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. 2020 Apr 21;9:e54074. doi: 10.7554/eLife.54074

Figure 2. Characterization of neuronal cluster markers.

(A) Functional analysis of neuronal cluster markers (DAVID) showing representative functional terms (>5 fold-change) and their corresponding enrichment scores (representing mean p-values). (B) Phylogenetic tree of IgSF neuronal cluster markers. IgSF subfamily members are highlighted in color. (C) Chord diagram comparing the relationship between Tale Homeobox TF cluster markers (left) and the clusters in which they are significantly enriched (right). (D) Chord diagram comparing the relationship between LIM Homeobox TF cluster markers (left) and the clusters in which they are significantly enriched (right). (B–D) Gene were classified based on Flybase Gene Group annotations (www.flybase.org). (C,D) Chord diagrams are visual aids based on data available in Figure 1—source data 1.

Figure 2.

Figure 2—figure supplement 1. Comparison of central nervous system single-cell data sets.

Figure 2—figure supplement 1.

(A) t-SNE of mid-brain DropSeq single-cell data generated in Croset et al. (2018); each cluster is defined by a unique number and color. (B) t-SNE of brain 10x single-cell data generated in Davie et al. (2018); each cluster is defined by a unique number and color. (C) Euler diagram showing the overlap of cluster markers (average log-fold change >0.5, adjusted p-value<0.05) between the VNC (blue) mid-brain (pink) and brain (green) datasets. (A–C) For comparison purposes, datasets were reanalyzed as described in the Methods.
Figure 2—figure supplement 1—source data 1. List of marker genes for the 32 clusters shown in Figure 2—figure supplement 1A of re-analyzed data from Croset et al. (2018).
Table showing the average log-fold change (>0.5) values of cluster-discriminative marker genes, including adjusted p-values (<0.05). pct.1 is the proportion of cells that express the gene in the cluster, pct.2 is the proportion of cells that express the gene in all other clusters.
Figure 2—figure supplement 1—source data 2. List of marker genes for the 88 clusters shown in Figure 2—figure supplement 1B of re-analyzed data from Davie et al. (2018).
Table showing the average log-fold change (>0.5) values of cluster-discriminative marker genes, including adjusted p-values (<0.05). pct.1 is the proportion of cells that express the gene in the cluster, pct.2 is the proportion of cells that express the gene in all other clusters.
Figure 2—figure supplement 2. Relationships between IgSF subfamilies in defining cluster identity.

Figure 2—figure supplement 2.

(A) Dot plot of the expression of IgSF cluster markers (left) across clusters (below). The fill color intensity represents the scaled, normalized expression level of each gene, and the radius of the dot represents the percent of cells in that cluster expressing the gene of interest (GOI). (B) Chord diagram comparing the relationship between dpr (left, brown) and DIP (left, blue) cluster markers genes and the clusters in which they are significantly enriched (right, clusters in grey). (C) Chord diagram comparing the relationship between Beat (left, green) and Side (left, pink) cluster marker genes and the clusters in which they are significantly enriched (right, clusters in grey) (B,C) Chord diagrams are visual aids based on data available in Figure 1—source data 1.
Figure 2—figure supplement 3. GPCR neuronal cluster markers.

Figure 2—figure supplement 3.

(A) Dot plot of the expression of GPCR cluster markers(left) across clusters (below). The fill color intensity represents the scaled, normalized expression level of each gene, and the radius of the dot represents the percent of cells in that cluster expressing the gene of interest (GOI). (B) Phylogenetic tree of Drosophila GPCR gene family. GPCRs found as neuronal cluster markers are highlighted in orange. The multiple sequence alignment (not shown) and the phylogenetic tree were created with Clustal Omega and FigTreeV1.4.4, respectively (adapted from Hanlon and Andrew, 2015).
Figure 2—figure supplement 4. Co-expression of gene family members in the VNC.

Figure 2—figure supplement 4.

Box plots of the number of co-expressed IgSF (A), GPCR (B), ion channel (C), and HD-TF (D) genes (number of genes) per cluster (varying thresholds for the proportion positive cells in cluster). For each threshold a series is shown with filtered data for increasing minimum UMI thresholds (min UMI 0–8). Co-expression in all single cells in shown on the right.
Figure 2—figure supplement 5. Ion channel neuronal cluster markers.

Figure 2—figure supplement 5.

Dot plot of the expression of ion channel cluster markers (left) across clusters (below). The fill color intensity represents the scaled, normalized expression level of each gene, and the radius of the dot represents the percent of cells in that cluster expressing the gene of interest (GOI).
Figure 2—figure supplement 6. TF neuronal cluster markers.

Figure 2—figure supplement 6.

(A) Dot plot of the expression of homeodomain TF cluster markers (left) across clusters (below). The fill color intensity represents the scaled, normalized expression level of each gene, and the radius of the dot represents the percent of cells in that cluster expressing the gene of interest (GOI). (B) Doughnut graphs representing proportion of TF types found in the entire Drosophila genome (left) versus those found as neuronal cluster markers (right), based on Flybase Gene Group annotations.