Large-scale gene co-expression network as a source of functional annotation for cattle genes

BMC Genomics

Table 2 Functional enrichment analysis of close neighbors (TOM > 0.01) of hub genes with no functional annotation in CGCN^a

Gene	#	Top BP GO term	p-value^b	Top Reactome pathway	p-value^c
LOC509513	1	T cell activation	1.58E-20	Adaptive Immune System	1.04E-21
	2	T cell aggregation	1.58E-20	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	3.55E-19
	3	lymphocyte aggregation	1.84E-20	Immune System	7.66E-19
LOC100848208	1	RNA processing	8.95E-07	Mitochondrial translation elongation	2.12E-08
	2	mRNA metabolic process	1.87E-04	Mitochondrial translation termination	2.12E-08
	3	mitochondrial translation	2.18E-04	Mitochondrial translation	2.50E-08
LOC100850151	1	RNA processing	3.82E-15	Cell Cycle	8.78E-11
	2	mRNA processing	6.36E-11	Processing of Capped Intron-Containing Pre-mRNA	3.91E-10
	3	mRNA metabolic process	1.56E-10	Cell Cycle, Mitotic	2.79E-08
MGC137211	1	carboxylic acid metabolic process	1.32E-41	Metabolism	4.96E-41
	2	monocarboxylic acid metabolic process	1.05E-23	Biological oxidations	2.20E-18
	3	alpha-amino acid metabolic process	6.84E-20	Metabolism of lipids and lipoproteins	3.72E-18

^aJust three top over-represented biological process (BP) and Reactome pathways are listed, More information related to these hubs and other un-known genes in the network are provided in Additional file 6: Table S5
^b,cThe p-value indicated the probability that a module contains equal or larger number of genes associated with the GO term under a hypergeometric distribution after Bonferroni step-down correction

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