EsoDetect: computational validation and algorithm development of a novel diagnostic and prognostic tool for dysplasia in Barrett’s esophagus by Migla Miskinyte, Benilde Pondeca, José B. Pereira-Leal, Joana Cardoso

“…Specifically, for the diagnostic application, three RNAseq datasets were employed, while for the prognostic application, nine microarray datasets were identified, and 25 previously described genes were validated. …”
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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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Copy Number Variation of Immune-Related Genes and Their Association with Iodine in Adults with Autoimmune Thyroid Diseases by Xing Jin, Yunfeng Guan, Hongmei Shen, Yi Pang, Lixiang Liu, Qingzhen Jia, Fangang Meng, Xiaoye Zhang

“…Blood samples from 15 patients with AITD and 15 controls were assessed by chromosome microarray to identify candidate genes. The copy number of candidate genes and urinary iodine level was determined in adults from areas of different iodine statuses including 158 patients and 181 controls. …”
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Molecular Signatures of Recurrent Hepatocellular Carcinoma Secondary to Hepatitis C Virus following Liver Transplantation by Trina Das, Deborah L. Diamond, Matthew Yeh, Sajida Hassan, Janine T. Bryan, Jorge D. Reyes, James D. Perkins

“…Microarray analysis containing more than 29,000 known genes was performed on formalin-fixed-paraffin-embedded (FFPE) liver tissue from explanted livers. …”
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Metastatic melanoma: An integrated analysis to identify critical regulators associated with prognosis, pathogenesis and targeted therapies. by Zeinab Chaharlashkar, Yousof Saeedi Honar, Meghdad Abdollahpour-Alitappeh, Sepideh Parvizpour, Abolfazl Barzegar, Effat Alizadeh

“…We conducted an integrated analysis to identify critical regulators associated with the prognosis, pathogenesis, and targeted therapies of metastatic-melanoma. A microarray dataset, GSE15605, including 12 metastatic-melanoma and sixteen normal skin (NS) samples, were obtained from the GEO database. …”
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MicroRNA controlled adenovirus mediates anti-cancer efficacy without affecting endogenous microRNA activity. by Ryan Cawood, Suet-Ling Wong, Ying Di, Dilair F Baban, Leonard W Seymour

“…These were then filtered to select mRNAs that were only altered by Ad5mir122 and the remaining 21 mRNAs were compared to predicted mir122 targets. …”
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Prolonged application of high fluid shear to chondrocytes recapitulates gene expression profiles associated with osteoarthritis. by Fei Zhu, Pu Wang, Norman H Lee, Mary B Goldring, Konstantinos Konstantopoulos

“…Confirmation of the expression patterns of select genes was obtained by qRT-PCR. Using significance analysis of microarrays with a 5% false discovery rate, 71 and 60 non-redundant transcripts were identified to be ≥2-fold up-regulated and ≤0.6-fold down-regulated, respectively, in sheared chondrocytes. …”
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Early Regulation of Profibrotic Genes in Primary Human Cardiac Myocytes by Trypanosoma cruzi. by Aniekanabassi N Udoko, Candice A Johnson, Andrey Dykan, Girish Rachakonda, Fernando Villalta, Sammed N Mandape, Maria F Lima, Siddharth Pratap, Pius N Nde

“…The transcriptome microarray data, validated by quantitative Real-Time PCR, was also confirmed by immunoblotting and customized Enzyme Linked Immunosorbent Assays (ELISA) array showing significant increases in the protein expression levels of fibrogenic EGR1, SNAI1 and IL 6. …”
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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

“…The upregulated growth factors TGFβ2, CXCL12 and FGF10 were selected for further analysis because of previous associations with morphology. …”
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Investigating Single-Molecule Molecular Inversion Probes for Medium-Scale Targeted DNA Methylation Analysis by Roy B. Simons, Hieab H. H. Adams, Manfred Kayser, Athina Vidaki

“…Considering CpGs with at least 20X coverage, we yielded robust methylation detection with levels comparable to those obtained from the gold standard EPIC microarray analysis (Pearsons’s r: 0.96). Conclusions: The observed low specificity and uniformity indicate that smMIPs in their current form are not compatible with the lowered complexity of bisulfite-converted DNA.…”
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HSPA6 augments garlic extract-induced inhibition of proliferation, migration, and invasion of bladder cancer EJ cells; Implication for cell cycle dysregulation, signaling pathway a... by Seung-Shick Shin, Jun-Hui Song, Byungdoo Hwang, Dae-Hwa Noh, Sung Lyea Park, Won Tae Kim, Sung-Soo Park, Wun-Jae Kim, Sung-Kwon Moon

“…In addition, GE impeded the migration and invasion of EJ cells via inhibition of MMP-9 expression followed by decreased binding activities of AP-1, Sp-1, and NF-κB motifs. Based on microarray datasets, we selected Heat shock protein A6 (HSPA6) as the most up-regulated gene responsible for the inhibitory effects of GE. …”
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Cuproptosis-related signature and immune infiltration in age-related macular degeneration by Chen Li, Yi-Cheng Lu, Ming-Xuan Chen

