Exploring Hypertrophic Cardiomyopathy Biomarkers through Integrated Bioinformatics Analysis: Uncovering Novel Diagnostic Candidates by Guanmou Li, Dongqun Lin, Xiaoping Fan, Bo Peng

“…We selected the GSE36961 and GSE180313 datasets from the Gene Expression Omnibus (GEO) database for differential analysis. …”
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Spherical harmonics texture extraction for versatile analysis of biological objects. by Oane Gros, Josiah B Passmore, Noa O Borst, Dominik Kutra, Wilco Nijenhuis, Timothy Fuqua, Lukas C Kapitein, Justin M Crocker, Anna Kreshuk, Simone Köhler

“…The Spherical Texture extraction characterizes biologically defined gene expression patterns in Drosophila melanogaster embryos, giving a quantitative read-out for pattern formation. …”
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Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells by Chang Pyo Hong, Moon Kyung Choe, Tae-Young Roh

“…The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac) were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. …”
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The Macrophage Inflammatory Proteins MIP1α (CCL3) and MIP2α (CXCL2) in Implant-Associated Osteomyelitis: Linking Inflammation to Bone Degradation by Ulrike Dapunt, Susanne Maurer, Thomas Giese, Matthias Martin Gaida, Gertrud Maria Hänsch

“…To address the question of how the local inflammatory response is linked to bone degradation, tissue samples were taken during surgery and gene expression of the macrophage inflammatory proteins MIP1α (CCL3) and MIP2α (CXCL2) was assessed by quantitative RT-PCR. …”
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Development of Delivery Systems Enhances the Potency of Cell-Based HIV-1 Therapeutic Vaccine Candidates by Amin Hadi, Abbas Rastgoo, Maryam Eskandarian, Nooshin Haghighipour, Azam Bolhassani

“…Also, chemical transfection performed two times with 48-hour intervals further increased gene expression in both cells. The groups immunized with Nef DC prime/rNef protein boost and then Nef MSC prime/rNef protein boost were able to stimulate high levels of IFN-γ, IgG2b, IgG2a, and Granzyme B directed toward Th1 responses in mice. …”
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KYNU as a Biomarker of Tumor-Associated Macrophages and Correlates with Immunosuppressive Microenvironment and Poor Prognosis in Gastric Cancer by Kaiyu Shen, Binyu Chen, Liu Yang, Wencang Gao

“…GC-associated single-cell RNA sequencing and bulk RNA sequencing (bulk-seq) data were obtained from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. …”
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A Cell Differentiation Trajectory-Related Signature for Predicting the Prognosis of Lung Adenocarcinoma by Fan Yang, Yan Zhao, Xiaohan Huang, Jin Zhang, Ting Zhang

“…TCGA-LUAD samples were divided into two cell differentiation trajectory-related gene-based clusters, GSEA found that cluster 1 was significantly related to 20 pathways, cluster 2 was significantly enriched in three pathways, and it was also shown that clusters could better predict immune checkpoint gene expression and immunotherapy response. A six cell differentiation-related genes-based prognostic signature was constructed, and the patients in the high-risk group had poorer prognosis than those in the low-risk group. …”
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Multichrome encoding-based multiplexed, spatially resolved imaging reveals single-cell RNA epigenetic modifications heterogeneity by Dongsheng Mao, Xiaochen Tang, Runchi Zhang, Song Hu, Hongquan Gou, Penghui Zhang, Wenxing Li, Qiuhui Pan, Bing Shen, Xiaoli Zhu

“…Abstract Understanding the heterogeneity of epigenetic modifications within single cells is pivotal for unraveling the nature of the complexity of gene expression and cellular function. In this study, we have developed a strategy based on multichrome encoding and “AND” Boolean logic recognition for multiplexed, spatially resolved imaging of single-cell RNA epigenetic modifications, termed as PRoximity Exchange-assisted Encoding of Multichrome (PREEM). …”
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circSPECC1 Promotes Proliferation and Migration of LNCaP Prostate Cancer Cells by Affecting Their Epithelial-Mesenchymal Transition by Fangmei Xie, Jian Shen, Zeping Han, Wenfeng Luo, Liyin Liao, Jinhua He

“…Stable circSPECC1 shRNA-expressing and circSPECC1-overexpressing LNCaP cell lines were constructed, and relative gene expression levels were determined by RT-PCR. MTT and clonogenic assays were used to assess proliferative ability while a scratch test was used to analyze cell migration. …”
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Krait2: a versatile software for microsatellite investigation, visualization and marker development by Lianming Du, Jiahao Chen, Dalin Sun, Kelei Zhao, Qianglin Zeng, Nan Yang

