ArticleBioinformatics advances2023
EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics.
Article in Bioinformatics advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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Who cites it
1 citing paper in PubMed.
- Exploring the Functional Consequences of Protein-Coding Alternative Splice Variants at a Genome Scale: A Guide to Utilizing EXPANSION.Methods in molecular biology (Clifton, N.J.) · 2026Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.