Clustering, Pathway Enrichment, and Protein-Protein Interaction Analysis of Gene Expression in Neurodevelopmental Disorders by Ruchi Yadav, Prachi Srivastava

“…In this study, we have used four samples of microarray neuronal developmental data: control, RV (resveratrol), NGF (nerve growth factor), and RV + NGF. …”
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Expression of Genes Related to Germ Cell Lineage and Pluripotency in Single Cells and Colonies of Human Adult Germ Stem Cells by Sabine Conrad, Hossein Azizi, Maryam Hatami, Mikael Kubista, Michael Bonin, Jörg Hennenlotter, Karl-Dietrich Sievert, Thomas Skutella

“…Genome-wide comparisons with microarray analysis confirmed that different haGSC colonies exhibited gene expression heterogeneity with more or less pluripotency. …”
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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. …”
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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. …”
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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.…”
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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. …”
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Tumor immune microenvironment permissive to metastatic progression of ING4-deficient breast cancer. by Emily Tsutsumi, Anne M Macy, Janine LoBello, Karen T Hastings, Suwon Kim

“…To characterize the tumor immune microenvironment associated with ING4-deficient tumors, three approaches were employed in this study: First, tissue microarrays composed of 246 primary breast tumors including 97 ING4-deficient tumors were evaluated for the presence of selective immune markers, CD68, CD4, CD8, and PD-1, using immunohistochemical staining. …”
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Mutation Spectrum of the ABCA4 Gene in a Greek Cohort with Stargardt Disease: Identification of Novel Mutations and Evidence of Three Prevalent Mutated Alleles by Kamakari Smaragda, Kokkinou Vassiliki, Koutsodontis George, Stamatiou Polixeni, Giatzakis Christoforos, Anastasakis Anastasios, Aslanides Ioannis Minas, Koukoula Stavrenia, Panagiotoglou Theoni, Datseris Ioannis, Tsilimbaris K. Miltiadis

“…A total of 59 patients were analyzed for ABCA4 mutations using the ABCR400 microarray and PCR-based sequencing of all coding exons and flanking intronic regions. …”
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Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker. by Aileen Marshall, Margus Lukk, Claudia Kutter, Susan Davies, Graeme Alexander, Duncan T Odom

“…Six genes identified by microarray as highly expressed in HH-HCC were confirmed by RT qPCR. …”
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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. …”
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The Necessity of Prenatal Diagnosis by CMA for the Women with NIPS-Positive Results by Jun Xu, Ying Xue, Jing Wang, Qin Zhou, Bin Zhang, Bin Yu, Ting Wang

“…Single nucleotide polymorphism array testing was performed on a commercial 750K microarray chip (Affymetrix CytoScan 750K Array). Results. …”
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Downregulation of sorting nexin 10 is associated with overexpression of miR-30d during liver cancer progression in rats by Nancy Cervantes-Anaya, Alberto Ponciano-Gómez, Guadalupe Soledad López-Álvarez, Christian Gonzalez-Reyes, Sergio Hernández-Garcia, María Asunción Cabañas-Cortes, José Efraín Garrido-Guerrero, Saúl Villa-Treviño

“…The identification of molecules that might be molecular markers or therapeutic targets is urgently needed to improve clinical management. Based on a microarray analysis performed in our laboratory, we selected six genes—namely, ANXA2, DYNLT1, PFKP, PLA2G7, KRT19 , and SNX10 —as candidates for validation as tumor markers of liver cancer in a rat model. …”
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HuoXueJieDu Formula Alleviates Diabetic Retinopathy in Rats by Inhibiting SOCS3-STAT3 and TIMP1-A2M Pathways by Hongliang Wang, Wei Xing, Shijie Tang, Zhenglin Wang, Tiantian Lv, Yan Wu, Shuzhen Guo, Chun Li, Jing Han, Ruixin Zhu, Wei Wang

“…Whole genome expression profiles in rat retinas were examined using microarray technology. Differential gene expression and pathway enrichment analysis were conducted on the microarray data, with validation through real-time PCR and immunohistochemical staining. …”
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ANALYSIS OF CELLULAR REACTION TO IFN-γ STIMULATION BY A SOFTWARE PACKAGE GeneExpressionAnalyser by A. V. Saetchnikov, M. M. Yatskou, P. V. Nazarov, L. Vallar, V. V. Apanasovich

“…The developed software has a number of advantages over the existing software: it is free, has a simple and intuitive graphical interface, allows to analyze different types of DNA microarrays, contains a set of methods for complete data analysis and performs effec-tive gene annotation for a selected list of genes.…”
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An Ensemble Classification Method for High-Dimensional Data Using Neighborhood Rough Set by Jing Zhang, Guang Lu, Jiaquan Li, Chuanwen Li

“…Efficient and effective sample classification and feature selection are challenging tasks due to high dimensionality and small sample size of microarray data. …”
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Bayesian weighted random forest for classification of high-dimensional genomics data by Oyebayo Ridwan Olaniran, Mohd Asrul A. Abdullah

“…In addition, BWRCF also has improved predictive and efficiency abilities over selected competing methods.…”
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Gene Expression Profiling in Organ Transplantation by Osama Ashry Ahmed Gheith

“…However, because microarray analyses are expensive and time consuming and their statistical evaluation is often very difficult, gene expression analysis using the RTPCR method is nowadays recommended. …”
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Rapid changes in transcription profiles of the Plasmodium yoelii yir multigene family in clonal populations: lack of epigenetic memory? by Deirdre Cunningham, Jannik Fonager, William Jarra, Celine Carret, Peter Preiser, Jean Langhorne

“…Using microarray and quantitative RT-PCR, we show that despite this very restricted transcription in a single cell, many yir genes are transcribed throughout the intra-erythrocytic asexual cycle. …”
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The Differential Gene Expression Pattern of Mycobacterium tuberculosis in Response to Capreomycin and PA-824 versus First-Line TB Drugs Reveals Stress- and PE/PPE-Related Drug Targ... by Li M. Fu, Shu C. Tai

“…Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. …”
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Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions. by Sergio Rojas-Galeano, Emily Hsieh, Dan Agranoff, Sanjeev Krishna, Delmiro Fernandez-Reyes

“…The resulting variable subsets achieved classification accuracies of 99% on Human African Trypanosomiasis, 91% on Tuberculosis, and 91% on Malaria serum proteomic profiles with fewer than 20% of variables selected. Our method scaled-up to dimensionalities of much higher orders of magnitude as shown with gene expression microarray datasets in which we obtained classification accuracies close to 90% with fewer than 1% of the total number of variables.…”
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