Simulated networks from "Gene regulatory network structure informs the distribution of perturbation effects"

Data overview

This is the data release for "Gene regulatory network structure informs the distribution of perturbation effects" (Aguirre M, Spence JP, Sella G, and Pritchard JK, bioRxiv 2024). Here, we provide data from each synthetic gene regulatory network produced in our study, including summary statistics from gene-level perturbations. 

Synthetic networks

We provide two files for each of the 1,920 synthetic GRNs in our study. One is a plaintext log file which contains the graph generating parameters used to simulate each network. These log files are also aggregated into the plaintext tab-separated table, `networks.tsv`.

The other file is a python object (in gpickle format) that contains the instantiated network. This object is of type "grn", which is implemented in our project repository. All modeling parameters and summary statistics for the network (e.g., model betas which specify regulatory effects, and log2 fold-changes from knockout experiments) are stored as attributes in this object. Please refer to the main page of our repository for further documentation. 

These two files for each network (3,840 in total) are provided as a gzipped tarball, which can be extracted by running the command 

tar -xzf grns.tar.gz

The uncompressed data will occupy ~94GB of space on disk. Please refer to the project repository for information on how to process these data into summary matrixes.

Intermediate data used for figures

We also provide processed data files which can be used to replicate figures for our manuscript. These files are referenced in figure notebooks on our project repository, and include, for example, graphs and summary statistics used to show that various graph properties are controlled by parameters of our generating algorithm (see the second cell of the Fig. 2 notebook). 

These files are also provided as a gzipped tarball, which can be extracted by running the command

tar -xzf figdata.tar.gz

and whose contents will occupy ~38GB of space on disk when uncompressed.