Table 2. Intersection set of significantly enriched pathways with DE lncRNAs, DE mRNAs and DE miRNAs.

Significantly enriched pathways	Q_V	C_Q	R_C	Significantly enriched pathways	Q_V	C_Q	R_C
Arginine and proline metabolism		√	√	mTOR signaling pathway	√	√	√
Base excision repair	√		√	Mucin type O-Glycan biosynthesis	√
Biosynthesis of amino acids	√	√		Neuroactive ligand–receptor interaction	√	√	√
Circadian rhythm - fly	√	√	√	N-Glycan biosynthesis	√	√
Cysteine and methionine metabolism	√	√		Nitrogen metabolism	√	√
Dorso-ventral axis formation	√	√	√	Notch signaling pathway	√	√	√
Drug metabolism - other enzymes	√	√		Other glycan degradation
ECM-receptor interaction	√	√		Peroxisome	√
Endocytosis	√	√		Phenylalanine metabolism	√	√
Folate biosynthesis		√		Phosphatidylinositol signaling system	√	√	√
FoxO signaling pathway	√	√	√	Phototransduction - fly	√	√	√
Galactose metabolism	√			Proteasome	√	√
Glycerolipid metabolism	√	√	√	Protein processing in endoplasmic reticulum		√
Glycerophospholipid metabolism	√	√	√	Purine metabolism	√	√	√
Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate		√		Retinol metabolism		√
Glycosaminoglycan biosynthesis - heparan sulfate / heparin		√	√	RNA degradation	√	√	√
Hedgehog signaling pathway	√	√		RNA transport	√	√	√
Hippo signaling pathway - fly	√	√	√	Spliceosome	√	√	√
Inositol phosphate metabolism	√	√	√	Starch and sucrose metabolism	√
Jak-STAT signaling pathway			√	Sulfur metabolism	√
Lysine degradation	√			TGF-beta signaling pathway	√	√	√
MAPK signaling pathway - fly	√	√	√	Tyrosine metabolism	√	√
Metabolic pathways	√	√	√	Ubiquinone and other terpenoid-quinone biosynthesis	√	√
mRNA surveillance pathway	√	√	√	Wnt signaling pathway	√	√	√

Notes.

V

group of virgin queens

Q

group of egg-laying queens

C

group of egg-laying inhibited queens

R

group of egg-laying recovery queens