“…METHODS: The expression profiles of cuproptosis-related genes and immune signature in AMD based on the microarray dataset GSE29801 were analyzed. A total of 142 AMD samples were used to identify the cuproptosis-related differentially expressed genes (Cu-DEGs), together with the immune cell infiltration. …”
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Chlamydiaceae in wild, feral and domestic pigeons in Switzerland and insight into population dynamics by Chlamydia psittaci multilocus sequence typing. by Prisca Mattmann, Hanna Marti, Nicole Borel, Martina Jelocnik, Sarah Albini, Barbara Renate Vogler

“…Subsequent species identification was performed by DNA-microarray assay, sequencing of a 16S rRNA gene fragment and a C. psittaci specific qPCR. …”
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Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. by Prabhakar Rajan, Caroline Dalgliesh, Phillippa J Carling, Thomas Buist, Chaolin Zhang, Sushma N Grellscheid, Kelly Armstrong, Jacqueline Stockley, Cedric Simillion, Luke Gaughan, Gabriela Kalna, Michael Q Zhang, Craig N Robson, Hing Y Leung, David J Elliott

“…Androgens drive the onset and progression of prostate cancer (PCa) by modulating androgen receptor (AR) transcriptional activity. Although several microarray-based studies have identified androgen-regulated genes, here we identify in-parallel global androgen-dependent changes in both gene and alternative mRNA isoform expression by exon-level analyses of the LNCaP transcriptome. …”
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Exploring the predictive values of SERP4 and FRZB in dilated cardiomyopathy based on an integrated analysis by Bin Qi, Hai-Yan Wang, Xiao Ma, Yu-Feng Chi, Chun Gui

“…Methods Five DCM-related microarray datasets were downloaded from the Gene Expression Omnibus (GEO). …”
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An immunomics approach to schistosome antigen discovery: antibody signatures of naturally resistant and chronically infected individuals from endemic areas. by Soraya Gaze, Patrick Driguez, Mark S Pearson, Tiago Mendes, Denise L Doolan, Angela Trieu, Donald P McManus, Geoffrey N Gobert, Maria Victoria Periago, Rodrigo Correa Oliveira, Fernanda C Cardoso, Guilherme Oliveira, Guilherme Oliveira, Rie Nakajima, Al Jasinskas, Chris Hung, Li Liang, Jozelyn Pablo, Jeffrey M Bethony, Philip L Felgner, Alex Loukas

“…Herein, we take advantage of recent advances in systems biology and longitudinal studies in schistosomiasis endemic areas in Brazil to pilot an immunomics approach to the discovery of schistosomiasis vaccine antigens. We selected mostly surface-derived proteins, produced them using an in vitro rapid translation system and then printed them to generate the first protein microarray for a multi-cellular pathogen. …”
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Complex patterns of chromosome 11 aberrations in myeloid malignancies target CBL, MLL, DDB1 and LMO2. by Thorsten Klampfl, Jelena D Milosevic, Ana Puda, Andreas Schönegger, Klaudia Bagienski, Tiina Berg, Ashot S Harutyunyan, Bettina Gisslinger, Elisa Rumi, Luca Malcovati, Daniela Pietra, Chiara Elena, Matteo Giovanni Della Porta, Lisa Pieri, Paola Guglielmelli, Christoph Bock, Michael Doubek, Dana Dvorakova, Nada Suvajdzic, Dragica Tomin, Natasa Tosic, Zdenek Racil, Michael Steurer, Sonja Pavlovic, Alessandro M Vannucchi, Mario Cazzola, Heinz Gisslinger, Robert Kralovics

“…Therefore, we studied chromosome 11 in a total of 813 samples from 773 individual patients with different myeloid malignancies by SNP microarrays and complemented the data with exome sequencing in selected cases exhibiting chromosome 11 defects. …”
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Identification of Novel Biomarkers in Huntington’s Disease Based on Differential Gene Expression Meta-Analysis and Machine Learning Approach by Nayan Dash, Md Abul Bashar, Jeonghan Lee, Raju Dash

“…Therefore, to discover the key biomarkers associated with the progression of HD, we employed bioinformatics and machine learning (ML) to create a robust pipeline that integrated differentially expressed gene (DEG) analysis with ML to select potential biomarkers. We performed a meta-analysis to identify DEGs using three Gene Expression Omnibus (GEO) microarray datasets from different platforms related to HD-affected brain tissue, applying both relaxed and strict criteria to identify differentially expressed genes. …”
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Circulating exosomal microRNAs as biomarkers of colon cancer. by Hiroko Ogata-Kawata, Masashi Izumiya, Daisuke Kurioka, Yoshitaka Honma, Yasuhide Yamada, Koh Furuta, Toshiaki Gunji, Hideki Ohta, Hiroyuki Okamoto, Hikaru Sonoda, Masatoshi Watanabe, Hitoshi Nakagama, Jun Yokota, Takashi Kohno, Naoto Tsuchiya

“…<h4>Experimental design</h4>Microarray analyses of miRNAs in exosome-enriched fractions of serum samples from 88 primary CRC patients and 11 healthy controls were performed. …”
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Integrated bioinformatic analysis of the shared molecular mechanisms between ANCA-associated vasculitis and atherosclerosis by Xun Hu, Inmaculada Xu Lou, Qilan Chen

“…This study aims to explore the mechanisms underlying the concurrent occurrence of ANCA and AS. Methods Microarray data of AAV and AS were examined in a comprehensive gene expression database. …”
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