Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola. by Xiao-bo Xue, Li-fang Zou, Wen-xiu Ma, Zhi-yang Liu, Gong-you Chen

“…In the present study, in silicon microarray data demonstrated that the expression of 17 HrpX-regulated protein (Xrp) genes of X. oryzae pv. oryzicola (Xoc), which causes bacterial leaf streak in rice, were either positively or negatively regulated by HrpX or/and HrpG. …”
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Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection. by Tomoki Yoshikawa, Terence E Hill, Naoko Yoshikawa, Vsevolod L Popov, Cristi L Galindo, Harold R Garner, C J Peters, Chien-Te Kent Tseng

“…Thus, a comprehensive evaluation of the complex epithelial signaling to SARS-CoV is crucial for paving the way to better understand SARS pathogenesis. Based on microarray-based functional genomics, we report here the global gene response of 2B4 cells, a cloned bronchial epithelial cell line derived from Calu-3 cells. …”
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Omalizumab Treated Urticaria Patients Display T Cell and Thrombocyte‐Associated Gene Regulation by Anna Smola, Heike C. Hawerkamp, Péter Oláh, Andreas Kislat, Nicole Duschner, Bernhard Homey, Stephan Meller

“…Results Our messenger RNA and microRNA microarray analyses revealed the greatest changes in expression levels on Day 2 after the first omalizumab dose. …”
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Morphological features and activity of estrogen receptors of endometrium and foci of adenomyosis in postmenopausal patients by V. A. Sitnikova, L. G. Rosha, G. Y. Honcharenko

“…IHC blocks were produced by the method of Tissue Microarray. The expression of estrogen markers was evaluated according to point system of general staining method for ER-status determining. …”
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Identification of responsive genes and analysis of genes with bacterial-inducible cis-regulatory elements in the promoter regions in Oryza sativa L. by Abbas SAIDI, Zohreh HAJIBARAT, Zahra HAJIBARAT

“…In order to study rice responsive genes to bacterial stress, microarray data were retrieved from GEO dataset. To identify the responsive genes to biotic stress (bacteria) bioinformatic tools were employed and the data presented in the forms of heatmap, gene ontology, gene network, and cis-element prediction were used. …”
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microRNA expression in peripheral blood cells following acute ischemic stroke and their predicted gene targets. by Glen C Jickling, Bradley P Ander, Xinhua Zhan, Dylan Noblett, Boryana Stamova, Dazhi Liu

“…Differentially expressed miRNA in patients with ischemic stroke were determined by microarray with qRT-PCR confirmation. The gene targets and pathways associated with ischemic stroke that may be regulated by the identified miRNA were characterized.…”
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The Aquaporin gene family of the yellow fever mosquito, Aedes aegypti. by Lisa L Drake, Dmitri Y Boudko, Osvaldo Marinotti, Victoria K Carpenter, Angus L Dawe, Immo A Hansen

“…Phylogenetic analysis showed that five of the six Ae. aegypti AQPs have high similarity to classical water-transporting AQPs of vertebrates. Using microarray, reverse transcription and real time PCR analysis we found that all six AQPs are expressed in distinct patterns in mosquito tissues/body parts. …”
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Molecular characterization of Pseudomyxoma peritonei with single-cell and bulk RNA sequencing by Ye Jin Ha, Seong-Hwan Park, Seon-Kyu Kim, Ka Hee Tak, Jeong-Hwan Kim, Chan Wook Kim, Yong Sik Yoon, Seon-Young Kim, Jong Lyul Lee

“…We also offer protein expression data from a tissue microarray (TMA) analysis of 90 samples (45 PMPs). Our single-cell and bulk transcriptomic profiles, along with TMA verifications, reveal the cellular diversity of PMP, highlighting the coexistence of epithelial and mesenchymal characteristics within PMP cells. …”
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In Silico Network Toxicology, Molecular Docking, and Multi‐Level Bioinformatics Reveal Methyl Eugenol‐Induced Hepatocellular Carcinoma Mechanisms in Humans by Fuat Karakuş, Zübeyde Tanrıverdi, Burak Kuzu

“…Molecular docking studies demonstrated weak binding affinities of ME to these targets compared to their specific inhibitors. However, microarray data and survival analyses of human HCC samples revealed that AURKB, CCNB1, CDK1, and PLK1 are upregulated in HCC, with higher expression levels correlating with poorer overall survival, particularly for CCNB1. …”
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Neurotransmission Sex Dichotomy in the Rat Hypothalamic Paraventricular Nucleus in Healthy and Infantile Spasm Model by Dumitru Andrei Iacobas, Jana Veliskova, Tamar Chachua, Chian-Ru Chern, Kayla Vieira, Sanda Iacobas, Libor Velíšek

“…Publicly available microarray data were used to characterize each gene in each condition for both sexes by the independent transcriptomic features: average expression level, control of the transcript abundance, and expression correlation with every other gene. …”
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The multicopy gene Sly represses the sex chromosomes in the male mouse germline after meiosis. by Julie Cocquet, Peter J I Ellis, Yasuhiro Yamauchi, Shantha K Mahadevaiah, Nabeel A Affara, Monika A Ward, Paul S Burgoyne

“…Here, we generate transgenic mice producing small interfering RNAs that specifically target the transcripts of the MSYq-encoded multicopy gene Sly (Sycp3-like Y-linked). Microarray analyses performed on these Sly-deficient males and on MSYq-deficient males show a remarkable up-regulation of sex chromosome genes in spermatids. …”
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Advanced Molecular-Genetic Methods and Prospects for Their Application for the Indication and Identification of <i>Yersinia pestis</i> Strains by K. A. Nikiforov

