Peripheral DNA Methylation of Cortisol- and Serotonin-Related Genes Predicts Hippocampal Volume in a Pediatric Population by Taena Hanson, Sophia Spencer, Samantha A. Harker, Fatoumata Barry, Phoebe Burton, Jennifer Beauchemin, Sarah E. Mennenga, B. Blair Braden, Viren D'Sa, Daphne Koinis-Mitchell, Sean C.L. Deoni, Candace R. Lewis

“…Methods: Bilateral hippocampal volume was computed from T2-weighted images through FreeSurfer, and DNA methylation was measured from saliva using the Illumina MethylationEPIC microarray in a pediatric population (N = 248, females = 112, meanage = 5.13 years, SDage = 3.60 years). …”
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Mitochondrial dysfunction and fatigue in Sjögren’s disease by Astrid Rasmussen, Christopher J Lessard, A Darise Farris, Kristi A Koelsch, Biji T Kurien, Joshua Cavett, Kathy Sivilis, Robert Hal Scofield, John Aubrey Ice, Rebecca A Wood, Gavin Pharaoh, Valerie Lewis, Shylesh Bhaskaran, Holly Van Remmen

“…Using Seahorse, we analysed T cells for mitochondrial oxygen consumption rate (OCR) and extracellular acidification rate, which we assessed for correlation with fatigue measures. Using public microarray data available for 190 SjD and 32 healthy subjects, we identified a mitophagic transcriptional signature that stratified SjD patients into 5 discrete clusters. …”
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IL-6-induced long noncoding RNA MIR3142HG promotes tumorigenesis by interacting with thioredoxin-1 and STAT3 in human colorectal cancer by Daoquan Fang, Qian Feng, Baojian Zhou, Yangyang Liu, Yichu Lian, Yihui Zhang, Dichen Yang, Xintong Liu, Xiaomeng Shi, Wuhua Ni, Lei Jiang

“…Bioinformatics analysis and tissue microarray were utilized for evaluating the clinical value of MIR3142HG in CRC. …”
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CircATP5C1 promotes triple-negative breast cancer progression by binding IGF2BP2 to modulate CSF-1 secretion by Hongbo Liu, Haoqi Wang, Wei Gao, Yang Yuan, Tiantian Tang, Meixiang Sang, Fei Liu, Cuizhi Geng

“…We found a novel circRNA named circATP5C1, whose function in TNBC remains uncovered. Tissue microarray was used to analyze the association between the expression of circATP5C1 and the prognoses of TNBC patients. …”
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The potential of MCM8 as a biomarker in esophageal carcinoma: a comprehensive analysis integrating m6a methylation and angiogenesis by Xu-Sheng Liu, Yong Xu, Li-Song Dai, Ao Li, Jie Liu, Yu Zhang, Jin Xie, Zhi-Jun Pei

“…MCM8 expression in ESCA tissues was evaluated by immunohistochemical staining on a tissue microarray. Pearson correlation analysis identified co-expressed genes, followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. …”
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Transcriptomic Signatures of Antibody-mediated Rejection in Early Biopsies With Negative Histology in HLA-incompatible Kidney Transplantation by Petra Hruba, PhD, Jiri Klema, PhD, Petra Mrazova, PhD, Eva Girmanova, PhD, Katerina Jaklova, MS, Ludek Voska, MD, Martin Kment, MD, Martina Mackova, PhD, Klara Osickova, MD, Vladimir Hanzal, MD, Philip F. Halloran, MD, PhD, Ondrej Viklicky, MD, PhD

“…RNA sequencing from biopsies selected from the biobank was used in cohort 1 (n = 32) and microarray, including the molecular microscope (Molecular Microscope Diagnostic System [MMDx]) algorithm, in recent cohort 2 (n = 30). …”
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Siglec-9+ tumor-associated macrophages delineate an immunosuppressive subset with therapeutic vulnerability in patients with high-grade serous ovarian cancer by Yan Huang, Chen Zhang, Wei Jiang, Moran Yang, Guodong Zhang, Yiying Wang, Mengdi He, Haiou Liu, Kankan Cao

