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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Quantification of the heterogeneity of prognostic cellular biomarkers in ewing sarcoma using automated image and random survival forest analysis. by Claudia Bühnemann, Simon Li, Haiyue Yu, Harriet Branford White, Karl L Schäfer, Antonio Llombart-Bosch, Isidro Machado, Piero Picci, Pancras C W Hogendoorn, Nicholas A Athanasou, J Alison Noble, A Bassim Hassan

“…Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithms. …”
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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

“…We examined the expression of PM genes in rat and mouse liver after exposure to 7 different PPCs (WY-14,643, clofibrate, fenofibrate, valproic acid, di-(2-ethylhexyl) phthalate, perfluorooctanoic acid, and perfluorooctane sulfonate) using Affymetrix microarrays. In rats and mice, 174 or 380 PM genes, respectively, were regulated by at least one PPC. …”
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Cell-cycle and Apoptosis Regulators (p16INK4A, p21CIP1, α-Catenin, Survivin, and hTERT) and Morphometry-Defined MPECs Predict Metachronous Cancer Development in Colorectal Adenoma... by Kjetil Soreide, Tirza C. E. Buter, Emiel A. Janssen, Einar Gudlaugsson, Ivar Skaland, Hartwig Körner, Jan P. A. Baak

“…Methods: Application of immunohistochemistry on tissue microarrays in consecutive, population-based colorectal adenomas. …”
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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

“…RNA from tumour biopsies taken from 104 postmenopausal women before and after 2 weeks treatment with an aromatase (oestrogen synthase) inhibitor was analyzed on Illumina 48K microarrays. Multiple-testing corrected Spearman correlation revealed that three previously uncharacterized open reading frames (ORFs) located immediately upstream of ESR1, C6ORF96, C6ORF97, and C6ORF211 were highly correlated with ESR1 (Rs =  0.67, 0.64, and 0.55 respectively, FDR<1 × 10(-7)). …”
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Genome-wide analysis of attention deficit hyperactivity disorder in Norway. by Tetyana Zayats, Lavinia Athanasiu, Ida Sonderby, Srdjan Djurovic, Lars T Westlye, Christian K Tamnes, Tormod Fladby, Heidi Aase, Pål Zeiner, Ted Reichborn-Kjennerud, Per M Knappskog, Gun Peggy Knudsen, Ole A Andreassen, Stefan Johansson, Jan Haavik

“…Genotyping was performed using Illumina Human OmniExpress-12v1 microarrays. Statistical analyses were divided into several steps: (1) genome-wide association in the form of logistic regression in PLINK and follow-up pathway analyses performed in DAPPLE and INRICH softwares, (2) SNP-heritability calculated using genome-wide complex trait analysis (GCTA) tool, (3) gene-based association tests carried out in JAG software, and (4) evaluation of previously reported genome-wide signals and candidate genes of ADHD.…”
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Parasite-derived microRNAs in host serum as novel biomarkers of helminth infection. by Anna M Hoy, Rachel J Lundie, Alasdair Ivens, Juan F Quintana, Norman Nausch, Thorsten Forster, Frances Jones, Narcis B Kabatereine, David W Dunne, Francisca Mutapi, Andrew S Macdonald, Amy H Buck

“…<h4>Methods/principal findings</h4>We used Exiqon miRNA microarrays to profile miRNA expression in the livers of mice infected with S. mansoni at 7 weeks post-infection. …”
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Advancing Precision Medicine: The Role of Genetic Testing and Sequencing Technologies in Identifying Biological Markers for Rare Cancers by Joviana Farhat, Lara Alzyoud, Mohammad AlWahsh, Animesh Acharjee, Basem Al‐Omari

“…Results In practice, fluorescence in situ hybridization, karyotype, microarrays and other genetic tests are mainly applied to identify specific genetic alterations and mutations associated with cancer progression. …”
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Prognostic value of B7-H3 expression in metastatic renal cell carcinoma and its impact on immunotherapy response by Faruk Recep Özalp, Kutsal Yörükoğlu, Eda Çalışkan Yıldırım, Mehmet Uzun, Hüseyin Salih Semiz

“…Methods Immunohistochemical analysis of B7-H3 expression was performed in 84 metastatic RCC patients. Tissue microarrays and separate sections of formalin-fixed paraffin-embedded tissue were used for immunohistochemical staining. …”
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The lncRNA H19/miR-766-3p/S1PR3 Axis Contributes to the Hyperproliferation of Keratinocytes and Skin Inflammation in Psoriasis via the AKT/mTOR Pathway by Yuexi He, Xiran Yin, Jianjun Yan, Xue Li, Qing Sun

“…Methods. miRNA and lncRNA microarrays were performed using IL-22-induced HaCaT cells and psoriatic lesions, respectively. …”
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Tumor immune microenvironment permissive to metastatic progression of ING4-deficient breast cancer. by Emily Tsutsumi, Anne M Macy, Janine LoBello, Karen T Hastings, Suwon Kim

