Figure 1. Schematic illustration of CSN and NDM construction and our statistic model. (A) CSN and NDM construction. (i) ... Figure 1. Schematic illustration.

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Figure 1. Schematic illustration of CSN and NDM construction and our statistic model. (A) CSN and NDM construction. (i) ... Figure 1. Schematic illustration of CSN and NDM construction and our statistic model. (A) CSN and NDM construction. (i) Make scatter diagrams for every two genes, where each point represents a cell, and x- and y-values are the expression values of the two genes in the n cells. Then m genes lead to m (m – 1)/2 scatter diagrams. (ii) In the scatter diagram of genes x and y, the plot i with red color means there is an edge between genes x and y in the cell i network based on our statistic model, and if the plot is blue, there is no edge. Then, we can construct n cell-specific networks corresponding to n cells, respectively. (iii) By counting the number of edges connected to each gene in each CSN, we can get the network degree matrix, which is still comprised of m rows and n columns, as the same as GEM, and thus it can be analyzed by any existing method. (B) Our statistic model for edge between genes x and y. Near the plot or cell k, make the light and medium grey boxes to represent the neighborhood of x<sub>k</sub> and y<sub>k</sub> respectively. The intersection of two boxes is the dark grey box, which represents the neighborhood of (x<sub>k</sub>, y<sub>k</sub>). The number of plots in the light, medium and dark grey boxes is n<sub>x</sub><sup>(</sup><sup>k</sup><sup>)</sup>, n<sub>y</sub><sup>(</sup><sup>k</sup><sup>)</sup> and n<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> respectively. Design the statistic as ρ<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup>. If x and y are independent of each other, the statistic follows normal distribution and the mean value and variance can be calculated. If the statistic ρ<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> is larger than a significant level, label plot k with red color, which means there is an edge between x and y in cell k; otherwise there is no edge. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. Probability density functions of the statistic ρxy(k) when (A) ... Figure 2. Probability density functions of the statistic ρ<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> when (A) genes x and y are independent of each other; (B) genes x and y are dependent in partial cells; (C) genes x and y are dependent in all cells. Red plots in the scatter diagrams of genes x and y represent that the statistic ρ<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> in these plots is larger than the significant level of 0.01 and edge<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> = 1, which corresponds to the red area in the density function graphs. Blue plots represent that ρ<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> in these plots is smaller than the significant level of 0.01 and edge<sub>xy</sub><sup>(</sup><sup>k</sup><sup>)</sup> = 0, which corresponds to the blue lines in the density function graphs. Sample size n = 500, and n<sub>x</sub><sup>(</sup><sup>k</sup><sup>)</sup> = n<sub>y</sub><sup>(</sup><sup>k</sup><sup>)</sup> = 0.1n. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. Illustration of network analyses of Chu-type dataset based on our CSN method. (A) Correlation network of ... Figure 3. Illustration of network analyses of Chu-type dataset based on our CSN method. (A) Correlation network of grouped cells (edge means correlation coefficient of two genes > 0.7) and CSN of a single cell (edge means normalized statistic of two genes > 8). The genes used in the network construction are all the same. (B) t-SNE plots of Chu-type dataset, where different cell types could be distinguished clearly (ARI = 0.98). (C) Scatter diagrams of genes POU5F1 and GATA6, colored by the cell types listed in (B). (D) Performance of edge POU5F1 - GATA6 in the t-SNE plots, colored by the normalized statistic. (E-J) Performance of genes FBXO33 and ZHX2 in the t-SNE plots, colored by (E) the gene expression level of FBXO33, (F) the network degree level of FBXO33, (G) the normalized statistic of edge FBXO33-KDR, (H) the gene expression level of ZHX2, (I) the network degree level of ZHX2, (J) the normalized statistic of edge ZHX2-PECAM1. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 4. Illustration of network analyses of Chu-time dataset based on our CSN method. (A) CSNs of some single cells ... Figure 4. Illustration of network analyses of Chu-time dataset based on our CSN method. (A) CSNs of some single cells with the 20 genes that are involved in human embryo development, where the larger normalized statistic leads to the darker edge. (B) Network degrees of POU5F1, NANOG and CDH1 along the six time points of embryo development. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. The clustering performances of NDM and GEM on four datasets Figure 5. The clustering performances of NDM and GEM on four datasets. t-SNE plots are used for visualization and ... Figure 5. The clustering performances of NDM and GEM on four datasets. t-SNE plots are used for visualization and different colors represent different cell types. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 6. Comparison of GEM and NDM based on TCGA adenocarcinoma and squamous cell carcinoma bulk RNA-seq data. (A) ... Figure 6. Comparison of GEM and NDM based on TCGA adenocarcinoma and squamous cell carcinoma bulk RNA-seq data. (A) Clustering performance (t-SNE) between GEM and NDM. Different colors represent different cell types. (B) The expression level FPKM and network degree of gene SPRR2E. (C) Squamous cell carcinoma can be divided into two parts S1 and S2 based on NDM, and the survival analysis shows the significant difference between S1 and S2. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 7. Cell type analysis of Xin dataset Figure 7. Cell type analysis of Xin dataset. (A) Clustering performance (t-SNE) of Xin dataset based on GEM and NDM. ... Figure 7. Cell type analysis of Xin dataset. (A) Clustering performance (t-SNE) of Xin dataset based on GEM and NDM. Different colors represent different cell types (pp cells, alpha cells, beta cells and delta cells). (B) Clustering performance of Xin dataset based on GEM and NDM. Different colors represent different cell sources (T2D and non-diabetic). (C) The expression levels of genes HSP90AB2P and PPY. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz172, https://doi.org/10.1093/nar/gkz172 The content of this slide may be subject to copyright: please see the slide notes for details.