SPP1 mRNA Expression Is Associated with M2 Macrophage Infiltration and Poor Prognosis in Triple-Negative Breast Cancer by Yu-Chia Chen, Chia-Ching Chen, Rong-Fu Chen, Hsin-Hung Chen, Po-Ming Chen

“…Additionally, we examined SPP1 mRNA expression datasets available in the Kaplan–Meier plotter and investigated the SPP1 protein expression patterns in our own tissue microarray cohort via immunohistochemistry. (3): The results revealed that genes associated with the Toll-like receptor signaling pathway showed a significant increase in activity in TNBC tissues when compared to normal breast tissues. …”
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A diet high in glucose and deficient in dietary fibre causes fat accumulation in the liver without weight gain by Sonoko Karino, Haruki Usuda, Shoma Kanda, Takayuki Okamoto, Tomomi Niibayashi, Takahisa Yano, Kohji Naora, Koichiro Wada

“…Hepatic triglycerides and areas of oil droplets increased in the HGD group both at day 7 and day 14, whereas weight gain, weight of epididymal fat, and plasma levels of triglycerides were unaffected by HGD consumption. A microarray analysis of the livers revealed that the expression of lipogenesis-related genes was the most affected by HGD consumption. …”
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Dermal fibroblast transcriptome indicates contribution of WNT signaling pathways in the pathogenesis of Apert syndrome by Arda Çetinkaya, Ekim Taşkıran, Tutku Soyer, Pelin Özlem Şimşek-Kiper, Gülen Eda Utine, Gökhan Tunçbilek, Koray Boduroğlu, Mehmet Alikaşifoğlu

“…For this purpose, primary skin fibroblast cultures obtained from 3 individuals with Apert syndrome and 3 controls without craniosynostosis were compared by transcriptome microarray, GeneChip Human Genome U133 Plus 2.0. As a result, 181 genes were shown to be differentially expressed between experimental groups. …”
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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. …”
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Distinctive profile of IsomiR expression and novel microRNAs in rat heart left ventricle. by Mary K McGahon, Janet M Yarham, Aideen Daly, Jasenka Guduric-Fuchs, Lyndsey J Ferguson, David A Simpson, Anthony Collins

“…The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. …”
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Dysregulation of human beta-defensin-2 protein in inflammatory bowel disease. by Marian C Aldhous, Colin L Noble, Jack Satsangi

“…<h4>Methodology/principal findings</h4>We examined HBD2 mRNA expression at three colonic locations by microarray analysis of biopsies from 151 patients (53 CD, 67 ulcerative colitis [UC], 31 controls). …”
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The cytochrome d oxidase complex regulated by fexA is an Achilles' heel in the in vivo survival of Vibrio vulnificus by Wenzhi Tan, Kwangjoon Jeong, Raghunath Pendru, Sao Puth, Seol Hee Hong, Shee Eun Lee, Joon Haeng Rhee

“…For deeper understanding the role of fexA gene on the successful V. vulnificus infection, we analyzed differentially expressed genes in ΔfexA mutant in comparison with wild type under aerobic, anaerobic or in vivo culture conditions by genome-scale DNA microarray analyses. Twenty-two genes were downregulated in the ΔfexA mutant under all three culture conditions. …”
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Reconstructing Dynamic Gene Regulatory Networks Using f-Divergence from Time-Series scRNA-Seq Data by Yunge Wang, Lingling Zhang, Tong Si, Sarah Roberts, Yuqi Wang, Haijun Gong

“…The existing methods have notable limitations as most are either designed for reconstructing time-varying networks from bulk microarray data or constrained to inferring stationary networks from scRNA-seq data, failing to capture the dynamic regulatory changes at the single-cell level. …”
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Comparison of monocyte gene expression among patients with neurocysticercosis-associated epilepsy, Idiopathic Epilepsy and idiopathic headaches in India. by Vasudevan Prabhakaran, Douglas A Drevets, Govindan Ramajayam, Josephine J Manoj, Michael P Anderson, Jay S Hanas, Vedantam Rajshekhar, Anna Oommen, Hélène Carabin

“…<h4>Methods/principal findings</h4>Patients aged 18 to 51 were recruited from the Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India, between January 2013 and October 2014. mRNA from CD14+ blood monocytes was isolated from 76 patients with NCC, 10 Recovered NCC (RNCC), 29 idiopathic epilepsy and 17 idiopathic headaches patients. A preliminary microarray analysis was performed on six NCC, six idiopathic epilepsy and four idiopathic headaches patients to identify genes differentially expressed in NCC-associated epilepsy compared with other groups. …”
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Biomarkers and potential therapeutic targets driving progression of non-alcoholic steatohepatitis to hepatocellular carcinoma predicted through transcriptomic analysis by Hui Fan, Rong Wang, Bin Wen, Jing Xiong

“…Despite its widespread impact, effective treatments to prevent the progression of NASH remain elusive, highlighting the critical importance of innovative molecular techniques in both the diagnosis and management of this disease.MethodsSix microarray datasets available in GEO were used to perform Robust Rank Aggregation (RRA) to identify differentially expressed genes (DEGs).We identified 62 robust upregulated genes and 24 robust downregulated genes. …”
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Repressor activator protein 1–promoted colorectal cell migration is associated with the regulation of Vimentin by Yongyong Yang, Chunxiang Ye, Lixin Wang, Guo An, Zhihua Tian, Lin Meng, Like Qu, Shenyi Lian, Chengchao Shou

