Gene Expression Profiling in Organ Transplantation by Osama Ashry Ahmed Gheith

“…It is important to note that the reproducibility of differently expressed genes might be affected by many factors such as gene ranking and selection methods, inherent differences between types, and the choice of thresholds. …”
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Exploration of autophagy-related molecular mechanisms underlying epilepsy using multiple datasets by Yongfei Wang, Haoxuan Zeng, Chongxu Liu, Jianjun Chen, Yihong Huang, Xianju Zhou

“…Further analyses including Least Absolute Shrinkage and Selection Operator regression, immune cell infiltration, and pathway enrichment were conducted. …”
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Pharmacologic inhibition of CSF-1R suppresses intrinsic tumor cell growth in osteosarcoma with CSF-1R overexpression by Cheng Dai, Bin Shen, Shenyan Liu, Cong Li, Shuqun Yang, Jie Wang, Jie Zhang, Manqi Liu, Zhixuan Zhu, Wan Shi, Qi Zhang, Zhui Chen, Nannan Zhang

“…Immunohistochemistry (IHC) was utilized to analyze human tissue microarray samples of osteosarcoma. We then investigated the anti-tumor effect and the mechanisms of action of pharmacologic inhibition of CSF-1R activity by pimicotinib (ABSK021), a highly potent and selective small molecule inhibitor of CSF-1R, in osteosarcoma models both in vitro and in vivo. …”
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A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression. by Kory R Johnson, C C T Hindmarch, Yasmmyn D Salinas, YiJun Shi, Michael Greenwood, See Ziau Hoe, David Murphy, Harold Gainer

“…In addition, we compare the SON transcriptomes resolved by RNA-Seq methods with the SON transcriptomes determined by Affymetrix microarray methods in rats under the same osmotic conditions, and find that there are 6,466 genes present in the SON that are represented in both data sets, although 1,040 of the expressed genes were found only in the microarray data, and 2,762 of the expressed genes are selectively found in the RNA-Seq data and not the microarray data. …”
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The transcription factors Snail and Slug activate the transforming growth factor-beta signaling pathway in breast cancer. by Archana Dhasarathy, Dhiral Phadke, Deepak Mav, Ruchir R Shah, Paul A Wade

“…Inhibition of the TGF-beta signaling pathway using selective small-molecule inhibitors following Snail or Slug addition resulted in decreased cell migration with no impact on the repression of cell junction molecules by Snail and Slug. …”
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Prevention of hypovolemic circulatory collapse by IL-6 activated Stat3. by Jeffrey A Alten, Ana Moran, Anna I Tsimelzon, Mary-Ann A Mastrangelo, Susan G Hilsenbeck, Valeria Poli, David J Tweardy

“…Pre-treatment of rats with a selective inhibitor of Stat3, T40214, reduced the IL-6-mediated increase in cardiac Stat3 activity, blocked successful resuscitation by IL-6 and reversed IL-6-mediated protection from cardiac apoptosis. …”
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R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting. by Takeshi Kawakami, Meghan K Jensen, Andrea Slavney, Petra E Deane, Ausra Milano, Vandana Raghavan, Brett Ford, Erin T Chu, Aaron J Sams, Adam R Boyko

“…We identified a putative causal variant in this region, an 11-kb tandem duplication (11,131,835-11,143,237) characterized by sequence read coverage and discordant reads of whole-genome sequence data, microarray probe intensity data, and a duplication-specific PCR assay. …”
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Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine. by Silvio D Brugger, Pascal Frey, Suzanne Aebi, Jason Hinds, Kathrin Mühlemann

“…Emergence of such previously rare serotypes under vaccine selection pressure may promote cocolonization in the future.…”
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Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions. by Sergio Rojas-Galeano, Emily Hsieh, Dan Agranoff, Sanjeev Krishna, Delmiro Fernandez-Reyes

“…The resulting variable subsets achieved classification accuracies of 99% on Human African Trypanosomiasis, 91% on Tuberculosis, and 91% on Malaria serum proteomic profiles with fewer than 20% of variables selected. Our method scaled-up to dimensionalities of much higher orders of magnitude as shown with gene expression microarray datasets in which we obtained classification accuracies close to 90% with fewer than 1% of the total number of variables.…”
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High prevalence of multidrug-tolerant bacteria and associated antimicrobial resistance genes isolated from ornamental fish and their carriage water. by David W Verner-Jeffreys, Timothy J Welch, Tamar Schwarz, Michelle J Pond, Martin J Woodward, Sarah J Haig, Georgina S E Rimmer, Edward Roberts, Victoria Morrison, Craig Baker-Austin