“…Microsatellite expansions play pivotal roles in gene expression regulation and are implicated in various neurological diseases and cancers. …”
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Expression of Otx Genes in Müller Cells Using an In Vitro Experimental Model of Retinal Hypoxia by Claudio Azzolini, Simone Donati, Giovanni Micheloni, Vittoria Moretti, Roberto Valli, Francesco Acquati, Lucy Costantino, Fulvio Ferrara, Davide Borroni, Elias Premi, Francesco Testa, Francesca Simonelli, Giovanni Porta

“…The HIF-1α protein and VEGF-A gene expression were quantified to verify the induction of a hypoxia-like state. …”
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Biochemistry of Bacterial Biofilm: Insights into Antibiotic Resistance Mechanisms and Therapeutic Intervention by Kashish Azeem, Sadaf Fatima, Asghar Ali, Ayesha Ubaid, Fohad Mabood Husain, Mohammad Abid

“…This encompasses the role of the extracellular matrix, altered gene expression, and the formation of persister cells, contributing to the recalcitrance of biofilms to eradication. …”
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The protective effect and crucial biological pathways analysis of Trametes lactinea mycelium polysaccharides on acute alcoholic liver injury in mice based on transcriptomics and me... by Jinbin Hao, Liyun Ye, Guoliang Meng, Yanjiao Song, Junsheng Fu, Xiaoping Wu

“…Assessment of the changes in gene expression and metabolites revealed the significantly different expression of several genes encoding key enzymes and metabolites in choline metabolism pathway. …”
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Comparative multiomics analyses reveal the breed effect on the colonic host–microbe interactions in pig by Liang Huang, Shiqi Luo, Shuqi Liu, Mingliang Jin, Yizhen Wang, Xin Zong

“…Detailed analysis revealed that the differences in colon gene expression signatures between the JXB and DLY are mainly enriched in metabolic and inflammatory responses, with Lactobacillus and Lachnospiraceae enriched in DLY and JXB, respectively. …”
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The Role of HMGB1 in the Pathogenesis of Type 2 Diabetes by Yanan Wang, Jixin Zhong, Xiangzhi Zhang, Ziwei Liu, Yuan Yang, Quan Gong, Boxu Ren

“…High-mobility group box 1 (HMGB1), a nonhistone nuclear protein regulating gene expression, was rediscovered as an endogenous danger signal molecule to trigger inflammatory responses when released into extracellular milieu in the late 1990s. …”
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Exploring the Mechanisms of Zhenbao Pills in the Treatment of Stroke through Network Pharmacology Combined with Mendelian Randomization by Yanhong Liu, Yunqi Hua, Xiaoe Jia

“…Furthermore, molecular docking and Gene Expression Omnibus (GEO) datasets were used for preliminary confirmation. …”
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Integrated Analysis of mRNA and lncRNA Expression Profiles Reveals Regulatory Networks Associated with Decompensated Cirrhosis by Li Zhang, Xiaoyu Fang, Suhua Wang, Shasha Ma, Jinyan Zhang, Xiang Dong, Jing Dai, Chuanmiao Liu, Yu Gao

“…By comparing differential gene expression, transcriptomic analysis is useful for exploring relevant functional changes during disease progression. …”
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Species- and strain-specific microbial modulation of interferon, innate immunity, and epithelial barrier in 2D air–liquid interface respiratory epithelial cultures by Mian Horvath, Ruoyu Yang, Diana Cadena Castaneda, Megan Callender, Elizabeth S. Aiken, Anita Y. Voigt, Ryan Caldwell, José Fachi, Blanda Di Luccia, Zoe Scholar, Peter Yu, Andrew Salner, Marco Colonna, Karolina Palucka, Julia Oh

“…Conclusions Microbial colonization differentially stimulates host gene expression with variations observed across phylogenetically diverse microbes and across different strains of the same species. …”
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MicroRNAs in Autoimmune Sjögren’s Syndrome by Seunghee Cha, Mahmoud Mona, Kyung Eun Lee, Dong Hee Kim, Kyudong Han

“…MicroRNAs (miRNAs), small non-coding RNAs, have been implicated in various diseases and cellular functions as microregulators of gene expression. Although the history of miRNA investigation in autoimmune Sjögren’s syndrome (SjS) is fairly short, a substantial amount of data has already been accumulated. …”
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The Potential Dual Role of H2.0-like Homeobox in the Tumorgenesis and Development of Colorectal Cancer and Its Prognostic Value by Shuo Chen, Lin Zhang, Kai Wang, Jizhen Huo, Siqi Zhang, Xipeng Zhang

“…In this study, the data were collected from The Cancer Genome Atlas and Gene Expression Omnibus databases. The diagnostic value of HLX was analyzed by the R package “pROC.” …”
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