“…The main groups of methods considered are as follows: based on the analysis of the lengths of restriction fragments (ribo- and IS-typing, pulse gel electrophoresis); based on the analysis of specific fragments (DFR typing, VNTR typing); based on sequencing (MLST, CRISPR analysis, SNP analysis); PCR methods (including IPCR, SPA); isothermal amplification methods (LAMP, HDA, RPA, SEA, PCA, SHERLOCK); DNA-microarray; methods using aptamer technology; bio- and nano-sensors; DNA origami; methods based on neural networks. …”
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Functional and transcriptional characterization of human embryonic stem cell-derived endothelial cells for treatment of myocardial infarction. by Zongjin Li, Kitchener D Wilson, Bryan Smith, Daniel L Kraft, Fangjun Jia, Mei Huang, Xiaoyan Xie, Robert C Robbins, Sanjiv S Gambhir, Irving L Weissman, Joseph C Wu

“…We investigated the transcriptional changes that occur during endothelial differentiation of hESCs using whole genome microarray, and compared to human umbilical vein endothelial cells (HUVECs). …”
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Putting into practice domain-linear motif interaction predictions for exploration of protein networks. by Katja Luck, Sadek Fournane, Bruno Kieffer, Murielle Masson, Yves Nominé, Gilles Travé

“…PDZ domains recognise short sequence motifs at the extreme C-termini of proteins. A model based on microarray data has been recently published for predicting the binding preferences of PDZ domains to five residue long C-terminal sequences. …”
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B-cell epitopes in NTS-DBL1α of PfEMP1 recognized by human antibodies in Rosetting Plasmodium falciparum. by Letusa Albrecht, Davide Angeletti, Kirsten Moll, Karin Blomqvist, Davide Valentini, Fabio Luiz D'Alexandri, Markus Maurer, Mats Wahlgren

“…The plasma-reactivity in a microarray, consisting of 96 overlapping 15-mer long peptides covering the NTS-DBL1α domain from IT4var60 sequence, was compared with their capacity to disrupt rosettes and we identified five peptides where the reactivity were correlated. …”
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FOXO4-DRI induces keloid senescent fibroblast apoptosis by promoting nuclear exclusion of upregulated p53-serine 15 phosphorylation by Yu-Xiang Kong, Zhi-Shuai Li, Yuan-Bo Liu, Bo Pan, Xin Fu, Ran Xiao, Li Yan

“…The up-regulated p53-serine15 phosphorylation (p53-pS15) in keloids is identified by phosphospecific protein microarray and western blotting. We further demonstrate that a senolytic FOXO4-D-retro-inverso-isoform peptide (FOXO4-DRI) promotes apoptosis and decreases G0/G1 phase cells in pro-senescence models of keloid organ cultures and fibroblasts, accompanied with p53-pS15 nuclear exclusion. …”
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Interleukin-27 is a potent inhibitor of cis HIV-1 replication in monocyte-derived dendritic cells via a type I interferon-independent pathway. by Qian Chen, Sanjay Swaminathan, De Yang, Lue Dai, Hongyan Sui, Jun Yang, Ronald L Hornung, Yanmei Wang, Da Wei Huang, Xiaojun Hu, Richard A Lempicki, Tomozumi Imamichi

“…Of note, other IL-12 family members (IL-12, IL-23 and IL-35) had no effect on HIV-1 replication. Microarray studies of IL-27 treated DCs showed no up-regulation of Type I (IFN) gene expression. …”
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Specific Inflammatory Stimuli Lead to Distinct Platelet Responses in Mice and Humans. by Lea M Beaulieu, Lauren Clancy, Kahraman Tanriverdi, Emelia J Benjamin, Carolyn D Kramer, Ellen O Weinberg, Xianbao He, Samrawit Mekasha, Eric Mick, Robin R Ingalls, Caroline A Genco, Jane E Freedman

“…At week 9, these cells individually localized to the spleen, while Western diet resulted in increased platelet-neutrophil aggregates in the spleen only. Microarray analysis of platelet RNA from infected or Western diet-fed mice at week 1 and 9 showed differential profiles. …”
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Treatment with Rhizoma Dioscoreae Extract Has Protective Effect on Osteopenia in Ovariectomized Rats by Zhiguo Zhang, Lihua Xiang, Dong Bai, Xiaowei Fu, Wenlai Wang, Yan Li, Hong Liu, Jinghua Pan, Ya’nan Li, Gary Guishan Xiao, Dahong Ju

“…Our results show that RDE could inhibit bone loss of OVX rats after a 12-week treatment. The microarray analysis showed that 68 genes were upregulated and that 100 genes were downregulated in femurs of the RDE group rats compared to those in the OVX group. …”
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Bioinformatics and network pharmacology-based study to elucidate the multi-target pharmacological mechanism of the indigenous plants of Medina valley in treating HCV-related hepato... by Mubarak A. Alamri

“…At first, the information related to active compounds of eight indigenous plants was retrieved from public databases and through literature review which was later combined with differentially expressed genes (DEGs) obtained through microarray datasets. Later, a compound-target genes-disease network was constructed which uncovered that kaempferol, rhazimol, beta-sitosterol, 12-Hydroxy-3-keto-bisnor-4-cholenic acid, 5-O-caffeoylquinic acid, 24-Methyldesmosterol, stigmasterone, fucosterol, and withanolide_J decisively contributed to the cell growth and proliferation by affecting ALB and PTGS2 proteins. …”
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