Differential expression of prognostic proteomic markers in primary tumour, venous tumour thrombus and metastatic renal cell cancer tissue and correlation with patient outcome. by Alexander Laird, Fiach C O'Mahony, Jyoti Nanda, Antony C P Riddick, Marie O'Donnell, David J Harrison, Grant D Stewart

“…As such, in this study a tissue microarray from 177 patients with primary renal tumour, renal vein tumour thrombus and/or RCC metastasis has been created and used with Automated Quantitative Analysis (AQUA) of immunofluorescence to study the prognostic significance of these markers in locally advanced and metastatic disease. …”
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A Novel Ensemble Feature Selection Technique for Cancer Classification Using Logarithmic Rank Aggregation Method by Hüseyin Öztoprak, Hüseyin Güney

“…Recent studies have shown that ensemble feature selection (EFS) has achieved outstanding performance in microarray data classification. However, some issues remain partially resolved, such as suboptimal aggregation methods and non-optimised underlying FS techniques. …”
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Pre-diagnostic Demographic, Lifestyle, and Health History Factors in Association with Secreted Protein Acidic and Rich in Cysteine (SPARC) Expression in Colorectal Cancer Tissue by Umaimah Zanif, Jaclyn Parks, Isabella Tai, Stephen Yip, Sindy Babinszky, Katy Milne, Peter Watson, Rachel A. Murphy, Parveen Bhatti

“…Methods: Tumor and normal tissue cores were taken from formalin-fixed paraffin-embedded (FFPE) blocks of incident CRC cases and were used to create tissue microarrays (TMAs). …”
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Coordinate Transcriptomic and Metabolomic Effects of the Insulin Sensitizer Rosiglitazone on Fundamental Metabolic Pathways in Liver, Soleus Muscle, and Adipose Tissue in Diabetic... by Sabrina Le Bouter, Marianne Rodriguez, Nolwen Guigal-Stephan, Sophie Courtade-Gaïani, Laura Xuereb, Catherine de Montrion, Vincent Croixmarie, Thierry Umbdenstock, Claire Boursier-Neyret, Michel Lonchampt, Manuel Brun, Catherine Dacquet, Alain Ktorza, Brian-Paul Lockhart, Jean-Pierre Galizzi

“…For this aim, transcriptional changes were measured in liver, inguinal adipose tissue (IAT) and soleus muscle using microarrays and real-time PCR. …”
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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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Therapeutic effects of adipose tissue-derived mesenchymal stem cells on ER stress in a murine model of metabolic dysfunction-associated steatohepatitis: an in vivo and in vitro stu... by Norihiko Ogawa, Akihiro Seki, Alessandro Nasti, Ho Yagi, Masatoshi Yamato, Hiiro Inui, Hiroki Nomura, Takuya Komura, Hidetoshi Nakagawa, Kouki Nio, Hajime Takatori, Tetsuro Shimakami, Masao Honda, Shuichi Kaneko, Yoshio Sakai, Taro Yamashita

“…Methods C57BL/6J mice were fed either an atherogenic high-fat diet (AT + HF) or a high-fat diet (HFD-60) to induce MASH and simple steatosis (SS), respectively. Liver tissues were analyzed for gene expression, protein levels, and apoptotic markers using DNA microarray, quantitative PCR, western blotting, histological staining, and caspase activity assays. …”
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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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Expression of Cancer‐Testis Antigens MAGE‐A1, MAGE‐A4, NY‐ESO‐1 and PRAME in Bone and Soft Tissue Sarcomas: The Experience From a Single Center in China by Anni Chen, Yuling Qiu, Ying‐Tzu Yen, Chun Wang, Xiaolu Wang, Chunhua Li, Zijian Wei, Lin Li, Lixia Yu, Fangcen Liu, Rutian Li

“…Conclusions CTA expression in bone and soft tissue sarcomas was correlated with both CTA type and sarcoma subtype, showing relatively high levels of expression in undifferentiated pleomorphic sarcoma (UPS) and osteosarcoma (OS). …”
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Cold-inducible RNA-binding protein is associated with subtype-specific breast cancer patient outcomes by Matthew Dankner, Veronique Ouellet, Jakob Lafon, Rima Ezzeddine, Matthew G. Annis, Afnan Abu-Thuraia, Quebec Breast Cancer Foundation Tissue Microarray Consortium, Peter M. Siegel

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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

