Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. by Kakajan Komurov, Michael A White, Prahlad T Ram

“…We also present NetWalk analysis of microarray gene expression data from MCF7 cells exposed to different doses of doxorubicin, which reveals a switch-like pattern in the p53 regulated network in cell cycle arrest and apoptosis. …”
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Histone methyltransferase KMT2A promotes pulmonary fibrogenesis via targeting pro‐fibrotic factor PU.1 in fibroblasts by Wenting Lyu, Hui Wang, Tong Ji, Ling Liu, Haoran Chen, Li Fan, Guanning Zhong, Naihui Wan, Suwan Chen, Jingyu Chen, Hourong Cai, Hongyang Xu, Dongjin Wang, Jinghong Dai

“…KMT2A is a member of the SET family which catalyses H3K4 methylation. Results Through microarray and single‐cell sequencing data, we discovered KMT2A‐positive fibroblasts were increased in IPF lung tissues. …”
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MiR-145-5p arrests the cell cycle by modulating SMAD5/cyclin D1 to inhibit gastric cancer progression by Li Wang, Li Wang, Jianghong Guo, Caixia Lv, Luke Kong, Luke Kong, Jing Cui, Zhongshuai Wang, Yuanyuan Guo, Ruirui Jia, Tao Guan, Tao Guan, Baofeng Yu, Feng Li

“…PurposeThis study aimed to explore the dysregulation of miR-145-5p in gastric cancer (GC) and its effects on the proliferation and cell cycle of GC cells, exploring the potential regulatory mechanism of miR-145-5p in GC.MethodsIn this study, the TCGA database combined with Microarray was used to detect differentially expressed microRNA (miRNA) in GC tissues and cells. …”
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Epigenetic Studies Point to DNA Replication/Repair Genes as a Basis for the Heritable Nature of Long Term Complications in Diabetes by Alexey A. Leontovich, Robert V. Intine, Michael P. Sarras

“…In the current study, control, DM, and MM excised fin tissues were further analyzed by MeDIP sequencing and microarray techniques. …”
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EMP1 as a Potential Biomarker in Liver Fibrosis: A Bioinformatics Analysis by Xuchen Chen, Xinliang Lv, Manman Han, Yexiao Hu, Wanqiong Zheng, Haibo Xue, Zhuokai Li, Kui Li, Wei Tan

“…In this study, we combined a publicly accessible single-cell transcriptome of human liver with microarray datasets to evaluate the cell-specific expression patterns of differentially expressed genes in the liver. …”
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Identification and analysis of neutrophil extracellular trap-related genes in periodontitis via bioinformatics and experimental verification by Miao Yu, Zhenqi Ye, Zixin Ye, Yaping Wu, Xiang Wu

“…This study intends to investigate the comprehensive effects of NET-related genes (NRGs) on periodontitis by bioinformatic analysis. Methods The microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. …”
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Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host A... by Yan Zhang, Juan He, Lei-Jie Jia, Ting-Lu Yuan, Dong Zhang, Yan Guo, Yufeng Wang, Wei-Hua Tang

“…Using laser microdissection and microarray analysis, we profiled changes in global gene expression during pathogen growth inside pith tissues of maize stalk from 12 h to six days after inoculation and documented transcriptomic patterns that provide further insights into the infection process. …”
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Androgen receptor (AR) antagonism triggers acute succinate‐mediated adaptive responses to reactivate AR signaling by Neetu Saxena, Eliana Beraldi, Ladan Fazli, Syam Prakash Somasekharan, Hans Adomat, Fan Zhang, Chidi Molokwu, Anna Gleave, Lucia Nappi, Kimberly Nguyen, Pavn Brar, Nicholas Nikesitch, Yuzhuo Wang, Colin Collins, Poul H Sorensen, Martin Gleave

“…Activation of this pathway was seen in tissue microarray analysis on prostatectomy tissues and patient‐derived xenografts. …”
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MyD88 deficiency alters expression of antimicrobial factors in mouse salivary glands. by Takeshi Into, Toshiya Takigawa, Shumpei Niida, Ken-ichiro Shibata

“…In the present study, we assessed the influence of MyD88 deficiency on the oral innate defense, particularly the expression of antimicrobial proteins in salivary glands and production of salivary basal immunoglobulins, in mice. Microarray analysis of the whole tissues of submandibular glands revealed that the expression of several genes encoding salivary antimicrobial proteins, such as secretory leukocyte peptidase inhibitor (SLPI), S100A8, and lactotransferrin, was reduced due to MyD88 deficiency. …”
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Exploration of autophagy-related molecular mechanisms underlying epilepsy using multiple datasets by Yongfei Wang, Haoxuan Zeng, Chongxu Liu, Jianjun Chen, Yihong Huang, Xianju Zhou

“…Methods We analyzed GSE143272 and GSE4290 microarray datasets from the NCBI Gene Expression Omnibus database, which is established based on evaluations of peripheral blood samples. …”
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Cytogenomic characterization of mosaic X-ring chromosomes in seventeen patients with Turner syndrome (TS)-42 years of experience at a single-site institution by Anita Madison, Carolyn Applegate, Victoria Stinnett, Diego Marrero Miranda, Chantal Cross, Kamaria Cayton Vaught, Ying S. Zou, Jaclyn B. Murry

