Genome-wide and rna-seq highlight genetic characteristics of rumpless signals in piao chicken by Wang Mei QI, Xing Fu ZHANG, Li Wen SONG, Zai Xia LIU, Yuan CHAI, Yan Yong SUN

“…In this study, transparent staining was performed on the bones of 16 tailed chickens and 16 Piao chickens to observe the dynamic bone formation process of embryos at different developmental stages. Microarray data of 988 chickens, resequencing results of 30 Piao chickens and 30 tailed chickens and 10 transcriptome samples were used for analysis. …”
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Identification of Novel Biomarkers in Huntington’s Disease Based on Differential Gene Expression Meta-Analysis and Machine Learning Approach by Nayan Dash, Md Abul Bashar, Jeonghan Lee, Raju Dash

“…We performed a meta-analysis to identify DEGs using three Gene Expression Omnibus (GEO) microarray datasets from different platforms related to HD-affected brain tissue, applying both relaxed and strict criteria to identify differentially expressed genes. …”
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MicroRNAs hsa-miR-99b, hsa-miR-330, hsa-miR-126 and hsa-miR-30c: Potential Diagnostic Biomarkers in Natural Killer (NK) Cells of Patients with Chronic Fatigue Syndrome (CFS)/ Myalg... by Robert D Petty, Neil E McCarthy, Rifca Le Dieu, Jonathan R Kerr

“…The CFS/ME associated miRNA identified by these experiments were then transfected into primary NK cells and gene expression analyses conducted to identify their gene targets.<h4>Results</h4>Microarray analysis identified differential expression of 34 miRNA, all of which were up-regulated. …”
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Machine learning-based transcriptmics analysis reveals BMX, GRB10, and GADD45A as crucial biomarkers and therapeutic targets in sepsis by Yanwei Cheng, Haoran Peng, Qiao Chen, Lijun Xu, Lijie Qin

“…This study leverages transcriptomics and machine learning (ML) to identify critical biomarkers and therapeutic targets in sepsis. Analyzing microarray data from the Gene Expression Omnibus (GEO) datasets GSE28750, GSE26440, GSE13205, and GSE9960, we discovered three pivotal biomarkers that BMX (bone marrow tyrosine kinase gene on chromosome X), GRB10 (growth factor receptor bound protein 10), and GADD45A (growth arrest and DNA damage inducible alpha), exhibiting exceptional diagnostic accuracy (AUC &gt;0.9). …”
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Identification of multicohort-based predictive signature for NMIBC recurrence reveals SDCBP as a novel oncogene in bladder cancer by Chen Zhang, Hubin Yin, Tinghao Li, Junrui Chen, Weiyang He, Ke Ren, Bo Li, Xudong Liu

“…Traditional clinical characteristics alone are inadequate for accurately assessing the risk of NMIBC recurrence, necessitating the development of novel predictive tools.Methods We analyzed microarray data of NMIBC samples obtained from the ArrayExpress and GEO databases. …”
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Integrated analysis of gene networks and cellular functions identifies novel heart failure biomarkers by Jiang Juncheng, Chen Lei, Lin Hao, Liang Fei

“…Methods Four public microarray datasets (GSE161472, GSE147236, GSE116250, and GSE46224) were retrieved from the Gene Expression Omnibus (GEO) database. …”
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Metabolomic characterisation of the glioblastoma invasive margin reveals a region-specific signature by James Wood, Stuart J. Smith, Marcos Castellanos-Uribe, Anbarasu Lourdusamy, Sean T. May, David A. Barrett, Richard G. Grundy, Dong-Hyun Kim, Ruman Rahman

“…Here, we use liquid chromatography–mass spectrometry and gene expression microarray to profile integrated intratumour metabolic heterogeneity, as a direct functional readout of adaptive responses of subclones to the tumour microenvironment. …”
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Distinct chromosome abnormality patterns for differential diagnosis of hepatocellular carcinoma and cholangiocarcinoma. by Wantakan Ngamsangiam, Sutheemon Techa-Ay, Prakasit Sa-Ngiamwibool, Sasithorn Watcharadetwittaya, Raksawan Deenonpoe, Anchalee Techasen, Natruja Sridakhun, Sureerat Padthaisong, Malinee Thanee

“…This study aimed to identify chromosomal abnormalities that could aid in differentiating these cancers using chromosome microarray analysis (CMA). We analyzed ten frozen tumor tissues each of HCC and CCA, identifying distinct patterns of chromosomal gains and losses. …”
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A Panel of Three MicroRNA Signatures as a Potential Biomarker for CRC Screening Based on Stages and Functional Prediction Using Bioinformatic Analysis by Syarah Syamimi Mohamed, Azmir Ahmad, Nurul Syakima Ab Mutalib, Tengku Ahmad Damitri Al-Astani Tengku Din, Md Salzihan Md Salleh, Andee Dzulkarnaen Zakaria, Zaidi Zakaria

“…Therefore, this study aims to identify the significantly deregulated miRNAs in CRC tumorigenesis. (2) Methods: Three upregulated miRNAs (hsa-miR-20a-5p, hsa-miR-21-5p, and hsa-miR210-3p) from 14 significant differentially expressed miRNAs (DEMs) were chosen from microarray profiling to be validated in plasma. Bioinformatics analyses showed that these miRNAs generally contributed to tumorigenesis, but only hsa-miR-20a-5p and hsa-miR-21-5p were specifically linked to CRC. …”
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The use of whole genome amplification for genomic evaluation of bovine embryos by K. S. Pantiukh, I. V. Rukin, S. V. Portnov, A. Khatib, S. L. Panteleev, A. M. Mazur

