Systematic analysis of alternative splicing in time course data using Spycone

Chit Tong Lio; Gordon Grabert; Zakaria Louadi; Amit Fenn; Jan Baumbach; Tim Kacprowski; Markus List; Olga Tsoy

doi:10.1093/bioinformatics/btac846

Systematic analysis of alternative splicing in time course data using Spycone

Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy

Assistant Professorship of Data Science in Systems Biology

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Motivation: During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. Results: Here, we propose 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.

Original language	English
Article number	btac846
Journal	Bioinformatics
Volume	39
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/btac846
State	Published - 1 Jan 2023

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title = "Systematic analysis of alternative splicing in time course data using Spycone",

abstract = "Motivation: During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. Results: Here, we propose 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.",

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AU - Lio, Chit Tong

AU - Grabert, Gordon

AU - Louadi, Zakaria

AU - Fenn, Amit

AU - Baumbach, Jan

AU - Kacprowski, Tim

AU - List, Markus

AU - Tsoy, Olga

PY - 2023/1/1

Y1 - 2023/1/1

N2 - Motivation: During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. Results: Here, we propose 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.

AB - Motivation: During disease progression or organism development, alternative splicing may lead to isoform switches that demonstrate similar temporal patterns and reflect the alternative splicing co-regulation of such genes. Tools for dynamic process analysis usually neglect alternative splicing. Results: Here, we propose 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.

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Systematic analysis of alternative splicing in time course data using Spycone

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