. 2022 Oct 6;31(22):5795–5812. doi: 10.1111/mec.16705

TABLE 2.

Candidate genes for regulating the temperature sensitivity of embryonic development rate – Continued

GeneID	When highly expressed at constant 10°C	Temperature effect compared to the control constant 10°C	D. melanogaster annotation
Within‐week temperature effect
MSTRG.20613	Module 13: week2 and week4	week6: downregulated after 3 h of warmth, log₂FC = −2.31, FDR = 0.009 week8: upregulated after 24 h of cold, log₂FC = 2.47, FDR = 0.007	tao, a Ser/Thr kinase involved in Hippo‐signalling (FlyBase, accessed May 24, 2022)
MSTRG.12645	Module 13: week2 and week4	week6: downregulated after 3 h of warmth, log₂FC = −4.97, FDR < .001	fdl, involved in restructuring the brain via hormonal control during metamorphosis (FlyBase, accessed May 24, 2022).
MSTRG.3087	Module 13: week2 and week4	week6: upregulated after 3 h of warmth, log₂FC = 3.34, FDR <0.001	tey, a protein that regulates neuromuscular target specificity, involved in the negative regulation of transcription and protein ubiquitination (FlyBase, accessed May 24, 2022).
MSTRG.22817	Module 13: week2 and week4	week6: upregulated after 3 h of warmth, log₂FC = 1.99, FDR = 0.001	gld, a glucose dehydrogenase involved in oxidoreductase activity (FlyBase, accessed May 24, 2022).
MSTRG.8284	Module 13: week2 and week4	week6: upregulated after 24 h of cold, log₂FC = 5.05, FDR = 0.001	cyp6a13, a cytochrome P450 involved in oxidoreductase activity that may be involved in the metabolism of insect hormones (FlyBase, accessed May 24, 2022).
MSTRG.32147	Module 13: week2 and week4	week6: upregulated after 24 h of cold, log₂FC = 4.20, FDR <0.001	sp7, a serine protease involved in the activation of the melanization cascade (FlyBase, accessed May 24, 2022)
MSTRG.13770	Module 13: week2 and week4	week8: upregulated after 3 h of cold, log₂FC = 3.37, FDR = 0.003 week8: upregulated after 24 h of cold, log₂FC = 3.74, FDR <0.001	atlastin, encodes a membrane‐bound GTPase that enables protein binding (FlyBase, accessed May 24, 2022)
MSTRG.11979	Module 13: week2 and week4	week8: upregulated after 24 h of cold, log₂FC = 1.21, FDR = 0.003	nanos, which codes for an RNA‐binding protein that forms part of a translational repressor complex (FlyBase, accessed April 13, 2022).
MSTRG.25766	Module 13: week2 and week4	week8: downregulated after 24 h of cold, log₂FC = −2.47, FDR = 0.002	cycC ^a , coactivator involved in regulating gene transcription of nearly all RNA polymerase II‐dependent genes (FlyBase, accessed May 24, 2022).
MSTRG.11006	Module 3: week6 and week8	week2: upregulated after 24 h of cold, log₂FC = 0.68, FDR <0.001	Psc, member of the polycomb gene group that regulates gene expression through epigenetic marks. Involved in chromatin binding, DNA binding, and cell cycle control (FlyBase, accessed May 24, 2022).
MSTRG.10930	Module 3: week6 and week8	week2: upregulated after 24 h of cold, log₂FC = 0.93, FDR = 0.001	polo, a Ser/Thr kinase thought to be a cell cycle regulator (FlyBase, accessed May 24, 2022)

Note: We highlight a number of genes with a significant response to a 5°C increase and/or decrease in temperature within a specific development week (within‐week temperature effect), which at the control constant 10°C were lowly expressed in that same development week, but highly expressed in another development week (see Table S8.3 for a full list including statistics). For each gene, we list when it was highly expressed during development at constant 10°C (belonging to one of four significant WCGNA gene modules, see Section 2), the temperature effect that was found (FDR <0.01), and its Drosophila melanogaster annotation with the related gene function obtained from FlyBase (Larkin et al., 2021). Expression profiles for these genes are visualized in Figure S7.2.

^{^a}

D. pseudoobscura annotation instead of D. melanogaster.