Table 3.

Differently enriched KEGG pathways with targeted genes of lncRNA of comparisons between chickens with different eggshell colors.

Comparison	Pathway	p	Targeted genes	lncRNA
DB vs. DP	Toll-like receptor signaling pathway	<0.001	TLR2A	TCONS_00055576
	Retinol metabolism	<0.001	RETSAT	ENSGALT00000081853
	Phagosome	<0.001	TLR2A	TCONS_00055576
	Spliceosome	<0.001	CTNNBL1	TCONS_00038047
	Glycosphingolipid biosynthesis-ganglio series	0.002	ST6GALNAC4	ENSGALT00000072290
	Glycerophospholipid metabolism	0.045	LCLAT1, DGKZ	ENSGALT00000048295
DB vs. LB	TGF-beta signaling pathway	<0.001	Sp1	TCONS_00054721
	Glycosphingolipid biosynthesis-ganglio series	<0.001	ST6GALNAC4	ENSGALT00000072290
	Pyruvate metabolism	0.002	ENSGALT00000074835	ENSGALT00000051137
	Propanoate metabolism	0.003	ENSGALT00000074835	ENSGALT00000051137
	Biosynthesis of secondary metabolites	0.016	LCLAT1	TCONS_00050772
	Selenocompound metabolism	0.034	TXNRD1	TCONS_00008143
	Metabolic pathways	0.039	ST6GALNAC4, DPM2, LCLAT1	ENSGALT00000072290
DP vs. LB	Retinol metabolism	<0.001	RETSAT	ENSGALT00000081853
	Other types of O-glycan biosynthesis	0.011	GXYLT1	ENSGALT00000069802
	Drug metabolism-other enzymes	0.016	HPRT1, MDM2	TCONS_00058295
	Cell cycle	0.029	YWHAE, MDM2	ENSGALT00000071577
	N-Glycan biosynthesis	0.033	MAN1C1, ALG1	TCONS_00040933
	Wnt signaling pathway	0.038	APC	TCONS_00040933
	Biosynthesis of secondary metabolites	0.045	HPRT1, MPI	ENSGALT00000009843
	p53 signaling pathway	0.046	MNM2, CASP14	ENSGALT00000071577
	Neurotrophin signaling pathway	0.046	-	ENSGALT00000077105
PK vs. DB	Proteasome	<0.001	PSMB1/3	ENSGALT00000088176
	TGF-beta signaling pathway	<0.001	Sp1	TCONS_00040436
	Selenocompound metabolism	<0.001	PAPSS1, TXNRD1	TCONS_00056173
	Retinol metabolism	<0.001	TXNRD1, RETSAT	ENSGALT00000081853
	Sulfur metabolism	<0.001	RETSAT, TXNRD1	TCONS_00056173
	Glycosphingolipid biosynthesis-ganglio series	0.003	RETSAT	ENSGALT00000072290
	Spliceosome	0.024	RBMXL1	ENSGALT00000070508
	Vitamin B6 metabolism	0.025	PHOSPHO2	ENSGALT00000085067
	Cell cycle	0.025	RB1	ENSGALT00000051325
PK vs. DP	beta-Alanine metabolism	<0.001	HIBCH	TCONS_00071353
	p53 signaling pathway	<0.001	SESN1, CASP14	ENSGALT00000078895
	Propanoate metabolism	<0.001	HIBCH	TCONS_00071353
	RNA degradation	0.001	XRN1	ENSGALT00000084047
	Porphyrin and chlorophyll metabolism	0.002	FECH	ENSGALT00000087341
	Valine, leucine and isoleucine degradation	0.002	HIBCH	TCONS_00071353
	Sulfur metabolism	0.003	PAPSS1	TCONS_00056173
PK vs. LB	Retinol metabolism	<0.001	RETSAT	ENSGALT00000081853
	N-Glycan biosynthesis	0.003	MAN1C1, ALG1	TCONS_00040933
	Cardiac muscle contraction	0.008	COX6A1	TCONS_00023198
	Metabolic pathways	0.013	MAN1C1, ALG1	TCONS_00040933
	Oxidative phosphorylation	0.014	COX6A1	TCONS_00023198
	Protein processing in endoplasmic reticulum	0.032	MAN1C1, ALG1	TCONS_00040933
	SNARE interactions in vesicular transport	0.048	VAMP3	TCONS_00039175

DB, DP, LB, and PK mean chickens producing dark blue, dark brown and greenish, light blue, and pink eggshell eggs, respectively.