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reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation

Stefano Manzini1, Marco Busnelli2, Alice Colombo2

  • 1Department of Pharmacological and Biomolecular Sciences, Università Degli Studi Di Milano, Milan, Italy. stefano.manzini@unimi.it.

Scientific Reports
|December 7, 2021
PubMed
Summary
This summary is machine-generated.

Functional enrichment analysis aids biological insight from gene expression data. The reString software simplifies retrieving and visualizing STRING database enrichments for researchers, streamlining complex data interpretation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Functional enrichment analysis is crucial for interpreting gene expression data from high-throughput experiments.
  • Existing methods can be complex and time-consuming for researchers without specialized bioinformatics skills.
  • Tools like STRING provide valuable protein-protein interaction networks and functional enrichment data.

Purpose of the Study:

  • To develop a user-friendly software tool, reString, for simplifying functional enrichment analysis.
  • To enable seamless retrieval and aggregation of functional enrichment data from the STRING database.
  • To facilitate the generation of publication-quality visualizations from complex gene sets.

Main Methods:

  • Developed reString, a cross-platform software application.
  • Integrated STRING database functionality for retrieving functional enrichments.
  • Implemented features for aggregating results into tables and generating clustermaps and bubble plots.

Main Results:

  • reString automates the retrieval of functional enrichments from multiple gene sets via the STRING database.
  • The software generates human-readable table summaries of enrichment findings.
  • User-customizable publication-grade clustermaps and bubble plots can be produced easily.

Conclusions:

  • reString significantly simplifies the process of functional enrichment analysis for biologists.
  • The software reduces the need for specialized bioinformatics expertise.
  • reString enhances the interpretation of large-scale gene expression datasets through accessible visualization.