Identification and validation of hub gene TNFAIP6 of fibroblast-like synoviocytes in rheumatoid arthritis by LEI Lei, LYU Yuxin, ZHANG Jing

“…Methods‍　‍Four independent synovial tissue microarray transcriptome sequencing datasets and one single cell sequencing dataset were downloaded from the Gene Expression Omnibus (GEO) database, and the hub gene of RA fibroblast-like synovial cells was identified by differential gene analysis, weighted gene co-expression network analysis (WGCNA) and single-cell sequencing data analysis. …”
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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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The proteomics of colorectal cancer: identification of a protein signature associated with prognosis. by Donna O'Dwyer, Lynda D Ralton, Aisling O'Shea, Graeme I Murray

“…Fifteen proteins that showed increased expression were validated by immunohistochemistry using a well characterised colorectal cancer tissue microarray containing 515 primary colorectal cancer, 224 lymph node metastasis and 50 normal colonic mucosal samples. …”
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Identification of circRNA Expression Profile and Potential Systemic Immune Imbalance Modulation in Premature Rupture of Membranes by Dongni Huang, Yuxin Ran, Ruixin Chen, Jie He, Nanlin Yin, Hongbo Qi

“…In this study, we displayed the expression profiles of circRNAs and mRNAs in plasma and fetal membranes of PROM and normal control (NC) groups based on circRNA microarray, the Gene Expression Omnibus database, and NCBI’s Sequence Read Archive. …”
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CDK5 Regulates Paclitaxel Sensitivity in Ovarian Cancer Cells by Modulating AKT Activation, p21Cip1- and p27Kip1-Mediated G1 Cell Cycle Arrest and Apoptosis. by Shu Zhang, Zhen Lu, Weiqun Mao, Ahmed A Ahmed, Hailing Yang, Jinhua Zhou, Nicholas Jennings, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, Roberto Miranda, Wei Qiao, Veera Baladandayuthapani, Zongfang Li, Anil K Sood, Jinsong Liu, Xiao-Feng Le, Robert C Bast

“…CDK5 protein was measured by immunohistochemical staining of an ovarian cancer tissue microarray to correlate CDK5 expression with overall patient survival. …”
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Deep sleep and parietal cortex gene expression changes are related to cognitive deficits with age. by Heather M Buechel, Jelena Popovic, James L Searcy, Nada M Porter, Olivier Thibault, Eric M Blalock

“…<h4>Conclusions</h4>The F344 rat appears to serve as a reasonable model for some common sleep architecture and cognitive changes seen with age in humans, including the cognitively disrupting influence of active period deep sleep. Microarray analysis suggests that the processes engaged by this sleep are consistent with its function. …”
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Inhibition of PDK modulates radiotherapy resistance in gastric cancer by Qi Zhang, Wanjia Qiao, Xiaoyu Liu, Jun Lu, Farooq Benish, Shuping Li, Xiaojun Liu

“…Abstract To explore the effect of sodium dichloroacetate (DCA), a pyruvate dehydrogenase kinase (PDK) inhibitor, on the progression of gastric cancer and resistance to radiotherapy, we analyzed histopathological microarrays from 60 gastric cancer and paracancerous tissues to determine PDK expression and its prognostic significance. 5-Ethynyl-2′-deoxyuridine (EdU) incorporation assay and Transwell migration assay were used to investigate the effects of PDK inhibition on gastric cancer cell proliferation and migration. …”
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Elevated expression of squamous cell carcinoma antigen (SCCA) is associated with human breast carcinoma. by Joseph M Catanzaro, Jennifer L Guerriero, Jingxuan Liu, Erica Ullman, Namratha Sheshadri, John J Chen, Wei-Xing Zong

“…Immunohistochemical analysis of SCCA expression was performed on tissue microarrays containing breast tumor tissues (n = 1,360) and normal breast epithelium (n = 124). …”
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Expression and correlation of Surfeit 4 gene in esophageal squamous cell carcinoma by Jun-xing Liu, Ting Lu, Yin Xia, Jun Yang, Ying-feng Jiang, Yan Zhao, Hong Yu

“…The results of the three methods indicated a significantly higher expression of SURF4 in the tumor group compared to both the adjacent paracancerous tissue group and the normal esophageal mucosal tissue group distant from the tumor. …”
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Prediction of CD8+ T cell infiltration in the tumor microenvironment of HGSOC patients by Jia Mai, Ling Yang, YuXin Chen, XiaoXu Zeng, HongJian Xie, XiaoJuan Liu

