HMGB1 Deficiency Occurs in a Broad Range of Human Cancers and Is Often Associated with Unfavorable Tumor Phenotype by Viktoria Chirico, Hena Sharifi, Maria Christina Tsourlakis, Seyma Büyücek, Clara Marie von Bargen, Katharina Möller, Florian Lutz, David Dum, Martina Kluth, Claudia Hube-Magg, Georgia Makrypidi-Fraune, Piero Caneve, Maximilian Lennartz, Morton Freytag, Sebastian Dwertmann Rico, Simon Kind, Viktor Reiswich, Eike Burandt, Till S. Clauditz, Patrick Lebok, Christoph Fraune, Till Krech, Sarah Minner, Andreas H. Marx, Waldemar Wilczak, Ronald Simon, Guido Sauter, Stefan Steurer, Kristina Jansen

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Construction, visualisation, and clustering of transcription networks from microarray expression data. by Tom C Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell J Grocock, Shiri Freilich, Janet Thornton, Anton J Enright

“…Such approaches are increasingly being applied to genomics data, where functional linkages are used to connect genes or proteins. However, while microarray gene expression datasets are now abundant and of high quality, few approaches have been developed for analysis of such data in a network context. …”
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Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology by Juwayria, Priyansh Shrivastava, Kaustar Yadav, Sourabh Das, Shubham Mittal, Sunil Kumar, Deepali Jain, Prabhat Singh Malik, Ishaan Gupta

“…Abstract 10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. …”
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Moderate degradation does not preclude microarray analysis of small amounts of RNA by Oliver Schoor, Toni Weinschenk, Jörg Hennenlotter, Stefan Corvin, Arnulf Stenzl, Hans-Georg Rammensee, Stefan Stevanović

“…We induced RNA degradation in human tumor and healthy tissue samples by endogeneous ribonucleases. Next, we amplified 20 ng total RNA degraded to different extents by two rounds of in vitro transcription and analyzed them using Affymetrix oligonucleotide microarrays. …”
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Prognostic role of high MTAP expression is reversed by the ERG status in prostate cancer treated by radical prostatectomy by Natalia Gorbokon, Seyma Büyücek, Henning Plage, Neele Heckmann, Ronald Simon, Maximilian Lennartz, Martina Kluth, Katharina Teljuk, Claudia Hube-Magg, Sarah Minner, Eike Burandt, Till S. Clauditz, Waldemar Wilczak, Guido Sauter, David Dum, Andrea Hinsch, Hans Heinzer, Alexander Haese, Thorsten Schlomm, Andreas M Luebke, Markus Graefen, Stefan Steurer, Christian Bernreuther, Luca Roma, Lukas Bubendorf, Sarah Weinberger

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MTAP deficiency is highly homogeneous in advanced, muscle-invasive urothelial carcinoma of the urinary bladder by Natalia Gorbokon, Katharina Teljuk, Viktor Reiswich, Florian Lutz, Sebastian Dwertmann Rico, Clara Lühr, Christian Bernreuther, Yaryna Klos Al Bunni, Cosima Völkel, Henning Plage, Maximilian Lennartz, Margit Fisch, Sarah Minner, Ronald Simon, Guido Sauter, Henrik Zecha, Stefan Steurer, Thorsten Schlomm, Tatjana Vlajnic, Lukas Bubendorf, Michael Rink, Martina Kluth, Florian Viehweger, Morton Freytag

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High NUSAP1 expression predicts poor survival in laryngeal squamous cell carcinoma by Shengkai Zhou, Haiyun Li, Li Zhang, Jinxiang Chen

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Microarray Data Analysis: From Hypotheses to Conclusions Using Gene Expression Data by Nicola J. Armstrong, Mark A. van de Wiel

“…We review several commonly used methods for the design and analysis of microarray data. To begin with, some experimental design issues are addressed. …”
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Chromosomal microarray on product of conception in early pregnancy loss: A case report by Snehal Mallakmir, Gauri Mulgund, Rashid Merchant

