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| http://dx.doi.org/10.1016/j.gendis.2024.101205 | DOI Listing |
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TRIAGE: an R package for regulatory gene analysis.
Brief Bioinform
November 2024
Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
Regulatory genes are critical determinants of cellular responses in development and disease, but standard RNA sequencing (RNA-seq) analysis workflows, such as differential expression analysis, have significant limitations in revealing the regulatory basis of cell identity and function. To address this challenge, we present the TRIAGE R package, a toolkit specifically designed to analyze regulatory elements in both bulk and single-cell RNA-seq datasets. The package is built upon TRIAGE methods, which leverage consortium-level H3K27me3 data to enrich for cell-type-specific regulatory regions.
View Article and Find Full Text PDFDeapioplatycodin D inhibits glioblastoma cell proliferation by inducing BNIP3L-mediated incomplete mitophagy.
Cancer Cell Int
January 2025
Department of Blood Transfusion, China-Japan, Union Hospital of Jilin University, Changchun, 130033, P.R. China.
Deapioplatycodin D (DPD) is a triterpenoid saponin natural compound isolated from the Chinese herb Platycodon grandiflorum that has antiviral and antitumor properties. This study aimed to investigate the effects of DPD on glioblastoma (GBM) cells and to determine its intrinsic mechanism of action. Using a CCK8 assay, it was found that DPD significantly inhibited the growth of GBM cells.
View Article and Find Full Text PDFGibberellin-3 induced dormancy and suppression of flower bud formation in pitaya (Hylocereus polyrhizus).
BMC Plant Biol
January 2025
Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
Background: Flowering is a complex, finely regulated process involving multiple phytohormones and transcription factors. However, flowering regulation in pitaya (Hylocereus polyrhizus) remains largely unexamined. This study addresses this gap by investigating gibberellin-3 (GA3) effects on flower bud (FB) development in pitaya.
View Article and Find Full Text PDFUnravelling the transcriptomic symphony of muscle ageing: key pathways and hub genes altered by ageing and caloric restriction in rat muscle revealed by RNA sequencing.
BMC Genomics
January 2025
Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK.
Age-related muscle wasting, sarcopenia is an extensive loss of muscle mass and strength with age and a major cause of disability and accidents in the elderly. Mechanisms purported to be involved in muscle ageing and sarcopenia are numerous but poorly understood, necessitating deeper study. Hence, we employed high-throughput RNA sequencing to survey the global changes in protein-coding gene expression occurring in skeletal muscle with age.
View Article and Find Full Text PDFAnalysis of differential gene expression of PBMC for the in vitro detection of drug sensitization.
Allergol Int
January 2025
Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany; Department of Dermatology and Allergy, University Hospital Aachen, Aachen, Germany.
Background: The detection of drug-specific activation of T cells in the lymphocyte transformation test (LTT) is mainly based on cell proliferation or cytokine secretion. However, the LTT presents with a varying sensitivity and specificity. The aim of our study was to analyse the genome wide gene expression of PBMC to identify drug allergy-specific gene regulation patterns.
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