Assumpção, Juan A. Rey, Rommel M. Rodríguez Burbano

“…The DEGs were picked using Sailfish software, followed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using KEGG. We found 11 significantly enriched gene sets by using enrichment score (ES), False Discovery Rate (FDR), and nominal P-values. …”
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Comprehensive Analysis of Competing Endogenous RNA Network Focusing on Long Noncoding RNA Involved in Cirrhotic Hepatocellular Carcinoma by Yuli Zhang, Dinggui Chen, Miaomiao Yang, Xianfeng Qian, Chunmei Long, Zhongwei Zheng

“…The lncRNA, miRNA, and mRNA expression datasets were obtained from Gene Expression Omnibus and The Cancer Genome Atlas. Based on miRanda and TargetScan, the HCC-specific ceRNA network was constructed to illustrate the coexpression regulatory relationship of lncRNAs, miRNAs, and mRNAs. …”
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Developmental Proteomics Reveals the Dynamic Expression Profile of Global Proteins of <i>Haemaphysalis longicornis</i> (Parthenogenesis) by Min-Xuan Liu, Xiao-Pei Xu, Fan-Ming Meng, Bing Zhang, Wei-Gang Li, Yuan-Yuan Zhang, Qiao-Ying Zen, Wen-Ge Liu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the differentially expressed proteins (DEPs) were used. …”
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The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran by Mehdi Shabani, Ahmad Nejati, Jila Yavarian, Jila Yavarian, Kaveh Sadeghi, Sevrin Zadheidar, Akram Sadat Ahmadi, Monire Ghadirali, Arghavan Zebardast, Adel Abedi, Mohammad Hossein Najmi, Nazanin-Zahra Shafiei-Jandaghi, Talat Mokhtari-Azad

“…The present study evaluated and compared these important variations among different Omicron sub-lineages in Iran.MethodologyFrom October 2023 to August 2024, high coverage whole genome sequences of 49 SARS-CoV-2 strains were subjected to phylogenetic analysis and evaluation of B cell, CD4+, and CD8+ T cell epitopes in Iran National Influenza Centre.ResultsThe phylogenetic tree exhibited eight Nextstrain clades (21L, 22F, 23B, 23H, 23D, 24A, 24B, and 24C) in 48 studied strains, and one recombinant strain (XDK.1). …”
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Transcriptome analysis of jejunal mucosal tissue in breeder hens exposed to acute heat stress by Yongcai Zhu, Satoshi Kubota, Phocharapon Pasri, Sitthipong Rakngam, Supattra Okrathok, Chayanan Pukkung, Shenglin Yang, Sutisa Khempaka

“…Functional analysis through gene ontology classification, pathway mapping via the Kyoto encyclopedia of genes and genomes, and protein interaction networks identified several important regulatory genes in thermal response (HSPA8 and HSPA2), energy homeostasis and fat metabolism (PDK4, PPARA, and CD36), glucose transport (SLC2A5), and cholesterol synthesis pathway (SQLE, CYP51A1, and HSD17B7). …”
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Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer’s disease by Waimao Gao, Guang Yang, Xinjuan Liu, Kaifan Hu, Jie Pan, Xingyu Wang, Yan Zhao, Ying Xu

“…Then we performed Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses on these common targets. …”
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