PyGNA: A unified framework for geneset network analysis

Viola Fanfani, Fabio Cassano, Giovanni Stracquadanio

Research output: Contribution to journalArticlepeer-review


Background: Gene and protein interaction experiments provide unique opportunities to study the molecular wiring of a cell. Integrating high-throughput functional genomics data with this information can help identifying networks associated with complex diseases and phenotypes. 

Results: Here we introduce an integrated statistical framework to test network properties of single and multiple gene sets under different interaction models. We implemented this framework as an open-source software, called Python Gene set Network Analysis (PyGNA). Our software is designed for easy integration into existing analysis pipelines and to generate high quality figures and reports. We also developed PyGNA to take advantage of multi-core systems to generate calibrated null distributions on large datasets. We then present the results of extensive benchmarking of the tests implemented in PyGNA and a use case inspired by RNA sequencing data analysis, showing how PyGNA can be easily integrated to study biological networks. PyGNA is available at can be easily installed using the PyPi or Anaconda package managers, and Docker. 

Conclusions: We present a tool for network-aware gene set analysis. PyGNA can either be readily used and easily integrated into existing high-performance data analysis pipelines or as a Python package to implement new tests and analyses. With the increasing availability of population-scale omic data, PyGNA provides a viable approach for largescale gene set network analysis
Original languageEnglish
Article number476
Number of pages22
JournalBMC Bioinformatics
Publication statusPublished - 22 Oct 2020


  • geneset network analysis
  • biological networks
  • network analysis workflow


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