Orthoweb: a software package for evolutionary analysis of gene networks by R. A. Ivanov, A. M. Mukhin, F. V. Kazantsev, Z. S. Mustafin, D. A. Afonnikov, Y. G. Matushkin, S. A. Lashin

“…These indices are important for understanding the dynamics of gene expression and its impact on the development and adaptation of organisms. …”
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Periductal Mastitis: An Inflammatory Disease Related to Bacterial Infection and Consequent Immune Responses? by Lu Liu, Fei Zhou, Pin Wang, Lixiang Yu, Zhongbing Ma, Yuyang Li, Dezong Gao, Qiang Zhang, Liang Li, Zhigang Yu

“…With 16S rRNA gene sequencing, we confirmed bacterial infections were found in all PDM patients, but none of the control patients was positive on the gene expression of 16S rRNA. Our results also demonstrated significant increases of the IFN-γ and IL-12A expression in PDM, but there was no difference in IL-17A expression in these two groups. …”
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Elucidating the role of pyrimidine metabolism in prostate cancer and its therapeutic implications by Liang Huang, Yu Xie, Shusuan Jiang, Kan Liu, Zhihao Ming, Hong Shan

“…Through transcriptomic and single-cell RNA sequencing analyses, we explored metabolic pathway enrichment, immune infiltration patterns, and differential gene expression in prostate cancer samples. The results showed that pyrimidine metabolism-related genes were significantly upregulated in the P2 subgroup compared to the P1 subgroup, with enhanced metabolic activity observed in basal and luminal epithelial cells. …”
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Negative Effects of High Glucose Exposure in Human Gonadotropin-Releasing Hormone Neurons by Annamaria Morelli, Paolo Comeglio, Erica Sarchielli, Ilaria Cellai, Linda Vignozzi, Gabriella B. Vannelli, Mario Maggi

“…In this study, we investigated the high glucose effects in the human GnRH-secreting FNC-B4 cells. Gene expression profiling by qRT-PCR, confirmed that FNC-B4 cells express GnRH and several genes relevant for GnRH neuron function (KISS1R, KISS1, sex steroid and leptin receptors, FGFR1, neuropilin 2, and semaphorins), along with glucose transporters (GLUT1, GLUT3, and GLUT4). …”
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Analysis of expression and transport activity of sugar transporter gene HpSWEET7 from red pitaya by ZHENG Qianming, YAN Shuang, XIE Pu, WANG Honglin, MA Yuhua

“…[Methods] HpSWEET7 gene was isolated from ‘Zihonglong’, and sequence alignment and phylogenetic relationship were analyzed. Gene expression was analyzed by qRT-PCR, and the subcellular localization was detected by fusing fluorescent protein. …”
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MicroRNAs in the DNA Damage/Repair Network and Cancer by Alessandra Tessitore, Germana Cicciarelli, Filippo Del Vecchio, Agata Gaggiano, Daniela Verzella, Mariafausta Fischietti, Davide Vecchiotti, Daria Capece, Francesca Zazzeroni, Edoardo Alesse

“…MicroRNAs are endogenous short noncoding molecules able to regulate gene expression at the post-transcriptional level. Due to their activity, microRNAs play a role in many fundamental physiological and pathological processes. …”
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Deficiency in Galectin-3 Promotes Hepatic Injury in CDAA Diet-Induced Nonalcoholic Fatty Liver Disease by Kazuhiro Nomoto, Takeshi Nishida, Yuko Nakanishi, Makoto Fujimoto, Ichiro Takasaki, Yoshiaki Tabuchi, Koichi Tsuneyama

“…Data generated by microarray analysis of gene expression suggested that galectin-3 deficiency causes alterations in the expression of various genes associated with carcinogenesis and lipid metabolism. …”
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Genome-wide identification of HbVQ proteins and their interaction with HbWRKY14 to regulate the expression of HbSRPP in Hevea brasiliensis by Jiahong Zhu, Long Qu, Liwang Zeng, Ying Wang, Huiliang Li, Shiqing Peng, Dong Guo

“…Gene structure analysis revealed that most of HbVQs had no introns except for HbVQ5 and HbVQ20. Gene expression analysis revealed that HbVQ4, 5, and 21 were expressed at relatively high levels in latex. …”
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5-Azacytidine Promotes an Inhibitory T-Cell Phenotype and Impairs Immune Mediated Antileukemic Activity by Thomas Stübig, Anita Badbaran, Tim Luetkens, York Hildebrandt, Djordje Atanackovic, Thomas M. C. Binder, Boris Fehse, Nicolaus Kröger

“…T-cells from healthy donors were treated with 5-Aza and analyzed by qRT-PCR and flow cytometry for changes in gene expression and phenotype. Functionality was assessed by a tumor lysis assay. …”
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A Narrative Review of Prognostic Gene Signatures in Oral Squamous Cell Carcinoma Using LASSO Cox Regression by Nur Fatinazwa Mohd Faizal, Saptarsi Shai, Bansi P. Savaliya, Lee Peng Karen-Ng, Rupa Kumari, Rahul Kumar, Vui King Vincent-Chong

