Bioinformatics-based screening and validation of PANoptosis-related biomarkers in periodontitis by Qing Sun, Qing Sun, JinYue Hu, JinYue Hu, RuYue Wang, RuYue Wang, ShuiXiang Guo, ShuiXiang Guo, GeGe Zhang, GeGe Zhang, Ao Lu, Ao Lu, Xue Yang, Xue Yang, LiNa Wang, LiNa Wang

“…RT-qPCR validation demonstrated that ZBP1 expression was significantly elevated in periodontitis tissues compared to healthy periodontal tissues (P < 0.05).ConclusionThis study provides bioinformatic evidence linking PANoptosis to periodontitis. …”
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Pan-cancer analysis identifies CD155 as a promising target for CAR-T cell therapy by Xiaohong Liu, Yue Sun, Boxu Lin, Hao Xiong, Xinyue Lu, Binghe Tan, Chenglin Zhang, Mingyao Liu, Juliang Qin, Na Zhang, Bing Du

“…Methods The expression of CD155 was analyzed across various cancer types using data from The Cancer Genome Atlas (TCGA) and validated by tissue microarray analysis. The impact of CD155 on T cell mediated cytotoxicity was analyzed using CD155 over-expression or knockout tumor cells. …”
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Implications of CYP1B1 in the treatment and prognosis of breast cancer by Maria Carolina Stipp, Jeanine Marie Nardin, José Claudio Casali-da-Rocha, Sérgio Ioshii, Alexandra Acco

“…Results The CYP1B1 enzyme was overexpressed in 75% of breast cancer tissues. This result remained consistent regardless of the treatment regimen. …”
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Construction of a macrophage-related prognostic signature and assessment of immune checkpoint inhibitor efficacy of HCC by Shouge Zang, Hongwei Chen, Yuqian Han, Di Cui, Jiangtao Yu

“…Functional assays were conducted to assess the effect of PLAUR knockdown on macrophage polarization, tumor cell behavior, and PI3K/AKT/mTOR pathway activity. Tissue microarray immunofluorescence validated PLAUR expression in situ. …”
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Stroma regulates increased epithelial lateral cell adhesion in 3D culture: a role for actin/cadherin dynamics. by Karen F Chambers, Joanna F Pearson, Naveed Aziz, Peter O'Toole, David Garrod, Shona H Lang

“…<h4>Background</h4>Cell shape and tissue architecture are controlled by changes to junctional proteins and the cytoskeleton. …”
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Involvement of tdTomato-Tagged RPE cells in a mouse PVR model with enzymatically compromised retina by Yao Chen, Xiao Liu, Ashwini Kini, John Y. Liu, Xiaoqin Lu, Ling Gao, Henry J. Kaplan, Douglas C. Dean, Yongqing Liu

“…Gene expression results of the mouse PVR model retinas are consistent with the microarray gene expression profile of human PVR retinas, validating that our mouse PVR model resembles human PVR and is thereby suitable for molecular mechanism and pharmaceutical studies.…”
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ALDOB is a prognostic biomarker and a potential immunotherapy target for clear cell renal cell carcinoma by Wu Xu, Dali Wu, Cuilian Li, Lingfei Yan, Bo Peng, Yang Luo, Dawei Liu, Qing Li, Tao Wang

“…Immunohistochemistry (IHC) was applied to identify the ALDOB level in a tissue microarray. Results The expression of ALDOB demonstrated a strong association with pathologic T stage, pathologic N stage, pathologic M stage, histologic grade, and gender. …”
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MicroRNA-135b Regulates Leucine Zipper Tumor Suppressor 1 in Cutaneous Squamous Cell Carcinoma. by Edit B Olasz, Lauren N Seline, Ashley M Schock, Nathan E Duncan, Argelia Lopez, Jozef Lazar, Michael J Flister, Yan Lu, Pengyuan Liu, Olayemi Sokumbi, Catherine A Harwood, Charlotte M Proby, Marcy Neuburg, Zelmira Lazarova

“…Immunohistochemical evaluation of 67 cSCC tumor tissues demonstrated that miR-135b expression inversely correlated with LZTS1 staining intensity and the tumor grade. …”
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Endothelial periostin regulates vascular remodeling by promoting endothelial dysfunction in pulmonary arterial hypertension by Dawn Lee, Heeyoung Lee, Ha-neul Jo, Eunsik Yun, Byung Su Kwon, Jongmin Kim, Aram Lee

“…Here, we demonstrated that POSTN upregulation correlates with PAH by analyzing a public microarray conducted on the lung tissues of patients with PAH and biological experimental results from in vivo and in vitro models. …”
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The Novel Action of miR-193b-3p/CDK1 Signaling in HCC Proliferation and Migration: A Study Based on Bioinformatic Analysis and Experimental Investigation by Xue Pang, Wei Wan, Xingxing Wu, Yu Shen

