EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics

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

doi:10.1093/bioadv/vbad135

EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics

Bioinform Adv. 2023 Sep 26;3(1):vbad135. doi: 10.1093/bioadv/vbad135. eCollection 2023.

Authors

Chakit Arora¹, Natalia De Oliveira Rosa¹, Marin Matic¹, Mariastella Cascone¹, Pasquale Miglionico¹, Francesco Raimondi¹

Affiliation

¹ Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy.

Abstract

Summary: EXPANSION (https://expansion.bioinfolab.sns.it/) is an integrated web-server to explore the functional consequences of protein-coding alternative splice 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 on canonical sequences to identify functionally relevant splicing events. We also retrieved isoform-specific protein-protein interactions and binding regions from IntAct to uncover isoform-specific functions via gene-set over-representation analysis. Through EXPANSION, users can analyze precalculated or user-inputted DE transcript datasets, to easily gain functional insights on any protein spliceform of interest.

Availability and implementation: EXPANSION is freely available at http://expansion.bioinfolab.sns.it/. The code of the scripts used for EXPASION is available at: https://github.com/raimondilab/expansion. Datasets associated to this resource are available at the following URL: https://doi.org/10.5281/zenodo.8229120. The web-server was developed using Apache2 (https://https.apache.org/) and Flask (v2.0.2) (http://flask.pocoo.org/) for the web frontend and for the internal pipeline to handle back-end processes. We additionally used the following Python and JavaScript libraries at both back- and front-ends: D3 (v4), jQuery (v3.2.1), DataTables (v2.3.2), biopython (v1.79), gprofiler-officia l(v1.0.0), Mysql-connector-python (v8.0.31). To construct the API, Fast API library (v0.95.1) was used.