“…The main purpose of this work is to assess the possibility of using embryo biopsy specimens (bsp) for embryo genotyping using microarray chips and predicting the carrier status of lethal haplotypes at the embryo stage. …”
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Identification and characterization of the GH3 gene family in maize by Dong-feng ZHANG, Nan ZHANG, Tao ZHONG, Chao WANG, Ming-liang XU, Jian-rong YE

“…In this study, the 12 maize GH3 proteins were primarily classified into two phylogenetic groups, similar to the 13 rice GH3 proteins, while 9 of the 19 Arabidopsis GH3 proteins were observed in the third phylogenetic group. Microarray analysis showed that expression of maize GH3 genes is temporally and spatially modulated. …”
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Prediction of CD8+ T cell infiltration in the tumor microenvironment of HGSOC patients by Jia Mai, Ling Yang, YuXin Chen, XiaoXu Zeng, HongJian Xie, XiaoJuan Liu

“…Two independent cohort were analyzed: (1) A multicenter tissue microarray (TMA) cohort of 105 epithelial ovarian cancer cases revealed that high CD8+ T cell density in tumor parenchyma, stroma, or whole tissue was significantly associated with good prognosis. (2) A retrospective cohort of 95 HGSOC patients from West China Second University Hospital (2016–2020) demonstrated that peripheral blood lymphocytes, globulin (GLB), lactate dehydrogenase (LDH), and low-density lipoprotein (LDL) correlated with CD8+ T cell infiltration in TME. …”
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MiR-136 inhibits gastric cancer–specific peritoneal metastasis by targeting HOXC10 by Jianyong Zheng, Peng Ge, Xiaonan Liu, Jiangpeng Wei, Guosheng Wu, Xiaohua Li

“…Functions of microRNAs have been characterized in the embryologic, physiologic, and oncogenic processes, but the role of microRNAs in mediating tumor-specific organ metastasis was addressed only recently and still absent in gastric cancer peritoneal metastasis. Here, we used the microarray analysis to define the gastric cancer peritoneal metastasis–related microRNAs from highly peritoneal metastatic derivatives (GC-9811P cells) and the parental GC-9811 human gastric cancer cells. …”
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Alternative splicing of TCF7L2 gene in omental and subcutaneous adipose tissue and risk of type 2 diabetes. by Ludmila Prokunina-Olsson, Lee M Kaplan, Eric E Schadt, Francis S Collins

“…A pathway enrichment analysis on transcripts significantly co-expressed with TCF7L2 in a microarray set combined with individual expression assays, suggested tissue-specific roles of TCF7L2 splicing forms in regulation of transcription, signal transduction and cell adhesion.…”
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Stromal Caveolin-1 and Caveolin-2 Expression in Primary Tumors and Lymph Node Metastases by Wladimir Gerstenberger, Michaela Wrage, Eeva Kettunen, Klaus Pantel, Sisko Anttila, Stefan Steurer, Harriet Wikman

“…The expression of these two genes was investigated at protein level on a tissue microarray (TMA) consisting of 161 primary tumor samples. 50.7% of squamous cell lung cancer (SCC) tumors showed strong expression of CAV1 in the tumor-associated stromal cells, whereas only 15.1% of adenocarcinomas (AC) showed a strong CAV1 expression (p<0.01). …”
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Association between the methyl-CpG-binding domain protein 5 gene and depressive symptoms in a Mexican population: results from the MxGDAR/Encodat cohort by Marco Antonio Sanabrais-Jiménez, Beatriz Camarena, Alejandro Aguilar-García, Alma Delia Genis-Mendoza, José Jaime Martínez-Magaña, Humberto Nicolini, Jorge Ameth Villatoro-Velázquez, Marycarmen Bustos-Gamiño, María de Lourdes Gutiérrez-López, María Elena Medina-Mora

“…The sample was genotyped with the commercial microarray PsychArray BeadChip. We identified 707 single nucleotide polymorphisms (SNPs) of 75 genes previously associated with AS and DS. …”
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Long-Term Aerobic Exercise Enhances Hepatoprotection in MAFLD by Modulating Exosomal miR-324 via ROCK1 by Yang Zhang, Qiangman Wei, Xue Geng, Guoliang Fang

“…Co-culture experiments evaluated the effects of exercise-derived exosomes on IR signaling pathways. miRNA microarray analysis identified miR-324, which was quantified in high-fat diet (HFD) mice with and without exercise and compared between athletes and sedentary controls. …”
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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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Expression signatures with specificity for type I and II IFN response and relevance for autoimmune diseases and cancer by Bogac Aybey, Benedikt Brors, Eike Staub

“…Our IFN-II signature is broader applicable than other published signatures as it demonstrates strong performance in detecting IFN-II response in more cell types. In three SLE microarray datasets our IFN-I signature was highly coherent and correlated with disease severity better than most published signatures. …”
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Plucked hair follicles from patients with chronic discoid lupus erythematosus show a disease-specific molecular signature by Miriam Wittmann, Edward M Vital, Mohammad Shalbaf, Adewonuola A Alase, Anna Berekmeri, Md Yuzaiful Md Yusof, Jelena Pistolic, Mark J Goodfield, Sara Edward, Natalia V Botchkareva, Martin Stacey

“…RNA was isolated from plucked anagen HFs and microarray, as well as quantitative real-time PCR was performed.Results Here, we report that gene expression analysis of only a small number of HF plucked from lesional areas of the scalp is sufficient to differentiate CDLE from psoriasis lesions or healthy HF. …”
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