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. 2020 May 1;34(9-10):701–714. doi: 10.1101/gad.335281.119

Figure 7.

Figure 7.

Coordinate transcriptional induction of metabolic pathways in late pupae. (A) Soft-clustering analysis was performed on transcripts from RNA-seq data for genes representing the major metabolic pathways in Drosophila using the Mfuzz package in R (Supplemental Table S2). FPKM normalized reads were used to account for gene size, with number of clusters set to four (up 1, up 2, down 1, and down 2). Temporal profiles with low membership value (yellow, green) and high membership value (red, purple) are depicted. The number of genes assigned to a given cluster is shown (n=) along with its percentage relative to the total set of metabolic genes analyzed. The first day of adulthood is marked with a dashed line. (B) Table of metabolic pathways with highest representation in the up clusters. Metabolic pathways are ordered vertically first by the percent total up, and then by the total number of genes in that pathway, shown in parentheses. The distribution of genes for each pathway in the four clusters is shown as a percentage of the total. Pathways in which every gene is in the up clusters (100%) are separated by a line from the top pathways where most genes are up (80%–95%). (C) Gene expression plots through time are shown for RNA-seq data from controls (blue) and dERR mutants (red) for six metabolic pathways: glycolysis, the pentose phosphate pathway (PPP), glycogenolysis, the electron transport chain (ETC), TCA cycle, and glycogen synthesis (n = 3 with 15 animals per sample). Mean expression values of the replicates of all genes at each time point are plotted to make the line, and the gray border represents the standard error bounds using a LOESS fitting. Expression levels are shown as transcripts per million (TPM) normalized expression values to account for gene size and total RNA in the sample. Animals were staged as white prepupae (WPP), day 1 pupae (P1), day 2 pupae (P2), day 3 pupae (P3), day 4 pupae (P4), day 1 adult (A1), and day 6 adult (A6).