miRNA-REGULATED PATHWAYS OF CD8+ T CELLS IN TNBC MOUSE MODEL by Müge Öçal Demirtaş, Bala Gür Dedeoğlu

“…Following RNA isolation, miRNA microarray analysis was performed. Differentially expressed miRNAs between the groups were detected. …”
Get full text

Transcriptional Profile of Kidney from Type 2 Diabetic db/db Mice by Haojun Zhang, Tingting Zhao, Zhiguo Li, Meihua Yan, Hailing Zhao, Bin Zhu, Ping Li

“…The top 10 hub genes were selected from the constructed PPI network of DEGs, including Ccnb2 and Nr1i2, which remained largely unclear in DN. …”
Get full text

Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease by Lu-Mei Chi, Li-Ping Wang, Dan Jiao

“…This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. …”
Get full text

Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72. by Abhijit Sarkar, Barbara Reinhold-Hurek

“…For selected genes, differential expression was corroborated by real time RT-PCR studies.…”
Get full text

Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation. by Alexandra Dumitriu, Jeanne C Latourelle, Tiffany C Hadzi, Nathan Pankratz, Dan Garza, John P Miller, Jeffery M Vance, Tatiana Foroud, Thomas G Beach, Richard H Myers

“…Single-nucleotide polymorphisms (SNPs) selected from a recent meta-analysis of PD genome-wide association studies (GWAS) were successfully genotyped in 50 out of the 53 microarray brains, allowing a targeted expression-SNP (eSNP) analysis for 52 SNPs associated with PD affection at genome-wide significance and the 189 probes from FoxO1 regulated genes. …”
Get full text

Molecular profiles of tumor contrast enhancement: A radiogenomic analysis in anaplastic gliomas by Xing Liu, Yiming Li, Zhiyan Sun, Shaowu Li, Kai Wang, Xing Fan, Yuqing Liu, Lei Wang, Yinyan Wang, Tao Jiang

“…Gene set enrichment analysis (GSEA), significant analysis of microarray, generalized linear models, and Least absolute shrinkage and selection operator algorithm were used to explore radiogenomic and prognostic signatures of AG patients. …”
Get full text

Identifying a unique chromosomal pattern to predict the gemcitabine response in patients with cholangiocarcinoma by Sutheemon Techa-ay, Sasithorn Watcharadetwittaya, Raksawan Deenonpoe, Prakasit Sa-ngiamwibool, Chanita Panwoon, Watcharin Loilome, Poramate Klanrit, Anchalee Techasen, Yaovalux Chamgramol, Manida Suksawat, Napat Armartmuntree, Thomas O’Connor, Hideyuki Saya, Malinee Thanee

“…This signature pattern could provide the knowledge to improve a predictive biomarker for GEM response, benefitting for individual CCA patient management and chemotherapeutic selection.…”
Get full text

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. by Katherine James, Shereen Al-Ali, Jessica Tarn, Simon J Cockell, Colin S Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin T Pease, Paul Emery, Peter Lanyon, John A Hunter, Monica Gupta, Michele Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, UK Primary Sjögren’s Syndrome registry, Anil Wipat, Julia Newton, David E Jones, John Isaacs, Jennifer Hallinan, Wan-Fai Ng

“…Finally, gene set enrichment analysis (GSEA) was used as a feature selection technique for input into a support vector machine (SVM) classifier. …”
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

Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine. by Carina Valente, Jason Hinds, Francisco Pinto, Silvio D Brugger, Katherine Gould, Kathrin Mühlemann, Hermínia de Lencastre, Raquel Sá-Leão

“…Co-colonization, serotype identification, and relative serotype abundance were detected by analysis of DNA of the total bacterial growth of the primary culture plate using the plyNCR-RFLP method and a molecular serotyping microarray-based strategy. …”
Get full text

Immune-related gene characterization and biological mechanisms in major depressive disorder revealed based on transcriptomics and network pharmacology by Shasha Wu, Shasha Wu, Qing Jiang, Jinhui Wang, Jinhui Wang, Daming Wu, Yan Ren

“…Subsequently, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cytoscape plugin CluGO, and Gene Set Enrichment Analysis (GSEA) were utilized to identify immune-related genes. The final selection of immune-related hub genes was determined through the least absolute shrinkage and selection operator (Lasso) regression analysis and PPI analysis. …”
Get full text

Differentially expressed miR-3680-5p is associated with parathyroid hormone regulation in peritoneal dialysis patients. by Sohyun Jeong, Jung Mi Oh, Kook-Hwan Oh, In-Wha Kim

