{"id":2799,"date":"2023-06-13T01:08:23","date_gmt":"2023-06-13T00:08:23","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&#038;p=2799"},"modified":"2023-06-14T18:37:24","modified_gmt":"2023-06-14T17:37:24","slug":"from-protein-protein-to-isoform-isoform-interactions-the-toolkit-to-map-alternative-splicing-to-interactome","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/from-protein-protein-to-isoform-isoform-interactions-the-toolkit-to-map-alternative-splicing-to-interactome\/","title":{"rendered":"From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome"},"content":{"rendered":"\n<p>Olga Tsoy<sup>1*<\/sup>, Zakaria Louadi<sup>2<\/sup>, Chit Tong Lio<sup>2<\/sup>, Jan Baumbach<sup>1<\/sup>, Olga Kalinina<sup>3,4<\/sup>, Alexander Gress<sup>3,4<\/sup>, Tim Kacprowski<sup>5,6<\/sup>, and Markus List<sup>2<\/sup><\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>1<\/sup>University of Hamburg, Notkestrasse 9, Hamburg, Germany<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>2<\/sup>Technical University of Munich, Maximus-von-Imhof-Forum 3, Freising, Germany<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>3<\/sup>Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, Saarbr\u00fccken, Germany. <\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>4<\/sup>Saarland University, Homburg, Germany<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>5<\/sup>PLRI of TU Braunschweig and MHH, Rebenring 56, Brunswick, Germany<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>6<\/sup>BRICS, TU Braunschweig, Rebenring 56, Brunswick, Germany <\/p>\n\n\n\n<p>olga.tsoy [at] uni-hamburg.de<\/p>\n\n\n\n<p><strong>Abstract<\/strong><\/p>\n\n\n\n<p class=\"abstract-para\">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.<\/p>\n\n\n\n<p class=\"abstract-para\">DIGGER (<a href=\"https:\/\/exbio.wzw.tum.de\/digger\">https:\/\/exbio.wzw.tum.de\/digger<\/a>) integrates PPIs, domain-domain, and residue-level interactions &#8211; 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 (<a href=\"https:\/\/github.com\/louadi\/NEASE\">https:\/\/github.com\/louadi\/NEASE<\/a>) identifies pathways that are significantly affected by network rewiring. NEASE extends classic gene set enrichment analysis by considering isoform-specific interactions affecting pathways. Spycone (<a href=\"https:\/\/github.com\/yollct\/spycone\">https:\/\/github.com\/yollct\/spycone<\/a>) 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.<\/p>\n\n\n\n<p class=\"abstract-para\">Overall, we offer a splicing-focused network analysis toolkit that allows for studying the mechanistic consequences of AS.<\/p>\n\n\n\n<p class=\"abstract-para\"><strong>Keywords:<\/strong> bioinformatics, protein-protein interactions, alternative splicing, network enrichment, time series analysis<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Olga Tsoy<sup>1*<\/sup>, Zakaria Louadi<sup>2<\/sup>, Chit Tong Lio<sup>2<\/sup>, Jan Baumbach<sup>1<\/sup>, Olga Kalinina<sup>3,4<\/sup>, Alexander Gress<sup>3,4<\/sup>, Tim Kacprowski<sup>5,6<\/sup>, and Markus List<sup>2<\/sup><\/p>\n<p class=\"affiliation-para\"><sup>1<\/sup>University of Hamburg, Notkestrasse 9, Hamburg, Germany<\/p>\n<p class=\"affiliation-para\"><sup>2<\/sup>Technical University of Munich, Maximus-von-Imhof-Forum 3, Freising, Germany<\/p>\n<p class=\"affiliation-para\"><sup>3<\/sup>Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, Saarbr\u00fccken, Germany. <\/p>\n<p class=\"affiliation-para\"><sup>4<\/sup>Saarland University, Homburg, Germany<\/p>\n<p class=\"affiliation-para\"><sup>5<\/sup>PLRI of TU Braunschweig and MHH, Rebenring 56, Brunswick, Germany<\/p>\n<p class=\"affiliation-para\"><sup>6<\/sup>BRICS, TU Braunschweig, Rebenring 56, Brunswick, Germany <\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/from-protein-protein-to-isoform-isoform-interactions-the-toolkit-to-map-alternative-splicing-to-interactome\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[18],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.0 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"Olga Tsoy1*, Zakaria Louadi2, Chit Tong Lio2, Jan Baumbach1, Olga Kalinina3,4, Alexander Gress3,4, Tim Kacprowski5,6, and Markus List21University of Hamburg, Notkestrasse 9, Hamburg, Germany2Technical University of Munich, Maximus-von-Imhof-Forum 3, Freising, Germany3Helmholtz Centre for Infection Research, Inhoffenstra\u00dfe 7, Saarbr\u00fccken, Germany. 4Saarland University, Homburg, Germany5PLRI of TU Braunschweig and MHH, Rebenring 56, Brunswick, Germany6BRICS, TU Braunschweig, Rebenring 56, Brunswick, Germany Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/from-protein-protein-to-isoform-isoform-interactions-the-toolkit-to-map-alternative-splicing-to-interactome\/\" \/>\n<meta property=\"og:site_name\" content=\"BelBi 2023\" \/>\n<meta property=\"article:modified_time\" content=\"2023-06-14T17:37:24+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/from-protein-protein-to-isoform-isoform-interactions-the-toolkit-to-map-alternative-splicing-to-interactome\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/from-protein-protein-to-isoform-isoform-interactions-the-toolkit-to-map-alternative-splicing-to-interactome\/\",\"name\":\"From protein-protein to isoform-isoform interactions: the toolkit to map alternative splicing to interactome - 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