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Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

Abstract

We present a systematic evaluation of state-of-the-art algorithms for inferring gene regulatory networks from single-cell transcriptional data. As the ground truth for assessing accuracy, we use synthetic networks with predictable trajectories, literature-curated Boolean models and diverse transcriptional regulatory networks. We develop a strategy to simulate single-cell transcriptional data from synthetic and Boolean networks that avoids pitfalls of previously used methods. Furthermore, we collect networks from multiple experimental single-cell RNA-seq datasets. We develop an evaluation framework called BEELINE. We find that the area under the precision-recall curve and early precision of the algorithms are moderate. The methods are better in recovering interactions in synthetic networks than Boolean models. The algorithms with the best early precision values for Boolean models also perform well on experimental datasets. Techniques that do not require pseudotime-ordered cells are generally more accurate. Based on these results, we present recommendations to end users. BEELINE will aid the development of gene regulatory network inference algorithms.

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Fig. 1: An overview of the BEELINE evaluation framework.
Fig. 2: Summary of results for datasets from synthetic networks.
Fig. 3: Visualization of t-SNE projections of simulations reveals trajectories leading to steady states that correspond to those of the curated models.
Fig. 4: Summary of results for ten datasets without dropouts from curated models.
Fig. 5: Summary of EPR results for experimental single-cell RNA-seq datasets.
Fig. 6: Summary of properties of GRN inference algorithms and results obtained from BEELINE.

Data availability

The datasets simulated from the synthetic networks and curated models and the processed experimental single-cell gene expression datasets are available on Zenodo at https://doi.org/10.5281/zenodo.3378975. The gene experimental scRNA-seq datasets we downloaded from Gene Expression Omnibus had the accession numbers GSE81252 (hHEP), GSE75748 (hESC), GSE98664 (mESC), GSE48968 (mouse dendritic cell) and GSE81682 (mHSC). Source data for Figs. 2 and 4–6 are provided with the paper.

Code availability

A Python implementation of the BEELINE framework is available under the GNU General Public License v.3 at https://github.com/murali-group/BEELINE.

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Acknowledgements

Grants from the National Science Foundation (nos. CCF-1617678 and DBI-1759858) and the National Cancer Institute (grant no. UH2CA203768) supported this work. The research is also based on work supported by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), via the Army Research Office (ARO) under cooperative agreement no. W911NF-17-2-0105. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of the ODNI, IARPA, ARO or the US Government. The US Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation thereon. The funding bodies played no role in the design of the study, the collection, analysis and interpretation of data or in writing the manuscript.

Author information

Authors and Affiliations

Authors

Contributions

A.P. and T.M.M. conceived and designed the analysis and selected the GRN algorithms. A.P. implemented BEELINE and led the analysis. A.P.J., A.P. and T.M.M. developed BoolODE and A.P.J. implemented it. A.P. and A.P.J. created and processed datasets. A.P., A.P.J., J.N.L. and A.B. contributed evaluation strategies. All authors analyzed the results. A.P., A.P.J. and T.M.M. wrote the paper. T.M.M. supervised the project.

Corresponding author

Correspondence to T. M. Murali.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nicole Rusk and Lin Tang were the primary editors on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Integrated supplementary information

Supplementary Figure 1 Comparison of datasets simulated from synthetic networks by using BoolODE and GeneNetWeaver.

Each row corresponds to the synthetic network indicated by the label on the left. (a) The network itself, with red edges representing inhibition and blue edges representing activation. (b) A 2D t-SNE visualization of one BoolODE-generated dataset for 2,000 cells. The color of each point indicates the simulation time: blue for earlier, green for intermediate, and yellow for later times. (c) Each colour corresponds to a different subset of cells obtained by using k-means clustering of the BoolODE-generated dataset, with k set to the number of expected steady states. (d) A 2-D t-SNE visualization of one GeneNetWeaver output.

Supplementary Figure 2 Box plots of AUPRC values for synthetic networks.

