Abstract
Alternative splicing (AS) generates functionally distinct transcripts and is involved in multiple cellular processes, including stem cell differentiation. Several epithelial-to-mesenchymal transition-related splicing factors have also been associated with pluripotency. Concomitantly with the interest in studying AS in stem cell biology, the advent of next-generation sequencing of RNA (RNA-seq) has increased the public availability of transcriptomic data and enabled genome-wide AS studies. To facilitate performing such analyses in large publicly available or user-provided transcriptomics datasets, the psichomics R package provides an easy-to-use interface and efficient data visualization tools for AS quantification and integrative analyses of AS and gene expression data.
psichomics is employed herein to study AS changes between human stem cells and fibroblasts, based on dimensionality reduction, and median- and variance-based differential AS and gene expression analyses. Putative RNA-binding protein regulators involved in those alterations are then identified based on correlation analyses in large cohorts of human tissue transcriptomes. We identified several alterations, both novel and previously reported, in alternative splicing events and in the expression of their candidate regulators that are associated with stem cell differentiation into fibroblasts.
Key words
- Differential gene expression analysis
- Differential splicing analysis
- psichomics
- RNA-seq
- Integrative analyses
- Stemness
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Acknowledgments
We would like to thank Marie Bordone, Mariana Ferreira, Sara Mendes, Marta Bica, and Arthur Schneider, for providing valuable feedback and other contributions to the chapter and psichomics.
This work is a result of the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT). This work was also supported by: UID/BIM/50005/2019, project funded by Fundação para a Ciência e a Tecnologia (FCT)/ Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado; European Molecular Biology Organization [EMBO Installation Grant 3057 to N.L.B.-M.]; Fundação para a Ciência e a Tecnologia [FCT Investigator Starting Grant IF/00595/2014 to N.L.B.-M., PhD Studentship SFRH/BD/131312/2017 to N.S.-A., project PERSEIDS PTDC/EMS-SIS/0642/2014].
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Saraiva-Agostinho, N., Barbosa-Morais, N.L. (2020). Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0301-7_10
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DOI: https://doi.org/10.1007/978-1-0716-0301-7_10
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