CanIsoNet: a database to study the functional impact of isoform switching events in diseases

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Authors
Karakulak, Tülay
Szklarczyk, Damian
Saylan, Cemil Can
Moch, Holger
von Mering, Christian
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Publication date
17.04.2023
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01A - Journal article
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Parent work
Bioinformatics Advances
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Volume
3
Issue / Number
1
Pages / Duration
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Publisher / Publishing institution
Oxford University Press
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Abstract
Motivation: Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases. Results: Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks. Availability and implementation: CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web.
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Subject (DDC)
600 - Technik, Medizin, angewandte Wissenschaften
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ISSN
2635-0041
Language
English
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Yes
Publication status
Published
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Peer review of the complete publication
Open access category
Gold
License
'https://creativecommons.org/licenses/by/4.0/'
Citation
KARAKULAK, Tülay, Damian SZKLARCZYK, Cemil Can SAYLAN, Holger MOCH, Christian VON MERING und Abdullah KAHRAMAN, 2023. CanIsoNet: a database to study the functional impact of isoform switching events in diseases. Aida OUANGRAOUA (Hrsg.), Bioinformatics Advances. 17 April 2023. Bd. 3, Nr. 1. DOI 10.1093/bioadv/vbad050. Verfügbar unter: https://doi.org/10.26041/fhnw-5342