Bioinformatic-based differential expression gene expressions of epithelial mesenchymal transformation in diabetic kidney disease and prediction of traditional Chinese medicine by Liu Wu, Zhou Yi, Yu Fang-ning, Zhang Ning

“…ObjectiveBased upon the bioinformatic analysis of gene chip data between patients with diabetic kidney disease （DKD） and normal controls， differentially expressed genes of epithelial mesenchymal transformation of DKD were screened for elucidating its pathogenesis and predicting the potential therapeutic Chinese medicine for DKD.MethodsGSE23338 microarray data were downloaded from gene expression omnibus， related differentially expressed genes screened by R language and differentially expressed genes analyzed by Gene Ontology， Kyoto Encyclopedia of Genes and Genomes. …”
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Cellular senescence-associated genes in rheumatoid arthritis: Identification and functional analysis. by You Ao, Qing Lan, Tianhua Yu, Zhichao Wang, Jing Zhang

“…In our study, we analyzed RA microarray data from the Gene Expression Omnibus (GEO) and focused on cellular senescence genes from the CellAge database. …”
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MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses. by Hongmei Zhu, Siu-Wai Leung

“…Biologically relevant microRNAs will then be selected through genomic database corroboration. Their association with T2D is further measured by area under the curve (AUC) of receive operating characteristic (ROC). …”
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Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas by Xueren Gao, Jianguo Wang, Shulong Zhang

“…The aim of the present study was to identify hub genes and pathways in ATC by microarray expression profiling. Two independent datasets (GSE27155 and GSE53072) were downloaded from GEO database. …”
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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. …”
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Bioinformatic identification of Single Nucleotide Polymorphisms (SNPs) in keratin-associated protein genes in alpacas (Vicugna pacos) by Deyanira Figueroa, Manuel More, Gustavo Gutiérrez, F. Abel Ponce de León

“…Of these, 35 SNPs were included in the 76K alpaca SNP microarray and 32 SNPs were confirmed in a population of 936 alpacas.…”
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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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Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression by Itai Yanai, L Ryan Baugh, Jessica J Smith, Casey Roehrig, Shai S Shen‐Orr, Julia M Claggett, Andrew A Hill, Donna K Slonim, Craig P Hunter

“…We used RNAi and time series, whole‐genome microarray analyses to systematically perturb and characterize components of a Caenorhabditis elegans lineage‐specific transcriptional regulatory network. …”
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Effect of Storage Temperature on Key Functions of Cultured Retinal Pigment Epithelial Cells by Lara Pasovic, Jon Roger Eidet, Berit S. Brusletto, Torstein Lyberg, Tor P. Utheim

“…Total RNA was isolated and the gene expression profile was determined using DNA microarrays. Comparison of the microarray expression values with qRT-PCR analysis of selected genes validated the results. …”
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Evaluation of LRIG1 Expression in Larynx Pathologies by Yavuz Gündoğdu, Orhan Asya, Ayşegül Gönen, Tajaddin Muradov, Selim Yiğit Erçetin, Zeliha Leyla Cinel, Ali Cemal Yumuşakhuylu

“…Patients’ data were obtained from the medical records. The tissue microarray method was used to evaluate specimens. Results: There was a statistically significant difference between the tumor differentiation, diagnosis, and the expression of LRIG1 (respectively p=0.045, p<0.001). …”
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Common gene-network signature of different neurological disorders and their potential implications to neuroAIDS. by Vidya Sagar, S Pilakka-Kanthikeel, Paola C Martinez, V S R Atluri, M Nair

“…An mRNA microarray analysis in HIV-infected monocytes showed significant changes in the expression of several genes of this in silico derived common pathway which suggests the possible physiological relevance of this gene-circuit in driving neuroAIDS condition. …”
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Cysteine‐rich intestinal protein 1 enhances the progression of hepatocellular carcinoma via Ras signaling by Hong‐Yu He, Li Hu

“…To further evaluate whether CRIP1 interacts with Ras, a specific siRNA targeting Ras was selected. We found that Ras knockdown reduced the activation of Ras/AKT signaling even in HepG2 cells transfected with CRIP1. …”
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Investigation of Underlying Biological Association and Targets between Rejection of Renal Transplant and Renal Cancer by Yinwei Chen, Zhanpeng Liu, Qian Yu, Xu Sun, Shuai Wang, Qingyi Zhu, Jian Yang, Rongjiang Jiang

“…Finally, the PLAC8 was selected for further research, including its clinical and biological role. …”
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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

“…Endogenous expression of selected genes linked to the abnormally methylated CGIs was correspondingly decreased or increased by as much as 4-19-fold. …”
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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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Bioinformatics-based analysis of autophagy-related genes and prediction of potential Chinese medicines in diabetic kidney disease by Yufeng Xing, Zining Peng, Chaoyang Ye

“…Methods: Data from sequencing microarrays GSE30528, GSE30529, and GSE1009 in the Gene Expression Omnibus (GEO) were employed. …”
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Polymorphisms in the mitochondrial DNA control region and frailty in older adults. by Ann Z Moore, Mary L Biggs, Amy Matteini, Ashley O'Connor, Sarah McGuire, Brock A Beamer, M Danielle Fallin, Linda P Fried, Jeremy Walston, Aravinda Chakravarti, Dan E Arking

“…At baseline, frailty was identified as the presence of three or more of five indicators (weakness, slowness, shrinking, low physical activity, and exhaustion). mtDNA variation was assessed in a pilot study, including 315 individuals selected as extremes of the frailty phenotype, using an oligonucleotide sequencing microarray based on the Revised Cambridge Reference Sequence. …”
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Digital spatial proteomic profiling reveals immune checkpoints as biomarkers in lymphoid aggregates and tumor microenvironment of desmoplastic melanoma by Ruth Halaban, Kelly Olino, James Clune, David L Rimm, Harriet M Kluger, Dijana Djureinovic, Wael Ibrahim, Raymond Baumann, Anjela Galan, David G Su, David A. Schoenfeld, Raysa Cabrejo, Sajid A Khan

“…These findings might have therapeutic implications and help guide treatment selection in addition to informing potential prognostic significance.…”
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The Role of Chromosomal Instability and Epigenetics in Colorectal Cancers Lacking β-Catenin/TCF Regulated Transcription by Wael M. Abdel-Rahman, Johanna E. Lotsari-Salomaa, Sippy Kaur, Anni Niskakoski, Sakari Knuutila, Heikki Järvinen, Jukka-Pekka Mecklin, Päivi Peltomäki

“…MFISH and CGH revealed distinct instability of chromosome structure in RKO. Gene expression microarray of RKO versus 7 colon cancer lines (with active Wnt signaling) and 3 normal specimens revealed 611 differentially expressed genes. …”
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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

“…But the findings were not validated in actual patients, so further investigation is needed to confirm the potential use of selected medicinal plants towards HCV-related HC.…”
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