Systematic analysis of alternative splicing in time course data using Spycone
Systematic analysis of alternative splicing in time course data using Spycone
Abstract During disease progression or organism development, alternative splicing (AS) may lead to isoform switches (IS) that demonstrate similar temporal patterns and reflect the AS co-regulation of such genes. Tools for dynamic process analysis usually neglect AS. Here we propose Spycone (https://github.com/yollct/spycone), a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection.
Baumbach Jan、Louadi Zakaria、Fenn Amit、List Markus、Lio Chit Tong、Tsoy Olga、Kacprowski Tim
Chair of Computational Systems Biology, University of Hamburg||Institute of Mathematics and Computer Science, University of Southern DenmarkChair of Computational Systems Biology, University of Hamburg||Chair of Experimental Bioinformatics, Technical University of MunichChair of Computational Systems Biology, University of Hamburg||Chair of Experimental Bioinformatics, Technical University of MunichChair of Experimental Bioinformatics, Technical University of MunichChair of Computational Systems Biology, University of Hamburg||Chair of Experimental Bioinformatics, Technical University of MunichChair of Computational Systems Biology, University of HamburgDivision Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universit?t Braunschweig and Hannover Medical School||Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig
生物科学研究方法、生物科学研究技术分子生物学遗传学
Alternative splicingtime seriesisoform switchomicsnetworksclustering
Baumbach Jan,Louadi Zakaria,Fenn Amit,List Markus,Lio Chit Tong,Tsoy Olga,Kacprowski Tim.Systematic analysis of alternative splicing in time course data using Spycone[EB/OL].(2025-03-28)[2025-04-30].https://www.biorxiv.org/content/10.1101/2022.04.28.489857.点此复制
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