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CanIsoNet: a database to study the functional impact of isoform switching events in diseases
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 a...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133402/ https://www.ncbi.nlm.nih.gov/pubmed/37123454 http://dx.doi.org/10.1093/bioadv/vbad050 |
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author | Karakulak, Tülay Szklarczyk, Damian Saylan, Cemil Can Moch, Holger von Mering, Christian Kahraman, Abdullah |
author_facet | Karakulak, Tülay Szklarczyk, Damian Saylan, Cemil Can Moch, Holger von Mering, Christian Kahraman, Abdullah |
author_sort | Karakulak, Tülay |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online. |
format | Online Article Text |
id | pubmed-10133402 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-101334022023-04-28 CanIsoNet: a database to study the functional impact of isoform switching events in diseases Karakulak, Tülay Szklarczyk, Damian Saylan, Cemil Can Moch, Holger von Mering, Christian Kahraman, Abdullah Bioinform Adv Application Note 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online. Oxford University Press 2023-04-17 /pmc/articles/PMC10133402/ /pubmed/37123454 http://dx.doi.org/10.1093/bioadv/vbad050 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Application Note Karakulak, Tülay Szklarczyk, Damian Saylan, Cemil Can Moch, Holger von Mering, Christian Kahraman, Abdullah CanIsoNet: a database to study the functional impact of isoform switching events in diseases |
title | CanIsoNet: a database to study the functional impact of isoform switching events in diseases |
title_full | CanIsoNet: a database to study the functional impact of isoform switching events in diseases |
title_fullStr | CanIsoNet: a database to study the functional impact of isoform switching events in diseases |
title_full_unstemmed | CanIsoNet: a database to study the functional impact of isoform switching events in diseases |
title_short | CanIsoNet: a database to study the functional impact of isoform switching events in diseases |
title_sort | canisonet: a database to study the functional impact of isoform switching events in diseases |
topic | Application Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133402/ https://www.ncbi.nlm.nih.gov/pubmed/37123454 http://dx.doi.org/10.1093/bioadv/vbad050 |
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