SPONGE: simple prior omics network GEnerator

• Published in: Bioinformatics (Oxford, England) Vol. 41; no. 7
• Main Authors: Hovan, Ladislav, Kuijjer, Marieke L
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2025; Oxford Publishing Limited (England)
• Subjects: Algorithms; Binding Sites; Computational Biology - methods; Databases, Genetic; Gene mapping; Gene Regulatory Networks; Information processing; Mapping; Modules; Networks; Peptide mapping; Protein interaction; Protein Interaction Mapping - methods; Proteins; Software; Transcription factors; Transcription Factors - metabolism
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btaf320

Abstract Summary Gene regulatory networks modelled from experimental data can be improved through the use of prior biological knowledge, e.g. transcription factor binding. There are several tools that utilize this information. However, the prior networks used with them are often not updated and may fail to reflect the most up-to-date information. Here we present SPONGE, a Python module designed to access information across biological databases, chiefly JASPAR and STRING, to model two types of networks—a prior gene regulatory network mapping transcription factors to genes based on their predicted binding sites, and a prior protein-protein interaction network mapping potential interactions between transcription factors. SPONGE is mainly designed to work with the PANDA algorithm and the corresponding NetZoo family of tools. However, the networks are provided in an easily adaptable format for other tools. SPONGE was designed with ease of use in mind, and it provides sensible default values for all of its parameters while giving the users the freedom to fine-tune them. Availability and implementation The code for the Python module and the documentation can be found in our GitHub repository.