“…These analyses require appropriate tissue preparations and are more difficult to perform on formalin-fixed, paraffin-embedded (FFPE) tissues. …”
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SPP1 mRNA Expression Is Associated with M2 Macrophage Infiltration and Poor Prognosis in Triple-Negative Breast Cancer by Yu-Chia Chen, Chia-Ching Chen, Rong-Fu Chen, Hsin-Hung Chen, Po-Ming Chen

“…Additionally, we examined SPP1 mRNA expression datasets available in the Kaplan–Meier plotter and investigated the SPP1 protein expression patterns in our own tissue microarray cohort via immunohistochemistry. (3): The results revealed that genes associated with the Toll-like receptor signaling pathway showed a significant increase in activity in TNBC tissues when compared to normal breast tissues. …”
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Chronic Exposure of Renal Progenitor Cells (HRTPT) to As (III) Implicates Microfibril Associated Protein 5 (MFAP5) in the Activation of Carcinoembryonic Antigen Related Cell Adhesi... by Md Ehsanul Haque, Donald A. Sens, Scott H. Garrett

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Neurotransmission Sex Dichotomy in the Rat Hypothalamic Paraventricular Nucleus in Healthy and Infantile Spasm Model by Dumitru Andrei Iacobas, Jana Veliskova, Tamar Chachua, Chian-Ru Chern, Kayla Vieira, Sanda Iacobas, Libor Velíšek

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The Construction of ceRNA Regulatory Network Unraveled Prognostic Biomarkers and Repositioned Drug Candidates for the Management of Pancreatic Ductal Adenocarcinoma by Busra Aydin, Keziban Okutan, Ozge Onluturk Aydogan, Raghu Sinha, Beste Turanli

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Reconstructing Dynamic Gene Regulatory Networks Using f-Divergence from Time-Series scRNA-Seq Data by Yunge Wang, Lingling Zhang, Tong Si, Sarah Roberts, Yuqi Wang, Haijun Gong

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Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways. by Andrew Filer, Philipp Antczak, Greg N Parsonage, Holly M Legault, Margot O'Toole, Mark J Pearson, Andrew M Thomas, Dagmar Scheel-Toellner, Karim Raza, Christopher D Buckley, Francesco Falciani

“…To test our hypothesis we utilized a bioinformatics approach to explore a publicly available microarray dataset including rheumatoid arthritis (RA), osteoarthritis (OA) and normal synovial tissue, then extended those findings in a new microarray dataset representing matched synovial, bone marrow and skin fibroblasts cultured from RA and OA patients undergoing arthroplasty. …”
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An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: functional, metabolic, and differential network analysis. by Sriram Devanathan, Timothy Whitehead, George G Schweitzer, Nicole Fettig, Attila Kovacs, Kenneth S Korach, Brian N Finck, Kooresh I Shoghi

“…Analysis of microarray data revealed differential variations in the expression of 208 genes affecting multiple transcriptional networks. …”
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Expression of RNA-binding motif 10 is associated with advanced tumor stage and malignant behaviors of lung adenocarcinoma cancer cells by Guofang Guan, Ranwei Li, Wenfang Tang, Tiecheng Liu, Zhenzhong Su, Yan Wang, Jingjin Tan, Shan Jiang, Ke Wang

“…Levels of RNA-binding motif 10 messenger RNA and protein were significantly lower in lung adenocarcinoma tissues than those in paired non-tumor tissues (p < 0.001). …”
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ADP-ribosylation factor 6 expression increase in oesophageal adenocarcinoma suggests a potential biomarker role for it. by Venkateswarlu Kanamarlapudi, Salman Tamaddon-Jahromi, Kate Murphy

“…We further evaluated ARF6 protein expression in oesophageal adenocarcinoma (EAC) tissue microarray cores by immunohistochemistry. The ARF6 gene expression levels are highly variable between healthy and cancer tissues. …”
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NuMA overexpression in epithelial ovarian cancer. by Anke Brüning-Richardson, Jaqueline Bond, Rawiah Alsiary, Julie Richardson, David A Cairns, Luci McCormac, Richard Hutson, Philip A Burns, Nafisa Wilkinson, Geoff D Hall, Ewan E Morrison, Sandra M Bell

“…Aneuploidy status in primary cultures was determined by FACS analysis.Affymetrix microarray data indicated that NuMA was overexpressed in tumour tissue, primary cultures and cell lines compared to normal ovarian tissue. …”
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