MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses. by Hongmei Zhu, Siu-Wai Leung

“…The corresponding reporting guidelines will be used to assess the quality of included studies according to their profiling methods (microarray, RT-PCR, and RNA-Seq).<h4>Ethics and dissemination</h4>No ethics approval is required since this study does not include identifiable personal patient data.…”
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Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS by Iwona Stelniec‐Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen, Reinhold Schäfer

“…We measured mRNA and protein levels in manipulated cells by microarray, RT–PCR and western blot analysis, respectively. …”
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Cysteine‐rich intestinal protein 1 enhances the progression of hepatocellular carcinoma via Ras signaling by Hong‐Yu He, Li Hu

“…Further study showed that the overexpression of CRIP1 enhanced the proliferation and migration of HepG2 cells, but the inhibition of CRIP1 decreased the proliferation and migration of HepG2 cells. Microarray assays and KyotoEncyclopedia of Genes and Genomes (KEGG) pathway analysis showed that overexpression of CRIP1 induced the activation of Ras signaling. …”
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Maternal cocaine administration in mice alters DNA methylation and gene expression in hippocampal neurons of neonatal and prepubertal offspring. by Svetlana I Novikova, Fang He, Jie Bai, Nicholas J Cutrufello, Michael S Lidow, Ashiwel S Undieh

“…Global DNA methylation, methylated DNA immunoprecipitation followed by CGI(2) microarray profiling and bisulfite sequencing, as well as quantitative real-time RT-PCR gene expression analysis, were evaluated in hippocampal pyramidal neurons excised by laser capture microdissection. …”
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Genetic variation and antioxidant response gene expression in the bronchial airway epithelium of smokers at risk for lung cancer. by Xuting Wang, Brian N Chorley, Gary S Pittman, Steven R Kleeberger, John Brothers, Gang Liu, Avrum Spira, Douglas A Bell

“…Prior microarray studies of smokers at high risk for lung cancer have demonstrated that heterogeneity in bronchial airway epithelial cell gene expression response to smoking can serve as an early diagnostic biomarker for lung cancer. …”
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Integrated analysis of hub genes and intrinsically disordered regions in triple-negative breast cancer by Azhar Iqbal, Faisal Ali, Sulaiman Ali Alharbi, Muhammad Sajid, Saleh Alfarraj, Momina Hussain, Tehmina Siddique, Rakhshanda Mustaq, Fakhra Shafique, Muhammad Sarfaraz Iqbal

“…Two microarray datasets were used to identify possible targets for TNBC, GSE38959 and GSE45827, retrieved from the Gene Expression Omnibus (GEO) database. …”
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HSPA6 augments garlic extract-induced inhibition of proliferation, migration, and invasion of bladder cancer EJ cells; Implication for cell cycle dysregulation, signaling pathway a... by Seung-Shick Shin, Jun-Hui Song, Byungdoo Hwang, Dae-Hwa Noh, Sung Lyea Park, Won Tae Kim, Sung-Soo Park, Wun-Jae Kim, Sung-Kwon Moon

“…In addition, GE impeded the migration and invasion of EJ cells via inhibition of MMP-9 expression followed by decreased binding activities of AP-1, Sp-1, and NF-κB motifs. Based on microarray datasets, we selected Heat shock protein A6 (HSPA6) as the most up-regulated gene responsible for the inhibitory effects of GE. …”
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EsoDetect: computational validation and algorithm development of a novel diagnostic and prognostic tool for dysplasia in Barrett’s esophagus by Migla Miskinyte, Benilde Pondeca, José B. Pereira-Leal, Joana Cardoso

“…Specifically, for the diagnostic application, three RNAseq datasets were employed, while for the prognostic application, nine microarray datasets were identified, and 25 previously described genes were validated. …”
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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. …”
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MicroRNA controlled adenovirus mediates anti-cancer efficacy without affecting endogenous microRNA activity. by Ryan Cawood, Suet-Ling Wong, Ying Di, Dilair F Baban, Leonard W Seymour

“…RT-QPCR for mature mir122 in infected livers showed that quantity of mir122 remained unaffected. Genome wide mRNA microarray profiling of infected livers showed that although the transcript level of >3900 different mRNAs changed more than 2-fold following Ad5WT infection, less than 600 were changed by Ad5mir122. …”
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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. …”
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Inhibition of ATG5-mediated autophagy maintains PMAIP1 stability to promote cell apoptosis and suppress triple-negative breast cancer progression by Fangjian Shang, Hongfeng Nie, Liyan Du, Jin Shang, Xiangquan Song, Ya Chen, Hui Li, Zhuo Wang, Yixin Qi, Liyan Zhao

“…Methods TNBC-related datasets were retrieved from The Cancer Genome Atlas and selected by Prediction Analysis of Microarray 50 analysis to assess the expression of PMAIP1 in the samples. …”
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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. …”
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Aberrant expression of shared master-key genes contributes to the immunopathogenesis in patients with juvenile spondyloarthritis. by Lovro Lamot, Fran Borovecki, Lana Tambic Bukovac, Mandica Vidovic, Marija Perica, Kristina Gotovac, Miroslav Harjacek

“…Microarray results and bioinformatical analysis revealed 745 differentially expressed genes involved in various inflammatory processes, while qRT-PCR analysis of selected genes confirmed data universality and specificity of expression profiles in jSpA patients. …”
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Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective by Fernanda Cornejo-Granados, Luigui Gallardo-Becerra, Sandra Romero-Hidalgo, Alonso A. Lopez-Zavala, Andrés Cota-Huízar, Melany Cervantes-Echeverría, Rogerio R. Sotelo-Mundo, Adrian Ochoa-Leyva

“…Results Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. …”
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A stratified transcriptomics analysis of polygenic fat and lean mouse adipose tissues identifies novel candidate obesity genes. by Nicholas M Morton, Yvonne B Nelson, Zoi Michailidou, Emma M Di Rollo, Lynne Ramage, Patrick W F Hadoke, Jonathan R Seckl, Lutz Bunger, Simon Horvat, Christopher J Kenyon, Donald R Dunbar

“…Selected candidate genes Npr3 and Thbs1, as well as Gys2, a non-QTL gene that otherwise passed our enrichment criteria were characterised, revealing novel functional effects consistent with a contribution to obesity.…”
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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. …”
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Gene network inference and biochemical assessment delineates GPCR pathways and CREB targets in small intestinal neuroendocrine neoplasia. by Ignat Drozdov, Bernhard Svejda, Bjorn I Gustafsson, Shrikant Mane, Roswitha Pfragner, Mark Kidd, Irvin M Modlin

“…High throughput techniques such as inference of gene regulatory networks from microarray experiments can objectively define signaling machinery in this disease. …”
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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

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Long Noncoding RNAs and mRNA Regulation in Peripheral Blood Mononuclear Cells of Patients with Chronic Obstructive Pulmonary Disease by Xiaoyan Qu, Xiaomin Dang, Weijia Wang, Ying Li, Dan Xu, Dong Shang, Ying Chang

“…Methods. lncRNA and mRNA profiling of PBMCs from 17 smokers and 14 COPD subjects was detected by high-throughput microarray. The expression of dysregulated lncRNAs was validated by qPCR. …”
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