“…This study aimed to elucidate the prognostic significance of Siglec-9 expression and its predictive value for immunotherapy in HGSC.Methods Study enrolled two cohorts, consisting of 120 tumor microarray specimens of HGSC for immunohistochemistry (IHC) and 40 fresh tumor specimens for flow cytometry (FCM). …”
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Characterization of breast cancer tumors in older patients who show de novo resistance to endocrine therapy by Yumiko Ishizuka, Yoshiya Horimoto, Men Yuan, Yuko Ueki, Hiroko Onagi, Harumi Saeki, Takuo Hayashi, Tsuyoshi Saito, Takahiko Kawate, Takashi Ishikawa, Hidetaka Eguchi, Junichiro Watanabe, Goro Kutomi

“…Among these, CDKN3 retained significantly high expression in the PD group, even after analyzing more samples (log2 fold change, 1.99; P = 0.005). Public mRNA microarray data analysis revealed that patients with high CDKN3 tumors had worse outcomes. …”
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TCL1A in naïve B cells as a therapeutic target for type 1 diabetesResearch in context by Siweier Luo, Lina Zhang, Chunfang Wei, Chipeng Guo, Zhe Meng, Honghui Zeng, Lele Hou, Le Wang, Zulin Liu, Yufei Du, Shiyu Tan, Yating Zhang, Xiaoding Xu, Liyang Liang, Yiming Zhou

“…Using a protein phosphorylation microarray, we confirmed that TCL1A knockdown specifically impaired AKT2 phosphorylation and affected B cell survival and proliferation. …”
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Penaeus vannamei Genetic Evaluation for Growth and Survival Traits During White Spot Syndrome Virus Infection Based on 55K SNP Chip by Yijing HE, Mianyu LIU, Sheng LUAN, Jie KONG, Xupeng LI, Baoxiang CAO, Kun LUO, Jian TAN, Jiawang CAO, Ping DAI, Guangfeng QIANG, Zhaoxin WANG, Juan SUI, Xianhong MENG

“…Based on the survival time of individual resistance to WSSV within the family line, 590 individuals were uniformly selected and typed using 55K SNP liquid-phase microarrays to obtain genotypic data for certain individuals. …”
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Clinical significance and gene prediction of a novel classification system based on tacrolimus concentration-to-dose ratio in the early post-liver transplant period by Junwei Fan, Junwei Fan, Peihao Wen, Liyun Yuan, Yan Xia, Shijie Hu, Xiaoqing Zhang, Zhihai Peng, Zhihai Peng

“…All recipients and their corresponding donor livers from center 1 were genotyped using an Affymetrix DMET Plus microarray, and association analysis was performed using trough blood concentration/weight-adjusted-dose ratios (CDR, (ng/mL)/(mg/kg)). …”
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Single Center Characterization of a Cohort of Salivary Gland Carcinomas by Ria Winkelmann, Maja Weißgerber, Peter J. Wild, Julia Bein, Maximilian Fleischmann, Melanie Demes, Panagiotis Balermpas, Andreas Loth, Katrin Bankov, Jens von der Grün

“…We aimed to characterize the cohort of salivary gland cancers in our institute and generate a tissue microarray (TMA) with clinical data available for immunohistochemical analysis. …”
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Revealing the role of natural killer cells in ankylosing spondylitis: identifying diagnostic biomarkers and therapeutic targets by Yuling Chen, Yan Li, Yuan Xu, Qing Lv, Yuanchun Ye, Jieruo Gu

“…This study integrated bioinformatics methods with experimental validation to explore the role of natural killer (NK) cells in AS.Methods Two microarray datasets, GSE25101 and GSE73754, were selected, and the scRNA-seq data were obtained from GSE194315 and Liu’s research. …”
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Exploration of the potential neurotransmitter or neuromodulator-like properties of harmine: evidence from synthesis to synaptic modulation by Zhejun Xie, Ning Cao, Manlin Li, Hanxue Wang, Huida Guan, Xuemei Cheng, Changhong Wang

“…Subsequently, the release, metabolism, and uptake pathways of harmine were investigated using rat brain synaptosomes and primary neural cells through mass spectrometry analysis. A human proteome microarray was employed to screen for harmine-binding receptors, followed by experimental validation.Results:Adipocyte plasma membrane-associated protein isoform X1 (APMAP-X1) could effectively catalyze the Pictet-Spengler reaction in mammals to generate tetrahydroharmine, which was subsequently oxidized by myeloperoxidase (MPO) to produce harmine. …”
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PLCH1 overexpression promotes breast cancer progression and predicts poor prognosis through the ERK1/2-EGR1 axis by Jing Li, Fenge Jiang, Congcong Wang, Ping Sun, Lei Song, Jiannan Liu