“…Various studies have now demonstrated the benefits of chromosomal microarray analysis (CMA) compared to conventional cytogenetic analysis in managing RPL. …”
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Comprehensive Review of Hybrid Feature Selection Methods for Microarray-Based Cancer Detection by Azka Khoirunnisa, Didit Adytia, Mustafa Mat Deris, Adiwijaya

“…Microarray data-based cancer detection advances early diagnosis and personalized medicine by utilizing gene expression data to develop comprehensive cancer profiles, measuring thousands of genes simultaneously. …”
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A review of independent component analysis application to microarray gene expression data by Wei Kong, Charles R. Vanderburg, Hiromi Gunshin, Jack T. Rogers, Xudong Huang

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High reproducibility using sodium hydroxide-stripped long oligonucleotide DNA microarrays by Zhiyuan Hu, Melissa Troester, Charles M. Perou

“…In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. …”
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ZODET: software for the identification, analysis and visualisation of outlier genes in microarray expression data. by Daniel L Roden, Gavin W Sewell, Anna Lobley, Adam P Levine, Andrew M Smith, Anthony W Segal

“…We compared the potential of ZODET to detect outlier genes in gene expression datasets with a previously described statistical method, gene tissue index (GTI), using a simulated expression dataset and a publicly available monocyte-derived macrophage microarray dataset. …”
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Robust Microarray Meta-Analysis Identifies Differentially Expressed Genes for Clinical Prediction by John H. Phan, Andrew N. Young, May D. Wang

“…Although microarrays have increased the rate of genomic data collection, sample size is still a major issue when identifying informative genetic biomarkers. …”
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Loss of MTAP expression is strongly linked to homozygous 9p21 deletion, unfavorable tumor phenotype, and noninflamed microenvironment in urothelial bladder cancer by Natalia Gorbokon, Niklas Wößner, Viktoria Ahlburg, Henning Plage, Sebastian Hofbauer, Kira Furlano, Sarah Weinberger, Paul Giacomo Bruch, Simon Schallenberg, Florian Roßner, Sefer Elezkurtaj, Maximilian Lennartz, Niclas C Blessin, Andreas H Marx, Henrik Samtleben, Margit Fisch, Michael Rink, Marcin Slojewski, Krystian Kaczmarek, Thorsten Ecke, Tobias Klatte, Stefan Koch, Nico Adamini, Sarah Minner, Ronald Simon, Guido Sauter, Henrik Zecha, David Horst, Thorsten Schlomm, Lukas Bubendorf, Martina Kluth

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Circular RNA microarray expression profile and potential function of circDOCK1 in colorectal cancer by Guojing Zhang, Xiaoyan Wu, Hongmin Fu, Daqing Sun

“…This study aimed to investigate the impact of circDOCK1 on CRC metastasis and prognosis as well as its underlying molecular mechanisms.MethodsWe explored circRNA expression profiles in four pairs of CRC tissues and adjacent non-carcinoma tissues via microarray analysis. …”
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Mathematical modelling and deep learning algorithms to automate assessment of single and digitally multiplexed immunohistochemical stains in tumoural stroma by Liam Burrows, Declan Sculthorpe, Hongrun Zhang, Obaid Rehman, Abhik Mukherjee, Ke Chen

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Microarray Gene Expression Analysis of Murine Tumor Heterogeneity Defined by Dynamic Contrast-Enhanced MRI by Nick G. Costouros, Dominique Lorang, Yantian Zhang, Marshall S. Miller, Felix E. Diehn, Stephen M. Hewitt, Michael V. Knopp, King C. P. Li, Peter L. Choyke, H. Richard Alexander, Steven K. Libutti

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Data analysis of high-throughput sequencing and microarray to identify key signatures of microribonucleic acids in glioblastoma by A. A. Pushkin, E. A. Dzenkova, N. N. Timoshkina, D. Yu. Gvaldin

“…A total of 156 glioblastoma samples with mRNA sequencing data, 571 samples with microarray microRNA analysis data, and 15 control samples were analyzed. …”
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Integrated Use of Statistical-Based Approaches and Computational Intelligence Techniques for Tumors Classification Using Microarray by Chia-Ding Hou, Yuehjen E. Shao

“…With the recent development of biotechnologies, cDNA microarray chips are increasingly applied in cancer research. …”
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