“…As the Cancer Genome Atlas (TCGA) dataset is available in HNSCC, the survival analysis prognosis of OSCC patients based on the TCGA dataset for discovering gene expression-based prognostic biomarkers is limited. …”
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Androgen Receptor-Target Genes in African American Prostate Cancer Disparities by Bi-Dar Wang, Qi Yang, Kristin Ceniccola, Fernando Bianco, Ramez Andrawis, Thomas Jarrett, Harold Frazier, Steven R. Patierno, Norman H. Lee

“…To elucidate the molecular mechanisms underlying PCa disparities, we employed an integrative approach combining gene expression profiling and pathway and promoter analyses to investigate differential transcriptomes and deregulated signaling pathways in AA versus CA cancers. …”
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Role of CXCL10 released from osteocytes in response to TNF-α stimulation on osteoclasts by Mariko Miura, Hideki Kitaura, Fumitoshi Ohori, Kohei Narita, Jiayi Ren, Takahiro Noguchi, Aseel Marahleh, Jinghan Ma, Angyi Lin, Ziqiu Fan, Itaru Mizoguchi

“…RNA sequencing (RNA-seq) revealed that TNF-α stimulation increased C-X-C motif chemokine ligand 10 (CXCL10) gene expression in osteocytes. Although CXCL10 did not affect osteoclast differentiation in vitro, it enhanced the migration of osteoclast precursors. …”
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Pantoprazole Decreases Cell Viability and Function of Human Osteoclasts In Vitro by Markus Prause, Claudine Seeliger, Marina Unger, Elizabeth Rosado Balmayor, Martijn van Griensven, Alexander Tobias Haug

“…Osteoclast-specific gene expression was evaluated after seven days and revealed no significant differences between all samples. …”
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STAT3 Genotypic Variant rs744166 and Increased Tyrosine Phosphorylation of STAT3 in IL-23 Responsive Innate Lymphoid Cells during Pathogenesis of Crohn’s Disease by Ying Tang, Sanda A. Tan, Atif Iqbal, Jian Li, Sarah C. Glover

“…Signal transducer and activator of transcription 3 (STAT3) regulates gene expression in a cell-specific, cytokine-dependent manner, involving multiple immune responses. …”
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A systematic screening assay identifies efficient small guide RNAs for CRISPR activation by Elin Arvidsson, Diana Duarte Lobo, Diana Duarte Lobo, Ermelinda Sabarese, Fabio Duarte, Rui Jorge Nobre, Rui Jorge Nobre, Rui Jorge Nobre, Luis Quintino, Cecilia Lundberg

“…The most efficient sgRNAs also demonstrated activation of endogenous gene expression at mRNA level. Correlation analysis of gene activation relative to sgRNA binding site distance to transcription start-site or nearby transcription factor binding sites failed to detect common characteristics influencing gene activation in the selected promoter regions. …”
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Expression study of Wnt/β-catenin signaling pathway associated lncRNAs in schizophrenia by Fatemeh Manafzadeh, Behzad Baradaran, Seyed Gholamreza Noor Azar, Kamran Javidi Aghdam, Reza Dabbaghipour, Asghar Shayannia, Soudeh Ghafouri-Fard

“…There was no significant difference in CTNNB1 gene expression in the medicated patients compared to controls (P value = 0.9754). …”
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Systematic review of bidirectional interaction between gut microbiome, miRNAs, and human pathologies by Lorenzo Drago, Lorenzo Drago, Luigi Regenburgh De La Motte, Loredana Deflorio, Delia Francesca Sansico, Michela Salvatici, Emanuele Micaglio, Manuele Biazzo, Fabiana Giarritiello, Fabiana Giarritiello

“…MicroRNAs (miRNAs) and the gut microbiome are key regulators of human health, with emerging evidence highlighting their complex, bidirectional interactions in chronic diseases. miRNAs, influence gene expression and can modulate the composition and function of the gut microbiome, impacting metabolic and immune processes. …”
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Evidence for Decreased Nucleolar PARP-1 as an Early Marker of Cognitive Impairment by Matthew Regier, Jiancong Liang, Alexander Choi, Kavita Verma, Jenny Libien, A. Iván Hernández

“…Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear protein that regulates gene expression through poly(ADP)-ribosylation, resulting in the loosening of chromatin structure. …”
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Transcriptomic analysis of the root system of Platycodon grandiflorum in response to the fallen leaves of Acer truncatum by FENG Chaoqun, RUAN Kunfei, SHI Shaotong, LI Sen, CHENG Shaoying, LIU Zhonghua

“…[Methods] We performed transcriptome sequencing using Illumina high throughput sequencing technology. Gene expression changes in the synthesis pathways of terpenes, flavonoids, and phenylpropanoid secondary metabolites were analyzed. …”
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Upregulated GSDMB in Clear Cell Renal Cell Carcinoma Is Associated with Immune Infiltrates and Poor Prognosis by Yuanshan Cui, Zhongbao Zhou, Yumeng Chai, Yong Zhang

“…The transcriptional expression profiles of GSDMB in ccRCC tissues in addition to normal tissues were retrieved from The Cancer Genome Atlas (TCGA) and additionally verified in a different independent cohort, which was obtained from the Gene Expression Omnibus (GEO) database. The Human Protein Atlas and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) were used to assess the protein expression of GSDMB. …”
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