“…A growing number of novel targets underlying HCC pathophysiology have been detected using microarray high throughput screening platforms. This study carried out bioinformatics analysis to explore underlying biomarkers in HCC and assessed the potential action of the miR-193b-3p/CDK1 signaling pathway in HCC progression. …”
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Rab27a was identified as a prognostic biomaker by mRNA profiling, correlated with malignant progression and subtype preference in gliomas. by Hongjun Wang, Yan Zhao, Chuanbao Zhang, Mingyang Li, Chuanlu Jiang, Yongli Li

“…<h4>Experimental design</h4>We used a whole-genome mRNA expression microarray dataset of 220 glioma samples from the Chinese Glioma Genome Atlas (CGGA) database (http://www.cgga.org.cn) as a discovery set. …”
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Complex Loci in human and mouse genomes. by Pär G Engström, Harukazu Suzuki, Noriko Ninomiya, Altuna Akalin, Luca Sessa, Giovanni Lavorgna, Alessandro Brozzi, Lucilla Luzi, Sin Lam Tan, Liang Yang, Galih Kunarso, Edwin Lian-Chong Ng, Serge Batalov, Claes Wahlestedt, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Christine Wells, Vladimir B Bajic, Valerio Orlando, James F Reid, Boris Lenhard, Leonard Lipovich

“…Bidirectional promoters were characterized by variable transcriptional start sites and an identifiable midpoint at which overall sequence composition changed strand and the direction of transcriptional initiation switched. In microarray data covering a wide range of mouse tissues, genes in cis-antisense and bidirectionally promoted arrangement showed a higher probability of being coordinately expressed than random pairs of genes. …”
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Characterization of transcriptional changes in ERG rearrangement-positive prostate cancer identifies the regulation of metabolic sensors such as neuropeptide Y. by Petra Massoner, Karl G Kugler, Karin Unterberger, Ruprecht Kuner, Laurin A J Mueller, Maria Fälth, Georg Schäfer, Christof Seifarth, Simone Ecker, Irmgard Verdorfer, Armin Graber, Holger Sültmann, Helmut Klocker

“…We validated our meta-analysis using data from our own independent microarray study (n = 57). 84% and 49% (fold-change>2 and >1.5, respectively) of all transcriptional changes between ERG+ and ERG- prostate cancer determined by meta-analysis were verified in the validation study. …”
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Exploration of the shared pathways and common biomarkers in cervical and ovarian cancer using integrated bioinformatics analysis by Fang Liu, Min Wang, Tian Zhu, Cong Xu, Guangming Wang

“…Abstract Objective Searching for potential biomarkers and therapeutic targets for early diagnosis of gynecological tumors to improve patient survival. Methods Microarray datasets of cervical cancer (CC) and ovarian cancer (OC) were downloaded from the Gene Expression Omnibus (GEO) database, then, differential gene expression between cancerous and normal tissues in the datasets was analyzed. …”
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Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. by Anatoly Urisman, Ross J Molinaro, Nicole Fischer, Sarah J Plummer, Graham Casey, Eric A Klein, Krishnamurthy Malathi, Cristina Magi-Galluzzi, Raymond R Tubbs, Don Ganem, Robert H Silverman, Joseph L DeRisi

“…A viral detection DNA microarray composed of oligonucleotides corresponding to the most conserved sequences of all known viruses identified the presence of gammaretroviral sequences in cDNA samples from seven of 11 R462Q-homozygous (QQ) cases, and in one of eight heterozygous (RQ) and homozygous wild-type (RR) cases. …”
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Machine learning reveals CAT gene as a novel potential diagnostic and prognostic biomarker in non-small cell lung cancer by Yi Tian, Wen-ya Zhao, Yi-ru Liu, Wen-wen Song, Qiao-xin Lin, Yan-na Gong, Yi-ting Deng, Dian-na Gu, Ling Tian

“…Furthermore, immunohistochemical staining was performed in an independent cohort from a tissue microarray. Additionally, cell culture and RT-qPCR were employed for external validation. …”
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SMART: unique splitting-while-merging framework for gene clustering. by Rui Fa, David J Roberts, Asoke K Nandi

“…Moreover, two real microarray gene expression datasets are studied using this approach. …”
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Improving machine learning detection of Alzheimer disease using enhanced manta ray gene selection of Alzheimer gene expression datasets by Zahraa Ahmed, Mesut Çevik

“…However, the late enriched understanding of the genetic underpinnings of AD has been made possible due to recent advancements in data mining analysis methods, machine learning, and microarray technologies. However, the “curse of dimensionality” caused by the high-dimensional microarray datasets impacts the accurate prediction of the disease due to issues of overfitting, bias, and high computational demands. …”
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RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats. by B Alex Merrick, Dhiral P Phadke, Scott S Auerbach, Deepak Mav, Suzy M Stiegelmeyer, Ruchir R Shah, Raymond R Tice

“…We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG) than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL). …”
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Prediction of gene expression in embryonic structures of Drosophila melanogaster. by Anastasia A Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma

“…Here, we present a widely applicable computational approach, integrating developmental time-course microarray data with annotated in situ hybridisation studies, that facilitates the de novo prediction of tissue-specific expression for genes that have no in vivo gene expression localisation data available. …”
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