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Motivation: graphics for RNA-sequencing and microarray gene expression analyses may contain upwards of tens of thousands of points. Details about certain genes or samples of interest are easily obscured in such dense summary displays. Incorporating interactivity into summary plots would enable additional information to be displayed on demand and facilitate intuitive data exploration.
Results: The open-source Glimma package creates interactive graphics for exploring gene expression analysis with a few simple R commands. It extends popular plots found in the limma package, such as multi-dimensional scaling plots and mean-difference plots, to allow individual data points to be queried and additional annotation information to be displayed upon hovering or selecting particular points. It also offers links between plots so that more information can be revealed on demand. Glimma is widely applicable, supporting data analyses from a number of well-established Bioconductor workflows ( limma , edgeR and DESeq2 ) and uses D3/JavaScript to produce HTML pages with interactive displays that enable more effective data exploration by end-users. Results from Glimma can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.
Availability And Implementation: The Glimma R package is available from http://bioconductor.org/packages/Glimma/ .
Contact: su.s@wehi.edu.au , law@wehi.edu.au or mritchie@wehi.edu.au.
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http://dx.doi.org/10.1093/bioinformatics/btx094 | DOI Listing |
Zhonghua Er Ke Za Zhi
March 2025
Department of Pediatrics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
To analyze a novel intronic variant in the SPTB gene and explore its effect on SPTB mRNA splicing. Clinical data of a child diagnosed with hereditary spherocytosis (HS) and admitted to the First Affiliated Hospital of Xi'an Jiaotong University in February 2022 were analyzed retrospectively. Whole genome sequencing was used to identify disease-causing mutations and the results were validated with Sanger sequencing, mRNA sequencing was used to determine the SPTB gene's mRNA expression level, and bioinformatics tools were used for splicing site prediction and analysis.
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Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9, Canada.
Fabrication of macroporous scaffolds with favorable mechanical and biological properties based on natural polysaccharides embedding inorganic components has emerged as a promising alternative for bone regeneration. We hypothesized that partially demineralized chitin containing natural calcium phosphate with suitable mechanical strength as the inorganic component is more favorable for this purpose than commonly used nano-hydroxyapatite (nHA). Therefore, a macroporous cryogel scaffold composed of gelatin (G), nanofibrillated cellulose (NFC), and partially demineralized chitin (PDCh), chemically crosslinked with oxidized dextran (ODex), was developed in this study.
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College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China. Electronic address:
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Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China. Electronic address:
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March 2025
Faculty of Medicine, Comenius University in Bratislava, 84215 Bratislava, Slovakia.
Endometrial cancer is a significant public health concern with rising incidence rates globally. Understanding the molecular mechanisms underlying this disease is crucial for developing effective therapeutic strategies. Our study aimed to characterize transcriptional changes in endometrial cancer tissues compared to adjusted healthy tissue.
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