urg1: a uracil-regulatable promoter system for fission yeast with short induction and repression times. by Stephen Watt, Juan Mata, Luis López-Maury, Samuel Marguerat, Gavin Burns, Jürg Bähler

“…<h4>Methodology/principal findings</h4>We used S. pombe microarrays to identify three neighbouring genes (urg1, urg2, and urg3) whose transcript levels rapidly and strongly increased in response to uracil, a condition which otherwise had little effect on global gene expression. …”
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Regulation of Proteome Maintenance Gene Expression by Activators of Peroxisome Proliferator-Activated Receptor α by Hongzu Ren, Beena Vallanat, Holly M. Brown-Borg, Richard Currie, J. Christopher Corton

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ESR1 is co-expressed with closely adjacent uncharacterised genes spanning a breast cancer susceptibility locus at 6q25.1. by Anita K Dunbier, Helen Anderson, Zara Ghazoui, Elena Lopez-Knowles, Sunil Pancholi, Ricardo Ribas, Suzanne Drury, Kally Sidhu, Alexandra Leary, Lesley-Ann Martin, Mitch Dowsett

“…Our observations suggest that some of the biological effects previously attributed to ER could be mediated and/or modified by these co-expressed genes. …”
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LncRNA MBNL1‐AS1 represses cell proliferation and enhances cell apoptosis via targeting miR‐135a‐5p/PHLPP2/FOXO1 axis in bladder cancer by Xiaosong Wei, Xiaoming Yang, Beibei Wang, Yang Yang, Zhiwei Fang, Chengzhi Yi, Lei Shi, Dongkui Song

“…Abstract LncRNAs have been shown to play essential roles in bladder cancer (BC) progress. Our microarrays of clinical samples firstly screened that lncRNA muscleblind‐like 1 antisense RNA 1 (MBNL1‐AS1) was poorly expressed in BC tissues. …”
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CPT1A/HIF-1α positive feedback loop induced fatty acid oxidation metabolic pathway contributes to the L-ascorbic acid-driven angiogenesis in breast cancer by Xiao Ma, Baojian Zhang, Xuezhe Yin, ShiPeng Yang, Zhenhua Lin, Yang Yang, Xianchun Zhou

“…Methods First, cell functional assays and animal models were employed to elucidate the pro-carcinogenic effects of CPT1A on BC and its role in metabolic alterations. …”
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Associations of circulating insulin-like growth factor-1 and insulin-like growth factor binding protein-3 with the expression of stem cell markers in benign breast tissue by Lusine Yaghjyan, Yujing J. Heng, Brian R. Sardella, Divya Murthy, Matt B. Mahoney, Bernard Rosner, Kornelia Polyak, Maisey Ratcliff, Rulla M. Tamimi

“…Immunohistochemistry (IHC) was done on tissue microarrays. For each core, the IHC expression was assessed using QuPath, and expressed as % of cells that stain positively for a specific marker out of the total cell count. …”
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Genome-wide DNA methylation and gene expression in human placentas derived from assisted reproductive technology by Pauliina Auvinen, Jussi Vehviläinen, Karita Rämö, Ida Laukkanen, Heidi Marjonen-Lindblad, Essi Wallén, Viveca Söderström-Anttila, Hanna Kahila, Christel Hydén-Granskog, Timo Tuuri, Aila Tiitinen, Nina Kaminen-Ahola

“…Methods We performed genome-wide DNA methylation (EPIC Illumina microarrays) and gene expression (mRNA sequencing) analyses for a total of 80 ART and 77 control placentas. …”
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GCKIII kinases control hepatocellular lipid homeostasis via shared mode of action by Emmelie Cansby, Mara Caputo, Emma Andersson, Rasool Saghaleyni, Marcus Henricsson, Ying Xia, Bernice Asiedu, Matthias Blüher, L. Thomas Svensson, Andrew J. Hoy, Margit Mahlapuu

