Prediction of gene expression in embryonic structures of Drosophila melanogaster. by Anastasia A Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma

“…Here, we present a widely applicable computational approach, integrating developmental time-course microarray data with annotated in situ hybridisation studies, that facilitates the de novo prediction of tissue-specific expression for genes that have no in vivo gene expression localisation data available. …”
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PLCH1 overexpression promotes breast cancer progression and predicts poor prognosis through the ERK1/2-EGR1 axis by Jing Li, Fenge Jiang, Congcong Wang, Ping Sun, Lei Song, Jiannan Liu

“…However, its specific role in breast cancer progression, its association with clinicopathological features, and its prognostic significance remain unclear.MethodsPLCH1 expression was analyzed across multiple tumor types using the TNMplot database, which integrates RNA-seq, microarray, and normalized data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO), encompassing 40,442 tumor and 15,648 normal samples. …”
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Bioinformatic analysis, clinical implications and experimental validation of ferroptosis-related feature gene in IgA nephropathy: focus on DUSP1 by Tingting Liu, Tingting Pan, Mingxin Chang, Shaojie Fu, Hongzhao Xu, Hao Wu, Zhonggao Xu, Yanli Cheng

“…The aim of this study was to identify ferroptosis-related feature gene (FFG) for the potential diagnosis of IgAN and to investigate its relationship with renal immune cell infiltration.MethodsRenal tissue microarray datasets (GSE93798, GSE104948, GSE99339) from IgAN patients and normal controls were retrieved from GEO database. …”
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Profiling of gastric cancer cell-surface markers to achieve tumour–normal discrimination by Henry Yang, Khek Yu Ho, Judith Toh, Michal Marek Hoppe, Teena Thakur, Kar Tong Tan, Brendan Pang, Sharmaine Ho, Rony Roy, Khay Guan Yeoh, Raghav Sundar, Anand Jeyasekharan

“…Promising candidates from this analysis were validated orthogonally using multispectral immunohistochemistry (mIHC) with automated quantitative analysis using the Vectra platform. mIHC was performed on a tissue microarray containing matched normal, marginal and tumour tissues. …”
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Acetylation suppresses breast cancer progression by sustaining CLYBL stability by Xinyue Deng, Chenglong Ma, Xingyu Chen, Ming Yi, Qianhua Cao, Ruocen Liao, Xingyu Lei, Longchang Bai, Bin Zhao, Yingnan Wang, Zhuoyang Shen, Liujing Wu, Chenfang Dong, Zhijun Dai

“…Methods CLYBL expression patterns in breast cancer were assessed using a breast cancer tissue microarray, immunohistochemistry, and publicly available datasets. …”
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Caveolin-1 inhibits the proliferation and invasion of lung adenocarcinoma via EGFR degradation by Jiahui Dong, Ruiping Du, Yani Zhang, Bo Hong, Gengyun Sun

“…The expressions of CAV1 and EGFR in LUAD tissues and adjacent tissues were detected by Western blotting, immunohistochemistry and microarray technology. …”
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Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. by Androniki Psifidi, Chrysostomos I Dovas, Georgios Bramis, Thomai Lazou, Claire L Russel, Georgios Arsenos, Georgios Banos

“…These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.…”
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Characterization of Human Knee and Chin Adipose-Derived Stromal Cells by Magali Kouidhi, Phi Villageois, Carine M. Mounier, Corinne Ménigot, Yves Rival, David Piwnica, Jérôme Aubert, Bérengère Chignon-Sicard, Christian Dani

“…Paired chin and knee fat depots were harvested from 11 subjects and gene expression profiles were determined by DNA microarray analyses. Adipose-derived stromal cells (ASCs) from both sites were isolated and analyzed for their capacity to proliferate, form clones, and differentiate. …”
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m6A reader IGF2BP2-stabilized lncRNA LHX1-DT inhibits renal cell carcinoma (RCC) cell proliferation and invasion by sponging miR-590-5p by Chunming Zhu, Ruiming Li, Xiangyun You, Jie Xu, Jiahe Wang, Dan Dong, Xiaonan Chen, Kefeng Wang

“…Differentially expressed lncRNAs and m6A levels were identified through microarray analysis. The interaction between IGF2BP2 and LHX1-DT was examined via RNA immunoprecipitation and luciferase reporter assays. …”
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Stromal expression of decorin, Semaphorin6D, SPARC, Sprouty1 and Tsukushi in developing prostate and decreased levels of decorin in prostate cancer. by Alexander Henke, O Cathal Grace, George R Ashley, Grant D Stewart, Antony C P Riddick, Henry Yeun, Marie O'Donnell, Richard A Anderson, Axel A Thomson

