Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases
Abstract Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integr...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-12-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-021-02538-1 |
| _version_ | 1818573840320561152 |
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| author | Zakaria Louadi Maria L. Elkjaer Melissa Klug Chit Tong Lio Amit Fenn Zsolt Illes Dario Bongiovanni Jan Baumbach Tim Kacprowski Markus List Olga Tsoy |
| author_facet | Zakaria Louadi Maria L. Elkjaer Melissa Klug Chit Tong Lio Amit Fenn Zsolt Illes Dario Bongiovanni Jan Baumbach Tim Kacprowski Markus List Olga Tsoy |
| author_sort | Zakaria Louadi |
| collection | DOAJ |
| description | Abstract Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with structural annotations of protein-protein interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis. |
| first_indexed | 2024-12-15T00:18:16Z |
| format | Article |
| id | doaj.art-4c0fecaa3f3d44588d58bb08e10ab366 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-15T00:18:16Z |
| publishDate | 2021-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-4c0fecaa3f3d44588d58bb08e10ab3662022-12-21T22:42:24ZengBMCGenome Biology1474-760X2021-12-0122112210.1186/s13059-021-02538-1Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseasesZakaria Louadi0Maria L. Elkjaer1Melissa Klug2Chit Tong Lio3Amit Fenn4Zsolt Illes5Dario Bongiovanni6Jan Baumbach7Tim Kacprowski8Markus List9Olga Tsoy10Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of MunichDepartment of Neurology, Odense University HospitalChair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of MunichChair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of MunichChair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of MunichDepartment of Neurology, Odense University HospitalDepartment of Internal Medicine I, School of Medicine, University hospital rechts der Isar, Technical University of MunichInstitute for Computational Systems Biology, University of HamburgDivision Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical SchoolChair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of MunichInstitute for Computational Systems Biology, University of HamburgAbstract Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with structural annotations of protein-protein interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis.https://doi.org/10.1186/s13059-021-02538-1Alternative splicingDifferential splicingFunctional enrichmentSystems biologyProtein-protein interactionsDisease pathways |
| spellingShingle | Zakaria Louadi Maria L. Elkjaer Melissa Klug Chit Tong Lio Amit Fenn Zsolt Illes Dario Bongiovanni Jan Baumbach Tim Kacprowski Markus List Olga Tsoy Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases Genome Biology Alternative splicing Differential splicing Functional enrichment Systems biology Protein-protein interactions Disease pathways |
| title | Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases |
| title_full | Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases |
| title_fullStr | Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases |
| title_full_unstemmed | Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases |
| title_short | Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases |
| title_sort | functional enrichment of alternative splicing events with nease reveals insights into tissue identity and diseases |
| topic | Alternative splicing Differential splicing Functional enrichment Systems biology Protein-protein interactions Disease pathways |
| url | https://doi.org/10.1186/s13059-021-02538-1 |
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