Analytic approaches to clinical validation of results from preclinical models of glioblastoma: A systematic review. by Beth Fitt, Grace Loy, Edward Christopher, Paul M Brennan, Michael Tin Chung Poon

“…In 14 studies published between 2017 and 2020 using TCGA RNA microarray data that should have the same cohort, the median number of patients was 464.5 (interquartile range 220.5-525). …”
Get full text

Bioinformatic identification of Single Nucleotide Polymorphisms (SNPs) in keratin-associated protein genes in alpacas (Vicugna pacos) by Deyanira Figueroa, Manuel More, Gustavo Gutiérrez, F. Abel Ponce de León

“…Of these, 35 SNPs were included in the 76K alpaca SNP microarray and 32 SNPs were confirmed in a population of 936 alpacas.…”
Get full text

Clinical experience of genome-wide non-invasive prenatal testing as a first-tier screening test in a cohort of 59,771 pregnancies. by Jianxin Zhen, Liting Zhang, Huilin Wang, Xi Chen, Weihong Wang, Lili Li, Quanfu Zhang

“…Fetal karyotype analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization were used for invasive diagnostic procedures, and postnatal outcomes were collected.…”
Get full text

MyD88 deficiency alters expression of antimicrobial factors in mouse salivary glands. by Takeshi Into, Toshiya Takigawa, Shumpei Niida, Ken-ichiro Shibata

“…In the present study, we assessed the influence of MyD88 deficiency on the oral innate defense, particularly the expression of antimicrobial proteins in salivary glands and production of salivary basal immunoglobulins, in mice. Microarray analysis of the whole tissues of submandibular glands revealed that the expression of several genes encoding salivary antimicrobial proteins, such as secretory leukocyte peptidase inhibitor (SLPI), S100A8, and lactotransferrin, was reduced due to MyD88 deficiency. …”
Get full text

Upregulated interleukin‐6 expression contributes to erlotinib resistance in head and neck squamous cell carcinoma by Aditya Stanam, Laurie Love-Homan, Tisha S. Joseph, Madelyn Espinosa-Cotton, Andrean L. Simons

“…Mechanisms of acquired resistance to the EGFR TKI erlotinib was investigated by developing erlotinib‐resistant HNSCC cell lines and comparing their gene expression profiles with their parental erlotinib‐sensitive HNSCC cell lines using microarray analyses and subsequent pathway and network analyses. …”
Get full text

Potential application of the bulk RNA sequencing in routine MPN clinics by Shenglong Li, Sanyun Wu, Mingli Xu, Xuedong Li, Xuelan Zuo, Yingying Wang

“…Additionally, data from the microarray datasets [GSE26049, GSE2191] were included in this study. …”
Get full text

Diagnostic value of C-reactive protein/ albumin ratio and TMTC1 in intracranial atherosclerotic stenosis in patients with acute cerebral infarction by Jinping Mo, Lin Liu, Zhe Li, Zongji Hu, Yuan Tan, Gen Long

“…Meanwhile, the differentially expressed genes (DEGs) in CI were identified through two Microarray profile GSE202518 and GSE180470. The receiver operating characteristics (ROC) curve analysis were performed to evaluate the sensitivity and specificity of CRP/ albumin ratio for the diagnosis of ICAS. …”
Get full text

Homozygous Microdeletion Involving Exon 1 of ERCC8 and NDUFAF2 With Uniparental Isodisomy of Chromosome 5 by Kaori Yamoto, Kosuke Yamada, Kenji Shimizu, Sachiko Miyamoto, Mitsuko Nakashima, Hirotomo Saitsu

“…Methods We performed chromosomal microarray analysis, exome sequencing (ES), and RNA sequencing (RNA‐seq) using the patient's urine‐derived cells on a patient with growth retardation and multiple congenital anomalies. …”
Get full text

Exploration of autophagy-related molecular mechanisms underlying epilepsy using multiple datasets by Yongfei Wang, Haoxuan Zeng, Chongxu Liu, Jianjun Chen, Yihong Huang, Xianju Zhou

“…Methods We analyzed GSE143272 and GSE4290 microarray datasets from the NCBI Gene Expression Omnibus database, which is established based on evaluations of peripheral blood samples. …”
Get full text

Mapping quantitative trait loci regions associated with Marek’s disease on chicken autosomes by means of selective DNA pooling by Ehud Lipkin, Jacqueline Smith, Morris Soller, David W. Burt, Janet E. Fulton

“…Allele substitution effects were calculated based on both pooled SNP microarray genotypes, and individual genotypes of QTLRs markers. …”
Get full text

