APPLICATIONS OF TRANSCRIPTOMICS METHODS IN BREAST CANCER by Yeşim Gökmen Polar

“…Gene expression studies using cDNA microarrays have revolutionized the breast cancer subclassification. …”
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p53 activation by knockdown technologies. by Mara E Robu, Jon D Larson, Aidas Nasevicius, Soraya Beiraghi, Charles Brenner, Steven A Farber, Stephen C Ekker

“…Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. …”
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MicroRNA-520a Suppresses Pathogenesis and Progression of Non-Small-Cell Lung Cancer through Targeting the RRM2/Wnt Axis by Yi Xie, Congyu Xue, Shuai Guo, Lei Yang

“…Differentially expressed miRNAs between tumor tissues and normal tissues were screened using microarrays, and miR-520a was screened to be significantly poorly expressed in tumor samples. …”
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Gene expression profiling identifies molecular pathways associated with collagen VI deficiency and provides novel therapeutic targets. by Sonia Paco, Susana G Kalko, Cristina Jou, María A Rodríguez, Joan Corbera, Francesco Muntoni, Lucy Feng, Eloy Rivas, Ferran Torner, Francesca Gualandi, Anna M Gomez-Foix, Anna Ferrer, Carlos Ortez, Andrés Nascimento, Jaume Colomer, Cecilia Jimenez-Mallebrera

“…To address this we have applied microarrays to analyse the transcriptome of UCMD muscle and compare it to healthy muscle and other muscular dystrophies. …”
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Diagnosing Autoimmune Bullous Diseases—An Indian Perspective by Adhyatm Bhandari, Dipankar De, Shikha Shah, Debajyoti Chatterjee, Vinod Kumar, Rahul Mahajan, Sanjeev Handa

“…BIOCHIP is a technique based on IIF that offers a sensitive and specific diagnostic alternative to ELISA. It uses microarrays with multiple antigenic substrates to simultaneously screen common AIBDs. …”
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Identification of components associated with thermal acclimation of photosystem II in Synechocystis sp. PCC6803. by John G Rowland, Xin Pang, Iwane Suzuki, Norio Murata, William J Simon, Antoni R Slabas

“…<h4>Methodology/findings</h4>We have analysed gene expression using whole-genome microarrays and monitored alterations in physiology during acclimation of PSII to elevated growth temperature in Synechocystis sp. …”
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Small deletion variants have stable breakpoints commonly associated with alu elements. by Adam J de Smith, Robin G Walters, Lachlan J M Coin, Israel Steinfeld, Zohar Yakhini, Rob Sladek, Philippe Froguel, Alexandra I F Blakemore

“…We investigated the breakpoints of 20 small, common deletions, representing a subset of those originally identified by array CGH, using Agilent microarrays, in 50 healthy French Caucasian subjects. …”
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An attempt at a molecular prediction of metastasis in patients with primary cutaneous melanoma. by Melanie Gschaider, Friederike Neumann, Bettina Peters, Florian Lenz, Michael Cibena, Malgorzata Goiser, Ingrid Wolf, Jörg Wenzel, Cornelia Mauch, Wolfgang Schreiner, Stephan N Wagner

“…Significance analysis of microarrays identified the top 50 differentially expressed genes. …”
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High Caveolin-1 mRNA expression in triple-negative breast cancer is associated with an aggressive tumor microenvironment, chemoresistance, and poor clinical outcome. by Christopher Godina, Somayeh Khazaei, Mattias Belting, Johan Vallon-Christersson, Björn Nodin, Karin Jirström, Karolin Isaksson, Ana Bosch, Helena Jernström

“…Tumor microenvironment composition of high- and low-expressing CAV1 tumors was estimated using ECOTYPER. Tumor tissue microarrays were used to evaluate CAV1 protein levels in stromal and malignant cells.…”
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Persistence of IgE-associated allergy and allergen-specific IgE despite CD4+ T cell loss in AIDS. by Katharina Marth, Eva Wollmann, Daniela Gallerano, Portia Ndlovu, Ian Makupe, Rudolf Valenta, Elopy Sibanda

“…Allergy was diagnosed according to case history, physical examination, skin prick testing (SPT), and serological analyses including allergen microarrays. HIV infection was confirmed serologically and the disease was staged clinically. …”
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MMP14 and DDR2 are potential molecular markers for metastatic triple-negative breast cancer by Rabeah Al-Temaimi, Rasheed Ahmad, Fahd Al-Mulla

“…Here, we utilized TNBC tissue microarrays to determine the protein expression of seven matrix metalloproteinases (MMPs) and Discoidin domain receptor 2 (DDR2) in metastatic and non-metastatic TNBC to identify potential targets for immunotherapy. …”
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Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. by Roy R Chaudhuri, Mohammed Sebaihia, Jon L Hobman, Mark A Webber, Denisse L Leyton, Martin D Goldberg, Adam F Cunningham, Anthony Scott-Tucker, Paul R Ferguson, Christopher M Thomas, Gad Frankel, Christoph M Tang, Edward G Dudley, Ian S Roberts, David A Rasko, Mark J Pallen, Julian Parkhill, James P Nataro, Nicholas R Thomson, Ian R Henderson