“…Finally, using in vitro kinase assays on microfluidic microarrays, we pinpointed various downstream targets that are phosphorylated by the GCKIII kinases, with known functions in lipogenesis, lipolysis, and lipid secretion, as well as glucose uptake, glycolysis, hexosamine synthesis, and ubiquitination. …”
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Overcoming immunotherapy resistance in bladder cancer with a novel antibody-drug conjugate RC48 by Xin Gao, Chunyu Zhang, Jinbo Chen, Zhi Liu, Jiao Hu, Xiongbing Zu, Jiatong Xiao, Jinhui Liu, Zhenyu Nie, Zhenglin Yi, Haisu Liang, Jinliang Huang, Zhiyong Cai, Luzhe Yan, Bingquan Wu, Zefu Liu

“…At the clinical level, bladder cancer immune therapy cohort tissue microarrays were used, and the aforementioned mechanisms were validated using immunohistochemistry and immunofluorescence.Results HER2 expression is associated with an inhibitory tumor immune microenvironment and resistance to immunotherapy. …”
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MARCKSL1 interacted with F‐actin to promote esophageal squamous cell carcinoma mobility by modulating the formation of invadopodia by Yue Zhao, Xiufeng Xie, Lusong Tian, Fang Liu, Yulin Sun, Haizhen Lu, Xiaohang Zhao, Yousheng Mao

“…Finally, the correlation between MARCKSL1 and the clinicopathological features of ESCC patients was assessed based on TCGA database analysis and immunohistochemistry staining of tissue microarrays. Results Knockdown of MARCKSL1 markedly attenuated the cell motility capacity of ESCC cells in vitro, while MARCKSL1 overexpression had the opposite effect. …”
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Integration of histopathological images and immunological analysis to predict M2 macrophage infiltration and prognosis in patients with serous ovarian cancer by Ling Zhao, Jiajia Tan, Qiuyuan Su, Yan Kuang, Yan Kuang

“…In addition, tissue microarrays from 106 patients with SOC patients were included as an external validation set. …”
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WD40 Protein NLE1 as a Novel Diagnostic Biomarker Promoting Hepatocellular Carcinoma Proliferation by Rutong Zhang, Dehua Liu, Xiaoxi Feng, Zhenye Yang, Kaiguang Zhang

“…We further evaluated NLE1 expression in patient tissue microarrays. Kaplan−Meier plots, Cox regression analyses, and receiver operating characteristic (ROC) curves were used to evaluate the prognostic relevance of NLE1. …”
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A nomogram for predicting 3-year total weight loss percentage following LSG: insights from visceral adipose tissue inflammatory methylation sites by Zhehong Li, Liang Wang, Zheng Wang, Qiqige Wuyun, Buhe Amin, Dongbo Lian, Guangzhong Xu, Nengwei Zhang, Dezhong Wang

“…Comparative analyses of 850K methylation microarrays from VAT samples were performed to identify methylation sites associated with INF-related genes. …”
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Inflammatory markers after supplementation with marine n-3 or plant n-6 PUFAs: A randomized double-blind crossover study by Elise Grytten, Johnny Laupsa-Borge, Kaya Cetin, Pavol Bohov, Jan Erik Nordrehaug, Jon Skorve, Rolf K. Berge, Elin Strand, Bodil Bjørndal, Ottar K. Nygård, Espen Rostrup, Gunnar Mellgren, Simon N. Dankel

“…These data point to tissue-specific proinflammatory effects of high n-6 intake, but a net systemic anti-inflammatory effect as for n-3.…”
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Constitutively nuclear FOXO3a localization predicts poor survival and promotes Akt phosphorylation in breast cancer. by Jie Chen, Ana R Gomes, Lara J Monteiro, San Yu Wong, Lai Han Wu, Ting-Ting Ng, Christina T Karadedou, Julie Millour, Ying-Chi Ip, Yuen Nei Cheung, Andrew Sunters, Kelvin Y K Chan, Eric W-F Lam, Ui-Soon Khoo