“…Four candidates (Decorin, SPARC, Spry-1, Tsukushi) were immunolocalised in human foetal prostate (weeks 14, 16, 19) and expression of Decorin was evaluated on a human prostate cancer tissue microarray. In embryonic and perinatal rats Decorin, Semaphorin6D, SPARC, Spry-1 and Tsukushi were expressed with varying distribution patterns throughout the mesenchyme at E17.5, E19.5, P0.5 and P6.5. …”
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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

“…Molecular subtypes were generated using “ConsensusClusterPlus” on identified genes, which were further assessed for tumor stage relevance, expression differences in adjacent and tumor tissues, and impact on survival in TCGA liver cancer patients. …”
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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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SPARC Promotes Aerobic Glycolysis and 5‐Fluorouracil Resistance in Colorectal Cancer Through the STAT3/HK2 Axis by Jingrong Xiang, Huan Zhang, Kanger Shen, Jie Feng, Kexi Yang, Tongguo Shi, Qinhua Xi

“…Methods Firstly, Secreted protein acidic and rich in cysteine (SPARC) expression and prognosis in CRC clinical samples were investigated using tissue microarray (TMAs) and GEPIA databases. Subsequently in vitro, SPARC knockdown or overexpression was used to explore the role of SPARC in 5‐fluorouracil (5‐FU) resistance in CRC cell lines. …”
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A Thorough Navigation of miRNA's Blueprint in Crafting Cardiovascular Fate by Abubakar Nazir, Olivier Uwishema, Sanobar Shariff, William Xochitun Gopar Franco, Noha El Masri, Nitsuh Dejene Ayele, Isabelle Munyangaju, Fatima Esam Alzain, Magda Wojtara

“…A variety of state‐of‐the‐art technologies have aided researchers in discovering, profiling, and analyzing miRNAs, including microarray analysis, next‐generation sequencing, and others. …”
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Thymidine Kinase 1 Expression Correlates with Tumor Aggressiveness and Metastatic Potential in OSCC by Chia-Jung Lee, Pei-Wen Peng, Chia-Yu Wu, Tsung-Ming Chang, Ju-Fang Liu, Kuan-Chou Lin

“…<b>Methods:</b> To identify key molecular drivers in OSCC, we performed an integrative bioinformatics analysis of five OSCC-related microarray datasets from the Gene Expression Omnibus (GEO). …”
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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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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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MiR-136 inhibits gastric cancer–specific peritoneal metastasis by targeting HOXC10 by Jianyong Zheng, Peng Ge, Xiaonan Liu, Jiangpeng Wei, Guosheng Wu, Xiaohua Li

“…We further confirmed that miR-136 expression is frequently downregulated in gastric cancer peritoneal metastasis cells and tissues and its low expression is significantly associated with more peritoneal metastasis and worse prognosis. …”
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High prevalence of p16 staining in malignant tumors. by Noémi De Wispelaere, Sebastian Dwertmann Rico, Marcus Bauer, Andreas M Luebke, Martina Kluth, Franziska Büscheck, Claudia Hube-Magg, Doris Höflmayer, Natalia Gorbokon, Sören Weidemann, Katharina Möller, Christoph Fraune, Christian Bernreuther, Ronald Simon, Christian Kähler, Anne Menz, Andrea Hinsch, Frank Jacobsen, Patrick Lebok, Till Clauditz, Guido Sauter, Ria Uhlig, Waldemar Wilczak, Stefan Steurer, Eike Burandt, Rainer Krech, David Dum, Till Krech, Andreas Marx, Sarah Minner

“…However, the prevalence of p16 expression in different cancer types is controversial. 15,783 samples from 124 different tumor types and 76 different normal tissue types were analyzed by immunohistochemistry in a tissue microarray format. p16 was detectable in 5,292 (45.0%) of 11,759 interpretable tumors. …”
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Integrative bioinformatic analysis identifies differentially expressed gene targets as potential biomarkers for anaplastic thyroid cancer by Angel Sebastian Treviño-Juarez, Jose Gerardo Gonzalez-Gonzalez, Rene Rodriguez-Gutierrez, Adriana Sanchez-Garcia, Camilo Daniel Gonzalez-Velazquez

“…Methods We analyzed five microarray datasets from the GEO database to compare gene expression profiles between ATC samples and normal thyroid tissues. …”
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