Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis

Table 6 Gene set enrichment analysis (GSEA) between HRFI and LRFI birds

Gene set		NES^a	FDR^b	Higher expression in HRFI or LRFI
GO-based list (C5, CC, C5.BP, C5.MP)
GO:0044455	Mitochondrial membrane part	2.60	< 0.001	LRFI
GO:0022900	Electron transport chain	2.09	0.011	LRFI
GO:0010822	Positive regulation of mitochondrion organization	1.80	0.027	LRFI
GO:0005740	Mitochondrial envelope	1.82	0.029	LRFI
GO:0009205	Purine ribonucleoside triphosphate metabolic process	1.85	0.031	LRFI
GO:0009144	Purine nucleoside triphosphate metabolic process	1.91	0.034	LRFI
GO:0046034	ATP metabolic process	1.85	0.039	LRFI
GO:0001960	Negative regulation of cytokine-mediated signaling pathway	−1.77	0.010	HRFI
GO:0060761	Negative regulation of response to cytokine stimulus	−1.76	0.011	HRFI
GO:0070588	Calcium ion transmembrane transport	−1.74	0.012	HRFI
GO:1903169	Regulation of calcium ion transmembrane transport	− 1.73	0.015	HRFI
GO:0042439	Ethanolamine-containing compound metabolic process	−1.71	0.019	HRFI
GO:0001776	Leukocyte homeostasis	−1.70	0.022	HRFI
GO:0008625	Extrinsic apoptotic signaling pathway via death domain receptors	−1.70	0.023	HRFI
KEGG-based list (C2.CP:KEGG)
KO00020	Citrate cycle (TCA cycle)	2.28	0.005	LRFI
KO04260	Cardiac muscle contraction	1.70	0.031	LRFI
KO04672	Intestinal immune network for IgA production	−1.60	0.020	HRFI
KO00510	N-Glycan biosynthesis	−1.57	0.022	HRFI
KO04210	Apoptosis	−1.57	0.025	HRFI
KO00532	Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate	−1.52	0.040	HRFI

^a NES normalized enriched score
^b FDR false discovery rate
Positive and negative NES indicate higher and lower expression in LRFI, respectively

ISSN: 1471-2164