“…<h4>Methodology/principal findings</h4>Examination of FOXO3a and phosphorylated-Akt (P-Akt) expression in breast cancer tissue microarrays showed nuclear FOXO3a was associated with lymph node positivity (p = 0.052), poor prognosis (p = 0.014), and P-Akt expression in invasive ductal carcinoma. …”
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Elucidation of Dysregulated Pathways Associated With Hypoxia in Oestrogen Receptor‐Negative Breast Cancer by Suad A. K. Shamis, Jean Quinn, Sara Al‐Badran, Molly McKenzie, Phimmada Hatthakarnkul, Gerard Lynch, Guang‐Yu Lian, Warapan Numprasit, Laszlo Romics Jr., Ditte Andersen, Elizabeth Mallon, Donald C. McMillan, Joanne Edwards

“…Methods Immunohistochemistry was performed to identify the prognostic role of CAIX protein expression in ER− tissue microarrays (TMAs) (n = 191). CAIX‐positive samples (n = 37) were transcriptionally profiled by TempO‐Seq and analysed by STRING. …”
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Vitamin K‐dependent gamma‐carboxyglutamic acid protein 1 promotes pancreatic ductal adenocarcinoma progression through stabilizing oncoprotein KRAS and tyrosine kinase receptor EGF... by Zheng Wu, Qing Ye, Shan Zhang, Li‐Peng Hu, Xiao‐Qi Wang, Lin‐Li Yao, Lei Zhu, Shu‐Yu Xiao, Zong‐Hao Duan, Xue‐Li Zhang, Shu‐Heng Jiang, Zhi‐Gang Zhang, De‐Jun Liu, Dong‐Xue Li, Xiao‐Mei Yang

“…Methods Analysis of pancreatic ductal adenocarcinoma (PDAC) datasets, including transcription profiles, clinical data, and tissue microarrays, was conducted to evaluate PRRG1 expression and its clinical relevance. …”
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UBE2N as a novel prognostic and therapeutic biomarker of lung adenocarcinoma by Haofeng Yin, Yibo Xue, Chen Wang, Yanqin Wu, Yuchen Guo, Chunzhen Li, Yunyan Zhang, Shulei Yin, Tiejun Zhao

“…Immunohistochemistry, cell viability, and apoptosis experiments were conducted to verify the oncogenic effects of UBE2N.ResultsUBE2N was identified as an independent prognostic biomarker for LUAD. …”
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Integrated hepatic transcriptomics and metabolomics identify Pck1 as a key factor in the broad dysregulation induced by vehicle pollutants by Gajalakshmi Ramanathan, Yuqi Zhao, Rajat Gupta, Siri Langmo, May Bhetraratana, Fen Yin, Will Driscoll, Jerry Ricks, Allen Louie, James A. Stewart, Timothy R. Gould, Timothy V. Larson, Joel Kaufman, Michael E. Rosenfeld, Xia Yang, Jesus A. Araujo

“…Methods Apolipoprotein E knockout (ApoE KO) mice were exposed to DE or filtered air (FA) for two weeks, or DE for two weeks followed by FA for 1 week. Expression microarrays and global metabolomics assessment were performed in the liver. …”
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Effector T cells under hypoxia have an altered transcriptome similar to tumor-stressed T cells found in non-responsive melanoma patients by Ahmad A Tarhini, Zhihua Chen, Dongliang Du, Joshua Davis, Justin C Boucher, Katarzyna A Rejniak, Jose A Guevara-Patino, Timothy I Shaw, Alyssa Obermayer, Mate Z Nagy, Lourdes B Plaza-Rojas, Elena Kostenko, Anna L Austin, Awino Maureiq E Ojwang'

“…As T cell-based therapies often fail to work in solid tumors, this study aims to investigate the effects of hypoxia on T cell topo-distribution in the TME, gene expression association with T cell states, and clinical responses in melanoma.Methods To generate detailed information on tumor oxygenation and T cell accessibility, we used mathematical modeling of human melanoma tissue microarrays that incorporate oxygen supply from vessels, intratumoral diffusion, and cellular uptake. …”
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