“…<h4>Methodology/principal findings</h4>To assess the potential effects of this sustained selection pressure, 127 Aeromonas spp. isolated from warm and cold water ornamental fish species were screened for tolerance to 34 antimicrobials. …”
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Apoptosis-associated genetic mechanisms in the transition from rheumatoid arthritis to osteoporosis: A bioinformatics and functional analysis approach by Hao-Ju Lo, Chun-Hao Tsai, Tsan-Wen Huang

“…Machine learning methods, including Lasso and Random Forest, refined the selection of key genes related to apoptosis. Immune infiltration analysis using CIBERSORT assessed immune cell differences between disease and normal samples. …”
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SMART: unique splitting-while-merging framework for gene clustering. by Rui Fa, David J Roberts, Asoke K Nandi

“…Moreover, two real microarray gene expression datasets are studied using this approach. …”
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Diagnosis of Coronary Heart Diseases Using Gene Expression Profiling; Stable Coronary Artery Disease, Cardiac Ischemia with and without Myocardial Necrosis. by Nabila Kazmi, Tom R Gaunt

“…We analyzed gene expression data from blood samples taken from normal people (n = 21), non-significant coronary artery disease (n = 93), patients with unstable angina (n = 16), stable coronary artery disease (n = 14) and myocardial infarction (MI; n = 207). We used a feature selection approach to identify a set of gene expression variables which successfully differentiate different cardiovascular diseases. …”
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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

“…Using a stratified transcriptome gene enrichment approach we attempted to identify adipose tissue-specific obesity genes in the unique polygenic Fat (F) mouse strain generated by selective breeding over 60 generations for divergent adiposity from a comparator Lean (L) strain.…”
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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

“…Isocitrate dehydrogenase wild-type glioblastoma (GBM) is characterised by a heterogeneous genetic landscape resulting from dynamic competition between tumour subclones to survive selective pressures. Improvements in metabolite identification and metabolome coverage have led to increased interest in clinically relevant applications of metabolomics. …”
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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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Combined Use of Gene Expression Modeling and siRNA Screening Identifies Genes and Pathways Which Enhance the Activity of Cisplatin When Added at No Effect Levels to Non-Small Cell... by Ada W Y Leung, Stacy S Hung, Ian Backstrom, Daniel Ricaurte, Brian Kwok, Steven Poon, Steven McKinney, Romulo Segovia, Jenna Rawji, Mohammed A Qadir, Samuel Aparicio, Peter C Stirling, Christian Steidl, Marcel B Bally

“…Being exposed to sub-lethal doses will induce changes in gene expression that contribute to the tumour cell's ability to survive and eventually contribute to the selective pressures leading to cisplatin resistance. …”
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Interpretable graph Kolmogorov–Arnold networks for multi-cancer classification and biomarker identification using multi-omics data by Fadi Alharbi, Nishant Budhiraja, Aleksandar Vakanski, Boyu Zhang, Murtada K. Elbashir, Harshith Guduru, Mohanad Mohammed

“…The proposed approach combines differential gene expression with DESeq2, Linear Models for Microarray (LIMMA), and Least Absolute Shrinkage and Selection Operator (LASSO) regression to reduce multi-omics data dimensionality while preserving relevant biological features. …”
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MOLECULAR AND GENETIC INSIGHTS OF ROOT-KNOT NEMATODES PATHOGENICITY: A REVIEW by Prabina Bhandari, Anjali Thapa, Anusha Ghimire, Sunil Ojha, Srijana Saud, Sanju Aryal

“…Protein analysis and molecular databases help identify down-regulated and up-regulated genes. Microarray technology can provide large-scale gene expression data on plant-nematode interaction, aiding in understanding nematode selection and feeding site alteration, thereby identifying genes controlling cell differentiation and division. …”
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Analytic approaches to clinical validation of results from preclinical models of glioblastoma: A systematic review. by Beth Fitt, Grace Loy, Edward Christopher, Paul M Brennan, Michael Tin Chung Poon

“…In 14 studies published between 2017 and 2020 using TCGA RNA microarray data that should have the same cohort, the median number of patients was 464.5 (interquartile range 220.5-525). …”
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