“…However, its specific role in breast cancer progression, its association with clinicopathological features, and its prognostic significance remain unclear.MethodsPLCH1 expression was analyzed across multiple tumor types using the TNMplot database, which integrates RNA-seq, microarray, and normalized data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO), encompassing 40,442 tumor and 15,648 normal samples. …”
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Pharmacogenomic testing implementation: Tertiary care center experience and results of a pilot of 512 patients by Dana Bakheet, Hana Al Alshaykh, Ghadi Askar, Sateesh Maddirevula, Samya Hagos, Nasir Hamad Alshahrani, Midrar Alhusseini, Amani Moharram, Faries Algadhi, Osama Alswailim, Moatasem Alsulaim, Bandar Alamro, Fadl Elmula Mohamed Fadl Elmula, Bahadur Khan, Ahmed Almustafa, Ahmed Alshehri, Dimpna Brotons, Fahad Alajlan, Mohammed Alnahedh, Abdullah Alsuwaidan, Salah Baz, Ahmed Alfares

“…We used the PharmacoScan microarray-based test to perform genotyping. Results: To date, 512 patients have been tested. 97.5% of all patients have at least 1 gene with altered function. …”
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DSN1 may predict poor prognosis of lower-grade glioma patients and be a potential target for immunotherapy by Yulong Jia, Meiling Liu, Han Liu, Wenjia Liang, Qingyun Zhu, Chao Wang, Yake Chen, Yanzheng Gao, Zhendong Liu, Xingbo Cheng

“…We obtained 1046 LGG samples from the The Cancer Genome Atlas, The Chinese Glioma Genome Atlas (CGGA) microarray, and CGGA RNA-Seq databases. Bioinformatic methods (gene set enrichment analysis (GSEA), chi-square test, multivariate), and laboratory validation were used to investigate DSN1 in LGG. …”
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Exosomes containing circSCP2 in colorectal cancer promote metastasis via sponging miR-92a-1-5p and interacting with PTBP1 to stabilize IGF2BP1 by Qing Meng, Haoyi Xiang, Yijing Wang, Kepeng Hu, Xin Luo, Jiawei Wang, Engeng Chen, Wei Zhang, Jiaxin Chen, Xiaoyu Chen, Huogang Wang, Zhenyu Ju, Zhangfa Song

“…A competing endogenous RNA microarray was used to analyze circRNA expression in serum exosomes in patients with CRC at early and late stages. circSCP2 expression was evaluated using qRT-PCR. …”
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A comprehensive bioinformatics analysis of pathways and biomarkers shared between type 2 diabetes mellitus and chronic obstructive pulmonary disease by Tingting Hu, Xiaomei Duan, Jiale Gao, Zheng Li, Dan Xu, Jing Jing, Fengsen Li, Jianbing Ding, Li Ma, Min Jiang, Jing Wang

“…In this study, we aimed to identify common diagnostic markers for T2DM and COPD and their therapeutic potential.MethodsMicroarray data from the GEO database were analyzed to identify DEGs, whereas WGCNA, co-differential gene analyses were employed to identify co-expression modules and DEGs functions. …”
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LILR genotype imputation with attribute bagging (LIBAG): leukocyte immunoglobulin-like receptor copy number imputation system by Seik-Soon Khor, Seik-Soon Khor, Kouyuki Hirayasu, Kouyuki Hirayasu, Yosuke Kawai, Hie Lim Kim, Hie Lim Kim, Masao Nagasaki, Masao Nagasaki, Katsushi Tokunaga

“…However, the presence of CNVs in the leukocyte receptor complex (LRC) region complicates single nucleotide polymorphism (SNP) association analysis within commercially available SNP microarray datasets. This study introduces LILR Genotype Imputation with Attribute Bagging (LIBAG), a novel method for determining CNVs in LILRB3, LILRA6, and LILRA3 from commercially available SNP genotyping array datasets. …”
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