“…To characterize the tumor immune microenvironment associated with ING4-deficient tumors, three approaches were employed in this study: First, tissue microarrays composed of 246 primary breast tumors including 97 ING4-deficient tumors were evaluated for the presence of selective immune markers, CD68, CD4, CD8, and PD-1, using immunohistochemical staining. …”
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Infiltration of CD3+ and CD8+ lymphocytes in association with inflammation and survival in pancreatic cancer. by Gerik W Tushoski-Alemán, Kelly M Herremans, Patrick W Underwood, Ashwin Akki, Andrea N Riner, Jose G Trevino, Song Han, Steven J Hughes

“…<h4>Methods</h4>Tissue microarrays were immunohistochemically stained for CD3+ and CD8+ lymphocytes and quantitatively assessed using QuPath. …”
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TPX2 promotes papillary renal cell carcinoma progression by forming a ceRNA with LINC00894 by Zhenshan Ding, Wenwei Ying, Ye Yan, Ying Zhao, Cheng Liu, Lulin Ma

“…Immunohistochemical analysis of tissue microarrays was performed to evaluate the associations between TPX2 expression and clinicopathological characteristics in type 2 pRCC patients. …”
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High Expression of Somatostatin Receptors 2A, 3, and 5 in Corticotroph Pituitary Adenoma by Felix Behling, Jürgen Honegger, Marco Skardelly, Irina Gepfner-Tuma, Ghazaleh Tabatabai, Marcos Tatagiba, Jens Schittenhelm

“…Paraffin-embedded tumor samples of 88 corticotroph pituitary adenomas and 30 nonadenomatous pituitary biopsies were analyzed after processing into tissue microarrays and immunohistochemical staining for SSTR 1, SSTR2A, SSTR3, SSTR4, and SSTR5. …”
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Prevalence of βIII-tubulin (TUBB3) expression in human normal tissues and cancers by Fermín Person, Waldemar Wilczak, Claudia Hube-Magg, Christoph Burdelski, Christina Möller-Koop, Ronald Simon, Mercedes Noriega, Guido Sauter, Stefan Steurer, Susanne Burdak-Rothkamm, Frank Jacobsen

“…To systematically investigate the epidemiology of TUBB3 expression in normal and neoplastic tissues, we used tissue microarrays for analyzing the immunohistochemically detectable expression of TUBB3 in 3911 tissue samples from 100 different tumor categories and 76 different normal tissue types. …”
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Evaluating the potential of anti-dsRNA antibodies as an alternative viral sensing tool in encephalitides of different species by Madeleine de le Roi, Hannah Gerhards, Adnan Fayyad, Adnan Fayyad, Mathias Boelke, Stefanie Christine Becker, Asisa Volz, Ingo Gerhauser, Wolfgang Baumgärtner, Christina Puff

“…Molecular methods like multiplex PCR and microarrays are considered to be often less sensitive than Next Generation Sequencing, whereas the latter is time-consuming and costly. …”
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Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies by Kyle A. Campbell, Justin A. Colacino, John Dou, Dana C. Dolinoy, Sung Kyun Park, Rita Loch-Caruso, Vasantha Padmanabhan, Kelly M. Bakulski

“…We collated new and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n = 36) with robust partial correlation based on the top 30 hyper- and hypomethylated sites identified per cell type. …”
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Spatially resolved proteomics surveys the chemo‐refractory proteins related to high‐grade serous ovarian cancer by Linyuan Fan, Yi Liu, Haichao Zhou, Yang Feng, Guangyi Jiang, Guixue Hou, Zhihan Cao, Zhiguo Zheng, Lu Sun, Hao Chen, Yuefei Zhang, Weiran Chen, Yun Xi, Benliang Cheng, Qinghai Yang, Yan Ren, Jianqing Zhu, Siqi Liu

“…Immunohistochemical validation of HGSC tissue microarrays confirmed the spatial proteomic localization of TFRC and PDLIM3, which are linked to tumour progression, while establishing their novel role as chemotherapy resistance biomarkers through this study, with broader predictive potential observed across additional targets in the discovery cohort. …”
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Resistance and aerobic training increases genome-wide DNA methylation in women with polycystic ovary syndrome by Cristiana Libardi Miranda Furtado, Megan Hansen, Gislaine Satyko Kogure, Victor Barbosa Ribeiro, Nathanael Taylor, Murilo Racy Soares, Rui Alberto Ferriani, Kenneth Ivan Aston, Timothy Jenkins, Rosana Maria dos Reis

“…Genome-wide leukocyte DNA methylation was analysed by Infinium Human MethylationEPIC 850K BeadChip microarrays (Illumina). Both resistance and aerobic exercise improved anthropometric indices, metabolic dysfunction, and hyperandrogenism in PCOS after the training programme, but no differences were observed between the two exercises. …”
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Biomarker-Based Nomogram to Predict Neoadjuvant Chemotherapy Response in Muscle-Invasive Bladder Cancer by Meritxell Pérez, Juan José Lozano, Mercedes Ingelmo-Torres, Montserrat Domenech, Caterina Fernández Ramón, J. Alfred Witjes, Antoine G. van der Heijden, Maria José Requena, Antonio Coy, Ricard Calderon, Begoña Mellado, Antonio Alcaraz, Antoni Vilaseca, Maria J. Ribal

“…Gene expression patterns were analysed in 34 samples from transurethral resection of the bladder (TURB) using Illumina microarrays. The expression levels of 45 selected differentially expressed genes between responders and non-responders to NAC were validated by quantitative PCR in an independent cohort of 157 patients. …”
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