“…Total RNA from 15 patients (7 and 8 patients in the low and high iPTH groups, respectively) underwent miRNA microarray analysis, and three differentially upregulated (>2-fold change) miRNAs previously associated with human disease were selected for real-time quantitative PCR (qPCR) analysis. …”
Get full text

Identification and validation of diagnostic genes IFI44 and IRF9 in insomnia-associated autoimmune uveitis by Chao Wu, Hui Feng, Meng Tian, Baorui Chu, Xianyang Liu, Shuhao Zeng, Yakun Wang, Hong Wang, Shengping Hou, Qingfeng Liang

“…Least absolute shrinkage and selection operator regression was employed to screen for candidate biomarkers, and their diagnostic performance was evaluated using receiver operating characteristic (ROC) curves and quantitative polymerase chain reaction (qPCR). …”
Get full text

Epidemiology of group B streptococcal infection in pregnant women and diseased infants in mainland China by Jing Huang, Xin-Zhu Lin, Yao Zhu, Chao Chen

“…Serotype III was the dominant serotype that was observed in GBS isolates. GBS detection and identification has become more commonplace, due to the availability of polymerase chain reaction and DNA microarray technologies. …”
Get full text

Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma. by Kimberly Stegmaier, Jenny S Wong, Kenneth N Ross, Kwan T Chow, David Peck, Renee D Wright, Stephen L Lessnick, Andrew L Kung, Todd R Golub

“…<h4>Methods and findings</h4>A gene expression signature for the EWS/FLI off state was determined with microarray expression profiling of Ewing sarcoma cell lines with EWS/FLI-directed RNA interference. …”
Get full text

Increased cycling cell numbers and stem cell associated proteins as potential biomarkers for high grade human papillomavirus+ve pre-neoplastic cervical disease. by Maurice Canham, Chara Charsou, June Stewart, Sharon Moncur, Laura Hoodless, Ramya Bhatia, Duanduan Cong, Heather Cubie, Camille Busby-Earle, Alistair Williams, Victoria McLoughlin, John D M Campbell, Kate Cuschieri, Sarah Howie

“…As cancer is increasingly presumed to develop from proliferative, tumour initiating, cancer stem cells (CSCs), and as other oncogenic viruses induce stem cell associated gene expression, we evaluated whether presence of mRNA (detected by qRT-PCR) or proteins (detected by flow cytometry and antibody based proteomic microarray) from stem cell associated genes and/or increased cell proliferation (detected by flow cytometry) could be detected in well-characterised, routinely collected cervical samples from high risk HPV+ve women. …”
Get full text

Immune Condition of Colorectal Cancer Patients Featured by Serum Chemokines and Gene Expressions of CD4+ Cells in Blood by Takuya Komura, Masaaki Yano, Akimitsu Miyake, Hisashi Takabatake, Masaki Miyazawa, Norihiko Ogawa, Akihiro Seki, Masao Honda, Takashi Wada, Shigeyuki Matsui, Shuichi Kaneko, Yoshio Sakai

“…The differences in gene expression profiles of whole blood cells and cell subpopulations between CRC patients and healthy controls were analyzed using DNA microarray. Serum cytokine/chemokine concentrations in CRC patients and healthy controls were measured via multiplex detection immunoassays. …”
Get full text

Inference of cell type content from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis. by Megan Hastings Hagenauer, Anton Schulmann, Jun Z Li, Marquis P Vawter, David M Walsh, Robert C Thompson, Cortney A Turner, William E Bunney, Richard M Myers, Jack D Barchas, Alan F Schatzberg, Stanley J Watson, Huda Akil

“…Using this database, we predicted the relative cell type content for 833 human cortical samples using microarray or RNA-Seq data from the Pritzker Consortium (GSE92538) or publicly-available databases (GSE53987, GSE21935, GSE21138, CommonMind Consortium). …”
Get full text

Diverse regulated cell death patterns and immune traits in kidney allograft with fibrosis: a prediction of renal allograft failure based on machine learning, single-nucleus RNA seq... by Yuqing Li, Jiandong Zhang, Xuemeng Qiu, Yifei Zhang, Jiyue Wu, Qing Bi, Zejia Sun, Wei Wang

“…A 9-gene signature, termed RCD risk score (RCDI), was constructed using the least absolute shrinkage and selection operator and multivariate Cox regression algorithms. …”
Get full text

The potential crosstalk genes and molecular mechanisms between systemic lupus erythematosus and periodontitis by Kai Zhao, Xiaolong Li, Qingmiao Zhu, Mengyu Zhu, Jinge Huang, Ting Zhao

“…Random forest (RF) and Least Absolute Shrinkage and Selection Operator (Lasso) regression were employed to identify key hub genes. …”
Get full text