Manuscript figures and tables

[dktanwar]

Main figures

Figure 1

• [x] A. PCA of samples from PND8, PND15, Adult
• [x] B. Heatmap of k-means clustering on gene expression data across time points
• [x] C. Dot plot of enriched GO terms from each cluster
• [x] D. Line plots of expression of genes

Figure 2

• [x] A. Volcano plot for DARs
• [x] B. Heatmap of enrichment values, clustered based on genomic annotations
• [x] C. Barplot of genomic annotation of DARs
• [x] D. Dot plots of GO terms for BP, MF and CC from GREAT on DARs. Separately for +ve and -ve enriched regions

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Supplementary figures

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Supplementary tables

[Irinalazar]

Input for Figure 1:

• [x] Fig B: the heat map looks weird, you cannot distinguish any differences between samples in terms of gene expression values, the intersample variability is lost...Can we maybe represent only the top differentially expressed genes in each cluster if the problem is the high number of genes? The issue now is that the reader cannot really see the proper delimitation between columns (samples) like it used to look like in the attached figure (change the z-scores scale and maybe the colour coding will look better?)

• [x] Fig B: move the "cluster" colour coding on the left side, cluster annotation is with numbers: 1-5 not a-e

• [x] Fig B: Decrease font size for "Group" and "Cluster" names; Replace "Gene expression" name with "Z-score" (or whatever that is), otherwise it doesn't tell the reader anything about what it means; "Gene expression", "Group", "Cluster" legends should be in one single column, one under the other

• [x] Fig C: I am quite confused about where you got these first 5 terms for each cluster, the top terms I get from your analysis are different, maybe we can discuss this tomorrow morning (again I filtered out the GO terms which have less than 10 genes); Also legend title "Count" doesn't say much, do you mean "Gene count"?

• [ ] Fig D: the melanoma antigen genes line plot should be the last; you don't need the legend title "Genes" repeated 3x, leave it just once at the top, otherwise it's uselessly crowding the figure

Overall, they need resizing, the PCA is too big for this figure, the heatmap too small, the line graphs too big I would suggest to save the subfigures separately ( high quality Png (>300pixels), sgv or pdf) so I can try to arrange them in inkscape (I'm learning it now)

That's all from my side for now, overall I think it looks good! we're definitely heading in the right direction 👍 Best, Irina