“…Studying the pattern of X-activation across tissues in this cohort could provide additional data on a postulated source of phenotypic variability. …”
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Zip4 (Slc39a4) expression is activated in hepatocellular carcinomas and functions to repress apoptosis, enhance cell cycle and increase migration. by Benjamin P Weaver, Yuxia Zhang, Stephen Hiscox, Grace L Guo, Udayan Apte, Kathryn M Taylor, Christian T Sheline, Li Wang, Glen K Andrews

“…Interestingly, meta-analysis of microarray data in the Geo and Oncomine databases suggests that Zip4 mRNA may also be elevated in many types of cancer. …”
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Identification of key genes and pathways in the following pancreatic ductal adenocarcinoma (PDAC) using integrated bioinformatics analysis by Manish Shukla, Jai Chand Patel, Meenakshi Shukla

“…This study analyzed microarray datasets (GSE16515, GSE28730, GSE62165, and GSE91035) from the Gene Expression Omnibus to identify differentially expressed genes (DEGs) in PDAC. …”
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Analysis of Long Noncoding RNAs-Related Regulatory Mechanisms in Duchenne Muscular Dystrophy Using a Disease-Related lncRNA-mRNA Pathway Network by Bing Xu, Chunlei Zheng

“…Finally, the proportions of immune cells infiltrating the muscle tissues in DMD were analyzed, and the correlation between the immune cells and expression of the DELs/DEMs was studied. …”
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Transgelin-2 is upregulated on activated B-cells and expressed in hyperplastic follicles in lupus erythematosus patients. by Kaori Kiso, Hajime Yoshifuji, Takuma Oku, Masaki Hikida, Koji Kitagori, Yoshitaka Hirayama, Toshiki Nakajima, Hironori Haga, Tatsuaki Tsuruyama, Aya Miyagawa-Hayashino

“…We found that TAGLN2-expressing B-cells were localized in the germinal center (GC) of secondary lymphoid tissues and TAGLN2 mRNA was significantly upregulated after IgM+IgG stimulation in primary human B-cells, suggesting that TAGLN2 was upregulated upon B-cell activation. …”
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The Aquaporin gene family of the yellow fever mosquito, Aedes aegypti. by Lisa L Drake, Dmitri Y Boudko, Osvaldo Marinotti, Victoria K Carpenter, Angus L Dawe, Immo A Hansen

“…Phylogenetic analysis showed that five of the six Ae. aegypti AQPs have high similarity to classical water-transporting AQPs of vertebrates. Using microarray, reverse transcription and real time PCR analysis we found that all six AQPs are expressed in distinct patterns in mosquito tissues/body parts. …”
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Spatial transcriptomic characteristics of gastric cancer in young and the expression and role of TMEM176B in gastric cancer cells by Zhenhua Jiang, Yongfeng Wang, Chi Zhang, Shuangyin Han

“…Methods The surgical specimens of six patients with GCY were included to construct a tissue microarray containing the tumor core region (TCR), cancer-adjacent tissue (CAT), and normal gastric tissue (NGT). …”
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ANGPTL4 exacerbates pancreatitis by augmenting acinar cell injury through upregulation of C5a by Kyung Hee Jung, Mi Kwon Son, Hong Hua Yan, Zhenghuan Fang, Juyoung Kim, Soo Jung Kim, Jung Hee Park, Ji Eun Lee, Young‐Chan Yoon, Myeong Seong Seo, Beom Seok Han, Soyeon Ko, Young Ju Suh, Joo Han Lim, Don‐Haeng Lee, Ziqiang Teo, Jonathan Wei Kiat Wee, Nguan Soon Tan, Soon‐Sun Hong

“…However, little is known about the genes associated with pancreatitis severity. Our microarray analysis of pancreatic tissues from mild and severe acute pancreatitis mice models identified angiopoietin‐like 4 (ANGPTL4) as one of the most significantly upregulated genes. …”
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QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis by Yulai Zhou, Yan Gao, Yinghui Peng, Changjing Cai, Ying Han, Yihong Chen, Gongping Deng, Yanhong Ouyang, Hong Shen, Shan Zeng, Yangfeng Du, Zemin Xiao

“…Here, we identified and characterized a circular RNA, circ_0001766 (hsa_circ_0001766), through microarray analysis of CRC tissues. Our results showed that circ_0001766 is downregulated in CRC tissues and closely associated with patient survival and metastasis. …”
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The potential of MCM8 as a biomarker in esophageal carcinoma: a comprehensive analysis integrating m6a methylation and angiogenesis by Xu-Sheng Liu, Yong Xu, Li-Song Dai, Ao Li, Jie Liu, Yu Zhang, Jin Xie, Zhi-Jun Pei

“…MCM8 expression in ESCA tissues was evaluated by immunohistochemical staining on a tissue microarray. …”
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