“…Knockdown of repressor activator protein 1 in colorectal cancer cells did not affect cell proliferation or colony formation, but dramatically decreased cell migration and F-actin-enriched membrane protrusions. Microarray screening revealed that Vimentin was downregulated after repressor activator protein 1 knockdown, which was validated by analysis of a colorectal cancer dataset. …”
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Circulating exosomal microRNAs as biomarkers of colon cancer. by Hiroko Ogata-Kawata, Masashi Izumiya, Daisuke Kurioka, Yoshitaka Honma, Yasuhide Yamada, Koh Furuta, Toshiaki Gunji, Hideki Ohta, Hiroyuki Okamoto, Hikaru Sonoda, Masatoshi Watanabe, Hitoshi Nakagama, Jun Yokota, Takashi Kohno, Naoto Tsuchiya

“…<h4>Experimental design</h4>Microarray analyses of miRNAs in exosome-enriched fractions of serum samples from 88 primary CRC patients and 11 healthy controls were performed. …”
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Multi-Omics analysis and in vitro validation reveal diagnostic and therapeutic roles of novel hub genes in ovarian cancer by Jianmin Wang, Guanghui Song, Lili Xing

“…We integrated four GEO microarray datasets (GSE54388, GSE40595, GSE18521, and GSE12470) to identify differentially expressed genes (DEGs) between OC and healthy tissues using the limma package. …”
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Comparative analysis of proteome and transcriptome variation in mouse. by Anatole Ghazalpour, Brian Bennett, Vladislav A Petyuk, Luz Orozco, Raffi Hagopian, Imran N Mungrue, Charles R Farber, Janet Sinsheimer, Hyun M Kang, Nicholas Furlotte, Christopher C Park, Ping-Zi Wen, Heather Brewer, Karl Weitz, David G Camp, Calvin Pan, Roumyana Yordanova, Isaac Neuhaus, Charles Tilford, Nathan Siemers, Peter Gargalovic, Eleazar Eskin, Todd Kirchgessner, Desmond J Smith, Richard D Smith, Aldons J Lusis

“…The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography-Mass Spectrometry using O(18)-reference-based isotope labeling approach. …”
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Autosomal Dominant Pseudohypoaldosteronism Type 1 in an Infant with Salt Wasting Crisis Associated with Urinary Tract Infection and Obstructive Uropathy by Sasigarn A. Bowden, Corin Cozzi, Scott E. Hickey, Devon Lamb Thrush, Caroline Astbury, Sushma Nuthakki

“…His serum aldosterone remained elevated at 5 months of age, despite resolution of salt wasting symptoms. Chromosomal microarray analysis revealed a deletion of exons 3–5 in NR3C2 in the patient and his asymptomatic mother who also had elevated serum aldosterone level, confirming that he had primary or autosomal dominant PHA1. …”
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mRNA ratios of AR to ESR1 and PGR distinguish breast cancer subtypes based on public datasets and experimental models by Diego Prieto, Milena Rondón-Lagos, Paola Cruz-Tapias, Andrés Rincón-Riveros, Wilson Rubiano, Jairo De la Peña, Elizabeth Vargas, Victoria E. Villegas, Nelson Rangel

“…Here, we conducted a meta-analysis of large-scale microarray transcriptomic datasets to evaluate whether the mRNA expression levels of the androgen receptor gene, relative to those of the estrogen receptor gene (AR/ESR1 ratio) and the progesterone receptor gene (AR/PGR ratio), can help differentiate BC tumor subtypes. …”
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TRIM13 prevents cardiomyocyte injury by affecting apoptosis through interacting with CD3D in myocardial infarction by Feipeng Wu, Xiandong Zheng, Qiyan Wu, Liju Hong, Lei Yue, Rui Yang, Dandan Chen, Youjun Zhou

“…A mouse model of MI was established, and cardiac tissue sample microarray data and GSE236374 dataset were collected to screen and 120 upregulation and 15 downregulation genes were obtained, and related to T cells and cell immunity. …”
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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. …”
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Cytokine and Antibody Based Diagnostic Algorithms for Sputum Culture-Positive Pulmonary Tuberculosis. by Tao Chen, Jinfei Lin, Wei Wang, Joy Fleming, Liang Chen, Yunxia Wang, Haicheng Li, Huixin Guo, Jie Zhou, Xunxun Chen, Yuhui Chen, Qinghua Liao, Yang Shu, Yaoju Tan, Meiling Yu, Guozhou Li, Lin Zhou, Qiu Zhong, Lijun Bi, Lina Guo, Meigui Zhao

“…TB-related cytokines and TB-specific antibodies were detected in parallel with microarray technology. The diagnostic performance of the new protocol for active TB was systematically compared with other traditional methods.…”
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Themis2/ICB1 is a signaling scaffold that selectively regulates macrophage Toll-like receptor signaling and cytokine production. by Matthew J Peirce, Matthew Brook, Nicholas Morrice, Robert Snelgrove, Shajna Begum, Alessandra Lanfrancotti, Clare Notley, Tracy Hussell, Andrew P Cope, Robin Wait

“…A second member of this family, Themis2 (Q91YX0), also known as ICB1 (Induced on contact with basement membrane 1), remains unreported at the protein level despite microarray and EST databases reporting Themis2 mRNA expression in B cells and macrophages.…”
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