New bioRχiv pre-print
We have a new BioRχiv pre-print by Ladislav, in which we present SPONGE, a new Python tool that simplifies generating up-to-date priors for gene regulatory network (GRN) modeling, boosting their reproducibility and accuracy.
Priors based on TF binding and protein interactions help integrate biological knowledge into GRN predictions. However, while databases update regularly, priors often circulate between users for years without updates, likely due to the challenges of generating them.
We therefore developed SPONGE, a tool to automatically create up-to-date priors for more consistent, reproducible results. SPONGE uses JASPAR and STRING data to build priors compatible with NetZoo (workflow overview in Figure A below), but can be easily adaptable to work with other tools and in other pipelines.
Using SPONGE, we compared priors generated on JASPAR2024 and JASPAR2022. We found that, while most prior edges were consistent between the two releases, there was still a substantial difference after data updates (Figure B-E). Thus, our findings show how SPONGE helps keep priors current with biological data advances.
SPONGE is designed with flexible parameters, allowing users to customize priors as needed. We released the code on GitHub (link) and the priors generated for the project on Zenodo (link). We hope SPONGE enables reproducible and up-to-date GRN research across platforms!
More information on the pre-print can be found here.
