EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice (AS) variants. We combined information from Differentially Expressed (DE) protein-coding transcripts from cancer genomics, together with domain architecture, protein interaction network, and gene enrichment analysis to provide an easy-to-interpret view of the effects of protein-coding splice variants. We retrieved all the protein-coding Ensembl transcripts and mapped Interpro domains and Post-translational modifications (PTMs) on canonical sequences to identify functionally relevant splicing events. We also retrieved isoform-specific protein-protein interactions (PPIs) and binding regions from IntAct to uncover isoform-specific functions via gene-sets over-representation analysis. Through EXPANSION, users can analyse pre-calculated or user-inputted DE transcript datasets, to easily gain functional insights on any protein spliceform of interest.

EXPANSION: A Webserver to Explore the Functional Consequences of Protein-Coding Alternative Splice Variants in Cancer Genomics

Arora, Chakit
;
De Oliveira Rosa, Natalia
;
Matic, Marin;Cascone, Mariastella;Miglionico, Pasquale;Raimondi, Francesco
2023

Abstract

EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice (AS) variants. We combined information from Differentially Expressed (DE) protein-coding transcripts from cancer genomics, together with domain architecture, protein interaction network, and gene enrichment analysis to provide an easy-to-interpret view of the effects of protein-coding splice variants. We retrieved all the protein-coding Ensembl transcripts and mapped Interpro domains and Post-translational modifications (PTMs) on canonical sequences to identify functionally relevant splicing events. We also retrieved isoform-specific protein-protein interactions (PPIs) and binding regions from IntAct to uncover isoform-specific functions via gene-sets over-representation analysis. Through EXPANSION, users can analyse pre-calculated or user-inputted DE transcript datasets, to easily gain functional insights on any protein spliceform of interest.
2023
Settore BIO/11 - Biologia Molecolare
Protein domains; protein interaction networks; alternative splicing; functional genomics
   Decoding and recoding onco-GPCR signaling through integrative bioinformatics and protein engineering
   Associazione Italiana per la ricerca sul Cancro
   My First Airc Grant 2020
   24317
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11384/134722
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