Integrated analysis of genomic and transcriptomic profiles identified a prognostic immunohistochemistry panel for esophageal squamous cell cancer by Yue Yu, Zhihua Li, Chenjun Huang, Haisheng Fang, Fei Zhao, Yue Zhou, Xianglong Pan, Qifan Li, Yu Zhuang, Liang Chen, Jing Xu, Wei Wang

“…Methods An integrated analysis was performed to screen and establish a prognostic panel using exome sequencing profile from 81 pairs of ESCC samples and RNA expression microarray data from 119 ESCC subjects. Two independent ESCC cohorts were recruited as training and validation groups to test the prognostic value. …”
Get full text

Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences. by A A Shea, R C Bernhards, C K Cote, C J Chase, J W Koehler, C P Klimko, J T Ladner, D A Rozak, M J Wolcott, D P Fetterer, S J Kern, G I Koroleva, S P Lovett, G F Palacios, R G Toothman, J A Bozue, P L Worsham, S L Welkos

“…Microscopic and colony morphology differences on six differential media were observed and only the Rough variant metabolized sugars in selective agar. Antimicrobial susceptibilities and lipopolysaccharide (LPS) features were characterized and phenotype microarray profiles revealed distinct metabolic and susceptibility disparities between the variants. …”
Get full text

A multi-omic meta-analysis reveals novel mechanisms of insecticide resistance in malaria vectors by Sanjay C. Nagi, Victoria A. Ingham

“…This study, employing a cross-species approach, integrates RNA-Sequencing, whole-genome sequencing, and microarray data to elucidate drivers of insecticide resistance in Anopheles gambiae complex and An. funestus. …”
Get full text

Deep learning-based spatial analysis on tumor and immune cells of pathology images predicts MIBC prognosis. by Chao Hu, Fan Wang, Hui Xu, XiQi Dong, XiuJuan Xiong, Yun Zhang, TianCheng Zhao, YuanQiao He, LiBin Deng, XiongBing Lu

“…Lymph_inside % can be an effective biomarker for predicting MIBC prognosis. …”
Get full text

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

“…Functional analyses do not fully explain the selective pressure causing ERG rearrangement during the development of prostate cancer. …”
Get full text

Research on the diagnosis model of osteoarthritis based on methylation-related genes using machine learning algorithms by Xu Cui, Houlin Ji, Shengyang Guo, Ju Liu, Linyuan Zhang, Yongwei Jia, Yin Cui, Xiaoxiao Zhou

“…ObjectiveTo construct a diagnostic model of osteoarthritis related to methylation genes using machine learning algorithms, and analyze its prognostic value and biological functions.MethodsThe GSE 63695 and GSE162484 datasets including human osteoarthritis (OA) and normal samples were downloaded from the GEO datasets. The microarray chip data of chondrocytes were analyzed using R software to obtain differentially methylated genes. …”
Get full text

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

“…The genetic correlation between the survival time of individuals against WSSV and SS50 was 0.95±0.03, which was not significantly different from 1 (P > 0.05).The study showed that the genetic assessment of the growth of P. vannamei by microarray can effectively improve the accuracy of the assessment, the evaluation of WSSV survival time traits may be affected by the selection of individuals and other factors, and the prediction accuracy was not significantly improved. …”
Get full text

A first large study of whole-exome sequencing (WES) in 489 patients with suspected rare genetic disorders at a tertiary centre in Malaysia by Lip Hen Moey, Go Hun Seo, Boon Eu Cheah, Wee Teik Keng, Hane Lee, Gaik Siew Ch’ng

“…Whole exome sequencing (WES) is a comprehensive test that can detect not only many of the same large deletions and duplications as CMA, but also detect other genetic variants that are detected by gene panels. …”
Get full text

Activation of PTGS2/NF‐κB signaling pathway enhances radiation resistance of glioma by Cheng Tan, Liang Liu, Xiaoyang Liu, Ling Qi, Weiyao Wang, Guifang Zhao, Libo Wang, Yimeng Dai

“…Methods We downloaded the microarray data from the Gene Expression Omnibus (GEO) database. …”
Get full text

NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes by Michael Chang, Mohamed Sherief, Maria Ioannou, Viveka Chinnasamy, Lucy Chen, Michael Frost, Michelle Mattson-Hoss, Herb Sarnoff, David O. Kamson, Matthias Holdhoff, Debraj Mukherjee, Chetan Bettegowda, Jordina Rincon-Torroella, Victoria Croog, Peng Huang, Fausto J. Rodriguez, Calixto-Hope G. Lucas, Karisa C. Schreck

