Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression Network

Table 3

Gene network and expression analysis of genes with large degree and BC. We selected 11 hub genes (6 genes with large degree and 5 with large BC) from the network topology analysis and confirmed gene expression for Hanwoo marbling using qRT-PCR.

Gene network^a	Gene	Full name		Expression^b		Relationship^c	𝑃 value^d
				Low	High
Large degree	MAEL	Maelstrom homolog	Turquoise	0.29	0.33	Positive	0.871
	HINT1	Histidine triad nucleotide binding Protein 1	Turquoise	0.41	0.25	Negative	0.118
	KIAA1712	KIAA1712	Turquoise	0.34	0.21	Negative	0.283
	TMEM60	Transmembrane protein 60	Turquoise	0.34	0.76	Positive	0.013
	RHEBL1	Ras homolog enriched in brain-like 1	Turquoise	0.45	0.31	Negative	0.544
	FAM40A	Hypothetical protein LOC511120	Turquoise	0.54	0.30	Negative	0.528
Large BC	S100A11	S100 calcium binding protein A11	Turquoise	0.34	0.36	Positive	0.616
	CD53	CD53 molecule	Red	0.41	0.28	Negative	0.901
	DPYD	Dihydropyrimidine dehydrogenase	Brown	0.26	0.84	Positive	0.001
	ELOVL4	Elongation of very long chain fatty acid-like 4	Turquoise	0.38	0.33	Negative	0.991
	CTSS	Cathepsin S	Red	0.33	0.23	Negative	0.765

aExpression and promotor binding indicate that the regulator changes the expression level and binds the promoter of the target.
bExpression showed means of normalized expression value of each gene within low- and high-marbled groups.
cRelationship indicated expression relationship of each gene against the intramuscular fat from PCA analysis.
^d𝑃-value was calculated by the regression analysis.
The bold type indicates significant differences at P ≤ 0.05 between high and low-marbled groups.