From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome
Authors
Tsoy, OlgaLouadi, Zakaria
Tong Lio, Chit
Baumbach, Jan
Kalinina, Olga
Gress, Alexander
Kacprowski, Tim
List, Markus
Contributors
Morić, IvanaĐorđević, Valentina
Conference object (Published version)
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© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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Alternative splicing (AS) can impact protein structure and lead to protein-protein
interaction (PPI) rewiring. Available PPI networks neglect alternative splicing isoforms: as
interactions might happen only between a subset of isoforms, the PPI network contains
both false-positive and false-negative interactions. Since it is not feasible to validate all
isoform-isoform interactions experimentally, we present a set of tools to investigate AS
on a network level: DIGGER to map splicing to the PPI network, as well as NEASE and
Spycone to evaluate the functional consequences of network rewiring.
DIGGER (https://exbio.wzw.tum.de/digger) integrates PPIs, domain-domain, and residuelevel
interactions - the structures that might be spliced in or out and result in interaction
gain or loss. Users can explore possible rewiring for an isoform or exon of interest and
extract relevant subnetworks. NEASE (https://github.com/louadi/NEASE) identifies pathways
that are significantly affected by... network rewiring. NEASE extends classic gene set
enrichment analysis by considering isoform-specific interactions affecting pathways.
Spycone (https://github.com/yollct/spycone) addresses the time-course changes in AS. It
searches for isoforms that demonstrate similar temporal splicing patterns and reflect the
splicing co-regulation. Spycone further integrates gene set, network, and splicing-aware
NEASE enrichment.
Overall, we offer a splicing-focused network analysis toolkit that allows for studying the
mechanistic consequences of AS.
Keywords:
bioinformatics / protein-protein interactions / alternative splicing / network enrichment / time series analysisSource:
4th Belgrade Bioinformatics Conference, 2023, 4, 51-51Publisher:
- Belgrade : Institute of molecular genetics and genetic engineering
Note:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
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Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Tsoy, Olga AU - Louadi, Zakaria AU - Tong Lio, Chit AU - Baumbach, Jan AU - Kalinina, Olga AU - Gress, Alexander AU - Kacprowski, Tim AU - List, Markus PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1993 AB - Alternative splicing (AS) can impact protein structure and lead to protein-protein interaction (PPI) rewiring. Available PPI networks neglect alternative splicing isoforms: as interactions might happen only between a subset of isoforms, the PPI network contains both false-positive and false-negative interactions. Since it is not feasible to validate all isoform-isoform interactions experimentally, we present a set of tools to investigate AS on a network level: DIGGER to map splicing to the PPI network, as well as NEASE and Spycone to evaluate the functional consequences of network rewiring. DIGGER (https://exbio.wzw.tum.de/digger) integrates PPIs, domain-domain, and residuelevel interactions - the structures that might be spliced in or out and result in interaction gain or loss. Users can explore possible rewiring for an isoform or exon of interest and extract relevant subnetworks. NEASE (https://github.com/louadi/NEASE) identifies pathways that are significantly affected by network rewiring. NEASE extends classic gene set enrichment analysis by considering isoform-specific interactions affecting pathways. Spycone (https://github.com/yollct/spycone) addresses the time-course changes in AS. It searches for isoforms that demonstrate similar temporal splicing patterns and reflect the splicing co-regulation. Spycone further integrates gene set, network, and splicing-aware NEASE enrichment. Overall, we offer a splicing-focused network analysis toolkit that allows for studying the mechanistic consequences of AS. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome EP - 51 SP - 51 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_1993 ER -
@conference{ author = "Tsoy, Olga and Louadi, Zakaria and Tong Lio, Chit and Baumbach, Jan and Kalinina, Olga and Gress, Alexander and Kacprowski, Tim and List, Markus", year = "2023", abstract = "Alternative splicing (AS) can impact protein structure and lead to protein-protein interaction (PPI) rewiring. Available PPI networks neglect alternative splicing isoforms: as interactions might happen only between a subset of isoforms, the PPI network contains both false-positive and false-negative interactions. Since it is not feasible to validate all isoform-isoform interactions experimentally, we present a set of tools to investigate AS on a network level: DIGGER to map splicing to the PPI network, as well as NEASE and Spycone to evaluate the functional consequences of network rewiring. DIGGER (https://exbio.wzw.tum.de/digger) integrates PPIs, domain-domain, and residuelevel interactions - the structures that might be spliced in or out and result in interaction gain or loss. Users can explore possible rewiring for an isoform or exon of interest and extract relevant subnetworks. NEASE (https://github.com/louadi/NEASE) identifies pathways that are significantly affected by network rewiring. NEASE extends classic gene set enrichment analysis by considering isoform-specific interactions affecting pathways. Spycone (https://github.com/yollct/spycone) addresses the time-course changes in AS. It searches for isoforms that demonstrate similar temporal splicing patterns and reflect the splicing co-regulation. Spycone further integrates gene set, network, and splicing-aware NEASE enrichment. Overall, we offer a splicing-focused network analysis toolkit that allows for studying the mechanistic consequences of AS.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome", pages = "51-51", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_1993" }
Tsoy, O., Louadi, Z., Tong Lio, C., Baumbach, J., Kalinina, O., Gress, A., Kacprowski, T.,& List, M.. (2023). From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 51-51. https://hdl.handle.net/21.15107/rcub_imagine_1993
Tsoy O, Louadi Z, Tong Lio C, Baumbach J, Kalinina O, Gress A, Kacprowski T, List M. From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome. in 4th Belgrade Bioinformatics Conference. 2023;4:51-51. https://hdl.handle.net/21.15107/rcub_imagine_1993 .
Tsoy, Olga, Louadi, Zakaria, Tong Lio, Chit, Baumbach, Jan, Kalinina, Olga, Gress, Alexander, Kacprowski, Tim, List, Markus, "From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome" in 4th Belgrade Bioinformatics Conference, 4 (2023):51-51, https://hdl.handle.net/21.15107/rcub_imagine_1993 .