Each row corresponds to one of the six synthetic networks. Each column corresponds to an algorithm. Red, blue, yellow, purple and green box plots correspond to AUPRC values for 10 datasets with 100, 200, 500, 2,000, and 5,000 cells, respectively. The gray dotted line indicates the AUPRC value for a random predictor, which is equal to the network’s density. In every boxplot, the box shows the 1st and 3rd quartile, and whiskers denote 1.5 times the interquartile range.

Supplementary Figure 3 Box plots of AUROC values for synthetic networks.

Each row corresponds to one of the six synthetic networks. Each column corresponds to an algorithm. Red, blue, yellow, purple and green box plots correspond to AUROC values for 10 datasets with 100, 200, 500, 2,000, and 5,000 cells, respectively. The gray dotted line indicates the AUROC value for a random predictor (0.5). In every boxplot, the box shows the 1st and 3rd quartile, and whiskers denote 1.5 times the interquartile range.

Supplementary Figure 4 Box plots of AUPRC values for curated models.

Each row corresponds to one of the four curated models. Each column corresponds to an algorithm. Red, blue and yellow box plots correspond to AUPRC values for 10 datasets with no dropouts, a dropout rate of q = 50, and a dropout rate of q = 70, respectively. The gray dotted line indicates the AUPRC value for a random predictor, i.e., the network density. In every boxplot, the box shows the 1st and 3rd quartile, and whiskers denote 1.5 times the interquartile range.

Supplementary Figure 5 Box plots of AUROC values for curated models.

Each row corresponds to one of the four curated models. Each column corresponds to an algorithm. Red, blue and yellow box plots correspond to AUROC values for 10 datasets with no dropouts, a dropout rate of q = 50, and a dropout rate of q = 70, respectively. The gray dotted line indicates the AUROC value for a random predictor (0.5). In all boxplots, the box shows the 1st and 3rd quartile, and whiskers denote 1.5 times the interquartile range.

Supplementary Figure 6 Box plots of early precision values for curated models.

Each row corresponds to one of the four curated models. Each column corresponds to an algorithm. Red, blue and yellow box plots correspond to early precision values for 10 datasets with no dropouts, a dropout rate of q = 50, and a dropout rate of q = 70, respectively. The gray dotted line indicates the early precision value for a random predictor (network density). In each boxplot, the box shows the 1st and 3rd quartile, and whiskers denote 1.5 times the interquartile range.

Supplementary Figure 7 Scalability of GRN algorithms on experimental single-cell RNA-Seq datasets.

Variation in running time and memory usage of GRN inference algorithms with respect to number of genes for three experimental single-cell RNA-Seq datasets. Each point represents the mean running time or memory across all three datasets and the shaded regions correspond to one standard deviation around the mean. Missing values indicate that the method either did not complete after one day or gave a runtime error. We did not consider SCNS since it took over a day on the 19-gene GSD Boolean model. We obtained these results on a computer with a 32-core 2.0GHz processor and 32GB of memory running Ubuntu 18.04.

Supplementary Figure 8 Summary of EPR values for experimental single-cell RNA-Seq datasets with 500 and 1000 genes.

Summary of EPR results for experimental single-cell RNA-seq datasets. The left half of the figure (500 genes) shows results for datasets composed of the 500 most-varying genes. Each row corresponds to one scRNA-seq dataset. The first three columns report network statistics. The next six columns report EPR values. The right half (1000 genes) shows results for the 1000 most-varying genes. In both sections, algorithms are sorted by median EPR across the datasets (rows) for the 500 gene set. For each dataset, the color in each cell is proportional to the corresponding value scaled between 0 and 1 (ignoring values that are less than that of a random predictor, which are shown as black squares). We display the highest and lowest values for each dataset inside the corresponding cells. Abbreviations: GENI: GENIE3, GRNB: GRNBoost2, PCOR: PPCOR, SINC: SINCERITIES.

