Table 1 Results of pathway enrichment of differentially expressed genes within and between state comparisons in the hypothalamus.

Category	Pathway#	Pathway description	Differentially expressed genes	P_adj	Bias group
*A. Hypothalamus: within state comparison (Photosensitive*: hour 10 vs. hour 14**)
KEGG	fab00190	Oxidative phosphorylation	3	0.0002	Hour 10
KEGG	fab01100	Metabolic pathways	4	0.0102	Hour 10
KEGG	fab04145	Phagosome	2	0.0102	–
KEGG	fab04150	mTOR signaling pathway	2	0.0102	–
(*Photosensitive: hour 10 vs. hour 18*)
KEGG	fab01200	Carbon metabolism	2	0.006	Hour 18
KEGG	fab01100	Metabolic pathways	3	0.019	Hour 18
(*Photorefractory: hour 10 vs. hour 14*)
KEGG	fab03013	RNA transport	2	0.009	–
(*Photorefractory: hour 10 vs. hour 18*)
KEGG	fab00010	Glycolysis/Gluconeogenesis	3	0.002	Hour 18
KEGG	fab01100	Metabolic pathways	8	0.002	Hour 18
KEGG	fab01230	Biosynthesis of amino acids	2	0.044	–
KEGG	fab03018	RNA degradation	2	0.044	–
(*Photorefractory: hour 10 vs. hour 22*)
KEGG	fab01200	Carbon metabolism	4	0.001	–
KEGG	fab01230	Biosynthesis of amino acids	3	0.003	Hour 22
KEGG	fab00030	Pentose phosphate pathway	2	0.011	Hour 22
KEGG	fab00051	Fructose and mannose metabolism	2	0.014	Hour 22
KEGG	fab00010	Glycolysis/Gluconeogenesis	2	0.024	Hour 22
KEGG	fab01100	Metabolic pathways	7	0.024	Hour 10
*B. Hypothalamus: Between state comparisons (hour 10*: photosensitive vs. photorefractory**)
KEGG	fab00280	Valine, leucine and isoleucine degradation	2	0.009	Photosensitive
KEGG	fab01100	Metabolic pathways	4	0.027	Photosensitive
KEGG	fab04145	Phagosome	2	0.027	Photosensitive
(*hour 22: photosensitive vs. photorefractory*)
UniProt	KW-0689	Ribosome	2	0.021	Photosensitive

The column on ‘bias group’ indicates the category with a higher number of upregulated genes.
The blanks (-) in ‘bias group’ column indicate that the number of up- and downregulated genes in that pathway were equal.

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