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. 2023 Jul 13;20(9):1355–1367. doi: 10.1038/s41592-023-01938-4

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a, Computational approach to infer differentiation drivers from a SCENIC+ analysis. First, differentiating cells are ordered by pseudotime. Second, for each eRegulon, a standardized GAM is fitted along the pseudotime axis for its expression and its target genes (or regions) enrichment scores and each cell in a certain quantile of the GAM TF expression curve is mapped to its future cells in the same quantile in the GAM regulon enrichment curve. Finally, the differentiation force of a cell and regulon is defined as the distance from the TF expression curve to its future cell in the regulon enrichment curve. b, Arrow grid representation along the differentiation of OPCs to mature oligodendrocytes in the mouse cortex (4,435 cells). c–e, UMAP dimensionality reduction of 3,104 pseudocells from the fly eye based on target gene and region enrichment scores, with a schematic representation of the fly eye-antennal disc (c), scVelo velocity arrows (d) and MultiVelo velocity arrows (e). f, Representation of svp dynamics along the two paths in eye disc differentiation. The gray horizontal line represents the TF expression threshold for arrows to be drawn. For cells below this threshold, the GRN velocity values are set to 0. The gray dashed line represents the penalization curve, which is the GAM fitted curve drawn using the standardized data across all possible paths for the cells in that path. Those points where the penalization and the TF expression curve disagree are considered artifacts (the TF gene seems to be expressed even if there is low expression, due to the standardization of the TF curve in that specific path). The red curve represents the GAM fitted curve using the standardized TF expression data (along the path) and the blue curve represents the GAM fitted curve using the standardized gene enrichment scores (along the path). g, Arrow grid representation along the eye disc differentiation.