“…Methods We assembled a single-institution, retrospective cohort of 542 IDH-wildtype GBM with somatic next generation sequencing to investigate the frequency and nature of detected NF1 alterations. We selected 69 GBMs from which to build a tissue microarray (TMA) of 44 NF1-wildtype and 25 NF1-mutant cases. …”
Get full text

A retrospective analysis of prenatal genetic results in fetal hydronephrosis. by Keqin Jin, Xiayuan Xu, Yue Qian, Liping Zhang, Min Hu, Jianfeng Luo

“…<h4>Objective</h4>To discuss the application value of technologies such as chromosome microarray analysis (CMA) in fetuses with hydronephrosis and pyelectasis.…”
Get full text

Evaluation of gene expression classification studies: factors associated with classification performance. by Putri W Novianti, Kit C B Roes, Marinus J C Eijkemans

“…The MAQC II study on cancer classification problems has found that performance was affected by factors such as the classification algorithm, cross validation method, number of genes, and gene selection method. In this paper, we study the hypothesis that the disease under study significantly determines which method is optimal, and that additionally sample size, class imbalance, type of medical question (diagnostic, prognostic or treatment response), and microarray platform are potentially influential. …”
Get full text

Sperm associated antigen 9 (SPAG9) a promising therapeutic target of ovarian carcinoma by Nirmala Jagadish, Rukhsar Fatima, Aditi Sharma, Sonika Devi, Vitusha Suri, Vikash Kumar, Anil Suri

Get full text

MicroRNA let-7f protects against H2O2-induced oxidative damage in neuroblastoma cells by targeting AKT-2 by Kuo Li, Zhan-Qiang Wang, Jun-Ling Zhang, Pei-Yuan Lv

“…Material and methods miRNA microarray analysis was performed to detect the miRNAs’ differential expression in AD patients and normal elderly volunteers. …”
Get full text

Endoplasmic reticulum stress-related CLIP4 plays a procarcinogenic role in hepatocellular carcinoma: an integrated analysis by Anqi Wang, Sitong Yan, Weijia Jiang, Xiang Chen, Yuhan Huang, Xiangyu Zu, Xiao Du, Lulu Fan, Jiatao Liu, Guoping Sun

“…CCK-8, colony formation, EdU staining, wound-healing, Transwell, western blotting and RT-qPCR were used to detect the effects of CLIP4 on the proliferation, migration and epithelial-mesenchymal transition (EMT) of HCC cells. …”
Get full text

Machine learning-based single-sample molecular classifier for cancer grading by Zoia Antysheva, Nikita Kotlov, Mariia V. Guryleva, Ivan Valiev, Viktor Svekolkin, Anna Belozerova, Sheila T. Yong, Dmitry Tabakov, Alexander Bagaev, Vladimir Kushnarev

“…Next, we showed that mGrades were effective in assessing risk levels for G2 samples. …”
Get full text

Identification of Hub Biomarkers and Immune and Inflammation Pathways Contributing to Kawasaki Disease Progression with RT-qPCR Verification by Hongjun Ba, Lili Zhang, Huimin Peng, Xiufang He, Yuese Lin, Xuandi Li, Shujuan Li, Ling Zhu, Youzhen Qin, Xing Zhang, Yao Wang

“…Patients and Methods. Gene microarray data were collected from the Gene Expression Omnibus database. …”
Get full text

HDAC1 Mediates Immunosuppression of the Tumor Microenvironment in Non-Small Cell Lung Cancer by Fan Y, Ji X, Yuan K, Wu Q, Lou M

“…However, there are no studies on the immunological aspects of HDAC1 in non-small cell lung cancer (NSCLC).Methods: In this research, we used the Cancer Genome Atlas (TCGA) public database combined with tissue microarray (TMA) to investigate HDAC1 expression and prognosis in NSCLC. …”
Get full text

Bioinformatics meets machine learning: identifying circulating biomarkers for vitiligo across blood and tissues by Qiyu Wang, Jingwei Yuan, Jingwei Yuan, Mengdi Zhang, Haiyan Jia, Hongjie Lu, Yan Wu

“…The merged microarray data were then used for WGCNA to identify modules of features genes. …”
Get full text

A retrospective analysis of 6942 amniocentesis cases by Qingsha An, Yuxiao Huang, Feifei Yu, Yilun Tao, Juan Li, Xiaoze Li

“…Among the single-method cases, Chromosomal Microarray Analysis (CMA) was the most frequently selected technique (14.18%). …”
Get full text