“…In addition, by using Biolog Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. …”
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Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid spo... by Paula Yagüe, Antonio Rodríguez-García, María Teresa López-García, Beatriz Rioseras, Juan Francisco Martín, Jesús Sánchez, Angel Manteca

“…The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. …”
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Endoplasmic reticulum protein ERp46 in renal cell carcinoma. by Wilhelmina C M Duivenvoorden, Athanasios Paschos, Sarah N Hopmans, Richard C Austin, Jehonathan H Pinthus

“…We demonstrated a higher ERp46/AdipoR1 expression ratio in metastatic compared to non-metastatic ccRCC, as determined by immunohistochemistry of tissue microarrays and subsequent image analysis. When ERp46 was stably knocked down using shRNA or overexpressed in murine RCC RAG cells, RCC growth after subcutaneous injection in BALB/c nude mice was inhibited and accelerated, respectively. …”
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An unbiased assessment of the role of imprinted genes in an intergenerational model of developmental programming. by Elizabeth J Radford, Elvira Isganaitis, Josep Jimenez-Chillaron, Joshua Schroeder, Michael Molla, Simon Andrews, Nathalie Didier, Marika Charalambous, Kirsten McEwen, Giovanna Marazzi, David Sassoon, Mary-Elizabeth Patti, Anne C Ferguson-Smith

“…We therefore analyse the role of imprinted genes in multiple tissues in two affected generations of an established murine model of the developmental origins of health and disease using microarrays and quantitative RT-PCR. We demonstrate that, despite the functional mono-allelicism of imprinted genes and their unique mechanisms of epigenetic dosage control, imprinted genes as a class are neither more susceptible nor protected from expression perturbation induced by maternal undernutrition in either the F1 or the F2 generation compared to other genes. …”
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Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. by Chunlei Wu, David L Delano, Nico Mitro, Stephen V Su, Jeff Janes, Phillip McClurg, Serge Batalov, Genevieve L Welch, Jie Zhang, Anthony P Orth, John R Walker, Richard J Glynne, Michael P Cooke, Joseph S Takahashi, Kazuhiro Shimomura, Akira Kohsaka, Joseph Bass, Enrique Saez, Tim Wiltshire, Andrew I Su

“…Recently, many studies have used microarrays to measure gene expression levels across genetic mapping populations. …”
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Phosphoribosyl transferase domain containing 1: A prognostic biomarker in testicular germ cell tumors by Peisheng Huang, Yihao Chen, Yongcheng Shi, Chuanfan Zhong, Huawei Lin, Xiaoxue Yu, Kai Chen, Zhuoya Huang, Le Zhang, Shumin Fang, Jianming Lu, Jiahong Chen

“…Immunohistochemistry on tissue microarrays validated PRTFDC1’s predictive value in clinical samples. …”
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Excavating regulated cell death signatures to predict prognosis, tumor microenvironment and therapeutic response in HR+/HER2- breast cancer by Shuangshuang Mao, Yuanyuan Zhao, Huihua Xiong, Chen Gong

“…The expressions and prognostic value of LEF1 and SFRP1were also validated in our tissue microarrays. The nomogram established basing on CDScore, age and TNM stage performed satisfactory in predicting overall survival, with an area under the ROC curve of 0.89, 0.82 and 0.8 in predicting 1-year, 3-year and 5-year overall survival rates, respectively. …”
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Association of PD-1, LAG-3 and TIM-3 expression on intratumoral CD8 T-cells with response to atezolizumab in a Real-World-Evidence biomarker study for advanced urothelial carcinoma... by Carlos E. de Andrea, Marta Abengozar-Muela, José Ángel Arranz, Miguel Angel Climent, Javier Puente, Ángel Vizcay, Ligia Montero de la Fuente, José Miguel Jurado, Teresa Bonfill, Carmen Santander, José Carlos Villa, Eduardo Pujol, Adriana Carolina Rosero, Jenifer Gomez, Eva María Fernández, Carlos Álvarez Fernández, Ignacio Ramirez, Pablo Arnáiz, Álvaro López-Janeiro, Ignacio Melero, Miguel F. Sanmamed, José Luis Pérez-Gracia

“…We assessed with Multiplexed Quantitative Immunofluorescence the expression of CD8, PD-1, TIM-3 and LAG-3 on T-cells in the different compartments of the TME (tumor, stroma and whole tissue) in pre-treatment tissue microarrays. We studied associations between the expression of the markers and clinical efficacy. …”
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History and prospects of flax genetic markers by Daiana A. Zhernova, Elena N. Pushkova, Tatiana A. Rozhmina, Elena V. Borkhert, Alexander A. Arkhipov, Alexander A. Arkhipov, Elizaveta A. Sigova, Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Ekaterina M. Dvorianinova, Alexey A. Dmitriev, Alexey A. Dmitriev, Nataliya V. Melnikova

“…Cost-effective and accurate analysis of large number of genotypes for multiple markers simultaneously using microarrays or targeted deep sequencing became available, as well as HRM, TaqMan, KASP, and other fluorescence-based high-throughput methods for detecting DNA polymorphisms. …”
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