Genetic variation and antioxidant response gene expression in the bronchial airway epithelium of smokers at risk for lung cancer. by Xuting Wang, Brian N Chorley, Gary S Pittman, Steven R Kleeberger, John Brothers, Gang Liu, Avrum Spira, Douglas A Bell

“…Prior microarray studies of smokers at high risk for lung cancer have demonstrated that heterogeneity in bronchial airway epithelial cell gene expression response to smoking can serve as an early diagnostic biomarker for lung cancer. …”
Get full text

Molecular profiles of HCV cirrhotic tissues derived in a panel of markers with clinical utility for hepatocellular carcinoma surveillance. by Ricardo C Gehrau, Kellie J Archer, Valeria R Mas, Daniel G Maluf

“…L(1)-penalized logistic regression model was fit for woHCC and wHCC microarrays, and tested against iHCC. Prediction model genes were validated in independent set by qPCR. …”
Get full text

Identification of the immune infiltration and biomarkers in ulcerative colitis based on liquid–liquid phase separation-related genes by Zhixing Hong, Shilin Fang, Haihang Nie, Jingkai Zhou, Yuntian Hong, Lan Liu, Qiu Zhao

“…Hub genes were screened that displayed high prediction accuracy of UC patients. Both the microarray and scRNA-seq datasets showed a strong correlation with immune cell infiltration and cytokines, especially GBP1, TRIM22, SRI. …”
Get full text

Seasonal changes in patterns of gene expression in avian song control brain regions. by Christopher K Thompson, John Meitzen, Kirstin Replogle, Jenny Drnevich, Karin L Lent, Anne Marie Wissman, Federico M Farin, Theo K Bammler, Richard P Beyer, David F Clayton, David J Perkel, Eliot A Brenowitz

“…We tested this by using the extracted RNA to perform a cDNA microarray hybridization developed by the SoNG initiative. …”
Get full text

Neutrophil Extracellular Traps Drive Kidney Stone Formation by Zhiming Yang, Xiong Chen, Guannan Qi, Jie Gu, Zheng Liu, Xiaobo Zhang

“… Introduction: This study aims to explore the contribution of neutrophil extracellular traps (NETs) to kidney stones. Methods: The microarray data from GSE73680 and bioinformatic analysis were applied to identify differentially expressed genes in patients with kidney stones. …”
Get full text

Development and validation of a programmed cell death index to predict the prognosis and drug sensitivity of gastric cancer by Feizhi Lin, Xiaojiang Chen, Chengcai Liang, Ruopeng Zhang, Guoming Chen, Ziqi Zheng, Bowen Huang, Chengzhi Wei, Zhoukai Zhao, Feiyang Zhang, Zewei Chen, Shenghang Ruan, Yongming Chen, Runcong Nie, Yuangfang Li, Baiwei Zhao

“…This study aimed to develop a novel prognostic indicator and marker of drug sensitivity in patients with gastric cancer (GC) based on PCD.MethodsWe analyzed genes associated with 14 distinct PCD patterns using bulk transcriptome data and clinical information from TCGA-STAD for model construction with univariate Cox regression and LASSO regression analyses. Microarray data from GSE62254, GSE15459, and GSE26901 were used for validation. …”
Get full text

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. by Shaun Mahony, Philip E Auron, Panayiotis V Benos

“…Prediction of the identity or the structural class of a protein that binds to a given DNA pattern will enhance the analysis of microarray and ChIP-chip data where frequently multiple putative targets of usually unknown TFs are predicted. …”
Get full text

Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas by Xueren Gao, Jianguo Wang, Shulong Zhang

“…The aim of the present study was to identify hub genes and pathways in ATC by microarray expression profiling. Two independent datasets (GSE27155 and GSE53072) were downloaded from GEO database. …”
Get full text

Rare Copy Number Variants Intersecting Parkinson’s-associated Genes in a Cohort of children With Autism Spectrum Disorders by Alina Erbescu, Sorina Mihaela Papuc, Magdalena Budișteanu, Maria Dobre, Catrinel Iliescu, Mihail Eugen Hinescu, Aurora Arghir, Monica Neagu

“…Our aim was to assess using a chromosomal microarray assay the frequency of rare exonic deletions that overlap with PD associated genes in a pediatric ASD group. …”
Get full text

A long non-coding RNA lncRNA-PE promotes invasion and epithelial–mesenchymal transition in hepatocellular carcinoma through the miR-200a/b-ZEB1 pathway by Yuan Shen, Shanshan Liu, Hanyu Yuan, Xiaomin Ying, Hanjiang Fu, Xiaofei Zheng

“…However, the detailed mechanisms underlying their activities are not fully understood. Using microarray technology, a number of long non-coding RNAs were previously identified to be aberrantly expressed in hepatocellular carcinoma. …”
Get full text