“…Two independent cohort were analyzed: (1) A multicenter tissue microarray (TMA) cohort of 105 epithelial ovarian cancer cases revealed that high CD8+ T cell density in tumor parenchyma, stroma, or whole tissue was significantly associated with good prognosis. (2) A retrospective cohort of 95 HGSOC patients from West China Second University Hospital (2016–2020) demonstrated that peripheral blood lymphocytes, globulin (GLB), lactate dehydrogenase (LDH), and low-density lipoprotein (LDL) correlated with CD8+ T cell infiltration in TME. …”
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α5-nAChR/NETO2 contributed to chronic stress-promoted lung adenocarcinoma progression by Jingting Wang, Jiaying Cai, Zengping Wang, Shuran Yang, Jing Wang, Yanfei Jia, Haiji Sun, Xiaoli Ma

“…Results α5-nAChR expression was related to NETO2 expression, low survival rate, staging as well as smoking status in LUAD dataset as well as tissue microarrays. The correlation between α5-nAChR and NETO2 was validated in nude mice xenograft tissues. α5-nAChR as well as NETO2 expression correlated in CRS and CUMS mice tissues. …”
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mRNA ratios of AR to ESR1 and PGR distinguish breast cancer subtypes based on public datasets and experimental models by Diego Prieto, Milena Rondón-Lagos, Paola Cruz-Tapias, Andrés Rincón-Riveros, Wilson Rubiano, Jairo De la Peña, Elizabeth Vargas, Victoria E. Villegas, Nelson Rangel

“…Here, we conducted a meta-analysis of large-scale microarray transcriptomic datasets to evaluate whether the mRNA expression levels of the androgen receptor gene, relative to those of the estrogen receptor gene (AR/ESR1 ratio) and the progesterone receptor gene (AR/PGR ratio), can help differentiate BC tumor subtypes. …”
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Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry by Farzad Ghafouri, Abolfazl Bahrami, Abolfazl Bahrami, Mostafa Sadeghi, Seyed Reza Miraei-Ashtiani, Maryam Bakherad, Herman W. Barkema, Samantha Larose

“…This approach revealed a new insight to better understand the biological processes associated with adipose tissue.…”
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Dermal fibroblast transcriptome indicates contribution of WNT signaling pathways in the pathogenesis of Apert syndrome by Arda Çetinkaya, Ekim Taşkıran, Tutku Soyer, Pelin Özlem Şimşek-Kiper, Gülen Eda Utine, Gökhan Tunçbilek, Koray Boduroğlu, Mehmet Alikaşifoğlu

“… Cranial sutures are unossified connective tissue structures between the cranial bones, which allow expansion of these bones during development. …”
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Stromal Caveolin-1 and Caveolin-2 Expression in Primary Tumors and Lymph Node Metastases by Wladimir Gerstenberger, Michaela Wrage, Eeva Kettunen, Klaus Pantel, Sisko Anttila, Stefan Steurer, Harriet Wikman

“…The expression of these two genes was investigated at protein level on a tissue microarray (TMA) consisting of 161 primary tumor samples. 50.7% of squamous cell lung cancer (SCC) tumors showed strong expression of CAV1 in the tumor-associated stromal cells, whereas only 15.1% of adenocarcinomas (AC) showed a strong CAV1 expression (p<0.01). …”
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Long-Term Aerobic Exercise Enhances Hepatoprotection in MAFLD by Modulating Exosomal miR-324 via ROCK1 by Yang Zhang, Qiangman Wei, Xue Geng, Guoliang Fang

“…Post-exercise, precursor and mature miR-324 increased in adipose tissue and decreased in muscle, suggesting its adipose origin and inverse regulation. …”
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HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. …”
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Adrenocortical carcinoma survival gene HMMR was identified as being targeted by fluorouracil and epirubicin using a gene coexpression network-based drug repositioning strategy by Zahra Jafari, Seyed-Morteza Javadirad, Seyede Elmira Yazdi Rouholamini

“…A total of 139 human specimens were examined, comprising 106 metastatic ACCs, 14 benign adrenocortical adenomas (ACAs), and 19 normal adrenal cortex tissues. Hub genes were identified using weighted correlation network analysis (WGCNA), and their differential expression was confirmed by microarrays and RNA sequencing. …”
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TRIM13 prevents cardiomyocyte injury by affecting apoptosis through interacting with CD3D in myocardial infarction by Feipeng Wu, Xiandong Zheng, Qiyan Wu, Liju Hong, Lei Yue, Rui Yang, Dandan Chen, Youjun Zhou

“…A mouse model of MI was established, and cardiac tissue sample microarray data and GSE236374 dataset were collected to screen and 120 upregulation and 15 downregulation genes were obtained, and related to T cells and cell immunity. …”
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Immunohistochemical evaluation of colorectal carcinoma: experience of a four-year study by Muchalapuri Sravani, Fatima Fatima, Rasheed Fatima, K. N. Deepthi, Shilpa Karamchedu, Shaikh Nishadbanu, Allam Swetha

“…A retrospective study was performed on 36 paraffin blocks of documented colorectal carcinomas were stained by immunohistochemical technique using a tissue microarray with CK7, CK20 and CDX2 markers. …”
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