Supplementary Figure 9 Summary of AUPRC ratio values for experimental single-cell RNA-Seq datasets with TFs + 500 and TFs + 1000 genes.

Summary of AUPRC ratio results for experimental single-cell RNA-seq datasets. The left half of the figure (TFs+500 genes) shows results for datasets composed of all significantly-varying TFs and the 500 most-varying genes. Each row corresponds to one scRNA-seq dataset. The first three columns report network statistics. The next six columns report AUPRC ratios. The right half (TFs+1000 genes) shows results for all significantly-varying TFs and the 1000 most-varying genes. In both sections, algorithms are sorted by median AUPRC ratio across the datasets (rows) for the TFs+500 gene set. For each dataset, the color in each cell is proportional to the corresponding value scaled between 0 and 1 (ignoring values that are less than that of a random predictor, which are shown as black squares). We display the highest and lowest values for each dataset inside the corresponding cells. Abbreviations: GENI: GENIE3, GRNB: GRNBoost2, PCOR: PPCOR, SINC: SINCERITIES.

Supplementary Figure 10 Summary of AUPRC ratio values for experimental single-cell RNA-Seq datasets with 500 and 1000 genes.

Summary of AUPRC ratio values for experimental single-cell RNA-seq datasets. The left half of the figure (500 genes) shows results for datasets composed of the 500 most-varying genes. Each row corresponds to one scRNA-seq dataset. The first three columns report network statistics. The next six columns report AUPRC ratios. The right half (1000 genes) shows results for the 1000 most-varying genes. In both sections, algorithms are sorted by median AUPRC ratios across the datasets (rows) for the 500 gene set. For each dataset, the color in each cell is proportional to the corresponding value scaled between 0 and 1 (ignoring values that are less than that of a random predictor, which are shown as black squares). We display the highest and lowest values for each dataset inside the corresponding cells. Abbreviations: GENI: GENIE3, GRNB: GRNBoost2, PCOR: PPCOR, SINC: SINCERITIES.

Supplementary Figure 11 Effect of pseudotime shuffling on AUPRC values for synthetic networks.

(a) Comparison of AUPRC values for networks inferred with original pseudotimes (blue) and shuffled within three window sizes 15% (light blue), 30% (beige) or 45% (orange). Each row corresponds to one of the three synthetic networks with single trajectories (Linear, Cycle, and Linear Long). Each boxplot represents 10 AUPRC values (10 datasets each containing 2,000 cells). The gray dotted line indicates the AUPRC value for a random predictor (i.e., the network density). In each boxplot, the box shows the 1st and 3rd quartile, and whiskers denote 1.5 times the interquartile range. (b) Median Pearson correlation between original and shuffled pseudotimes. For each network and window-size the median is over 10 datasets.

Supplementary information

Supplementary Information

Supplementary Figs. 1–11 and notes.

Reporting Summary

Supplementary Table 1

Summary of synthetic networks

Supplementary Table 2

Summary of published Boolean models.

Supplementary Table 3

Statistics on experimental single-cell RNA-seq datasets.

Supplementary Table 4

Statistics on networks used to evaluate experimental single-cell RNA-seq datasets

Supplementary Table 5

Truth table and parameter values for the BoolODE example.

Supplementary Table 6

Kinetic parameters used in BoolODE.

Supplementary Table 7

Parameters used to generate synthetic datasets.

Supplementary Table 8

Median Pearson correlation between simulation time and pseudotime computed using Slingshot for different dropout rates.

Supplementary Table 9

Software version details for the 12 GRN inference algorithms in BEELINE.

Source data

Source Data Fig. 2

Synthetic networks.

Source Data Fig. 4

Curated models.

Source Data Fig. 5

Experimental.

Source Data Fig. 6

Summary.

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Pratapa, A., Jalihal, A.P., Law, J.N. et al. Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nat Methods 17, 147–154 (2020). https://doi.org/10.1038/s41592-019-0690-6

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