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

Table 5 The biological function enrichment analysis of the three protein-protein interaction (PPI) hub network modules

Module	Database	GO term / pathway	B-H P-value	Genes^a
Module 1	GO	Cell activation	3.13E-06	PTPRC, SPI1, IKZF1, RAC2, DOCK2, PTPN6, PLEK, DOCK8, TLR4, ITGB2
		Immune system process	5.23E-06	PTPRC, SPI1, IKZF1, BLK, RAC2, CCR2, DOCK2, PTPN6, PLEK, IL16, DOCK8, TLR4, ITGB2
		Leukocyte activation	7.68E-06	PTPRC, SPI1, IKZF1, RAC2, DOCK2, PTPN6, DOCK8, TLR4, ITGB2
	KEGG	Phagosome	0.024684	CTSS, TLR4, ITGB2
	KEGG	Cell adhesion molecules (CAMs)	0.024684	PTPRC, VCAM1, ITGB2
Module 2	GO	Cellular respiration	1.35E-09	*ND4L, ND4, ND5, ND1, COX3, CYTB*
		ATP synthesis coupled electron transport	1.63E-09	*ND4L, ND4, ND5, COX3, CYTB*
		ATP metabolic process	2.70E-09	*ATP6, ND4L, ND4, ND5, COX3, CYTB*
	KEGG	Oxidative phosphorylation	1.85E-08	*ATP6, ND3, ND4L, ND4, ND1*
	KEGG	Metabolic pathways	0.001906	*ATP6, ND3, ND4L, ND4, ND1*
Module 3	GO	Regulation of actin filament length	7.35E-10	DSTN, WDR1, ARPC5, GMFB, ARPC1B, ACTR3
		Regulation of actin polymerization or depolymerization	7.35E-10	DSTN, WDR1, ARPC5, GMFB, ARPC1B, ACTR3
		Actin polymerization or depolymerization	9.09E-10	DSTN, WDR1, ARPC5, GMFB, ARPC1B, ACTR3
	KEGG	Salmonella infection	0.002892	ARPC5, ARPC1B
	KEGG	Regulation of actin cytoskeleton	0.010779	ARPC5, ARPC1B

^a Up-regulated genes in LRFI birds are highlighted in bold and down-regulated genes in normal typeface

ISSN: 1471-2164