Inferelator 3.0 Yeast Single-Cell Benchmarking Data
Description
Yeast single-cell gene expression data, database-derived prior knowledge network, and hand-curated gold standard network. Used to benchmark the Inferelator 3.0, SCENIC, and CellOracle.
Expression data (GSE144820_GSE125162.tsv.gz) is an integer count matrix [44343 rows x 6763 columns] with an index column (0) assembled from GSE144820 and GSE125162. Included is a paired metadata file (GSE144820_GSE125162_META_DATA.tsv.gz).
A database-derived prior knowledge network (YEASTRACT_20190713_BOTH.tsv) is a boolean connectivity matrix [6885 rows x 220 columns] with an index column (0) obtained from the YEASTRACT database on 07132019. It consists of edges which have both DNA localization evidence and evidence of changes to gene expression after TF perturbation.
A curated gold standard network (Tchourine_2018_yeast_gold_standard.tsv) is a signed connectivity matrix [993 rows x 98 columns] with an index column (0). Details of its construction have been published.
Files
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Additional details
References
- Jackson, C.A., Castro, D.M., Saldi, G.-A., Bonneau, R., and Gresham, D. (2020). Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. ELife 9, e51254.
- Jariani, A., Vermeersch, L., Cerulus, B., Perez-Samper, G., Voordeckers, K., Van Brussel, T., Thienpont, B., Lambrechts, D., and Verstrepen, K.J. (2020). A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast. ELife 9, e55320.
- Tchourine, K., Vogel, C., and Bonneau, R. (2018). Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. Cell Reports 23, 376–388.
- Teixeira, M.C., Monteiro, P.T., Palma, M., Costa, C., Godinho, C.P., Pais, P., Cavalheiro, M., Antunes, M., Lemos, A., Pedreira, T., et al. (2018). YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. Nucleic Acids Res 46, D348–D353.