Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Table 2 Candidate biomarkers distinguishing S. uberis positive cows from control (healthy) cows: fifteen DMCs

DMCs^a	Degree of methylation^b	meth.diff^c	q value^d	Importance^e	Gene symbol	log₂FC^f	FDR^g	Other overlapping elements^h
chr1_116798477	hypo	−41.94	3.06E-04	0.29	MED12L	2.03	2.72E-02	downstream of GPR87
chr1_116798702	hypo	−47.50	1.60E-05	0.01	MED12L	2.03	2.72E-02	downstream of GPR87
chr1_81755303	hypo	−22.22	3.61E-02	0.09	MAP3K13	2.00	2.49E-02
chr2_36910011	hypo	−52.63	5.56E-06	0.11	BAZ2B	2.40	1.21E-05	BovB^h
chr5_113635313	hypo	−28.00	4.20E-02	0.21	ARFGAP3	1.32	3.11E-02
chr5_9029509	hypo	−47.37	2.20E-04	0.29	SYT1	−4.62	9.72E-03
chr7_26444558	hyper	65.00	1.55E-06	−0.10	PRRC1	1.44	2.68E-02
chr14_67946960	hyper	35.90	1.03E-02	−0.39	PTDSS1	−1.50	4.02E-03	Bov-tA1^h
chr15_28521852	hypo	−50.00	1.08E-04	0.21	FXYD6	1.89	8.01E-03
chr19_22014105	hyper	27.27	4.42E-02	−0.16	NXN	2.34	5.96E-03
chr19_33218275	hypo	−27.50	2.08E-02	0.28	TRPV2	−2.46	1.39E-07	L2a^h
chr20_56637267	hypo	−30.00	4.92E-02	0.13	RETREG1	2.38	1.84E-06
chr21_61174672	hyper	54.55	1.32E-05	−0.28	ATG2B	1.93	8.14E-04	L1ME3C^h
chr26_7684695	hyper	43.59	1.48E-03	−0.40	PRKG1	3.77	3.41E-04
chrX_123509578	hypo	−26.32	3.49E-02	0.44	SH3KBP1	−1.90	1.84E-04

^aDMC: differentially methylated cytosines in the context of CpG; ^bhypo and hyper represents hypomethylated and hypermethylated, respectively, in S. uberis-positive group; ^cmeth-diff: difference in the methylation level of DMC between groups. The negative value indicates lower expression and positive value indicates higher expression in S. uberis-positive group; ^dq value: adjusted p value for the false discovery rate; ^eImportance: loading weight calculated by DIABLO method indicates the importance of corresponding selected DE gene or dMHB. The negative value indicates higher DE gene expression or dMHB methylation levels in S. uberis-positive group, while the positive value represents lower DE gene expression or dMHB methylation levels in S. uberis-positive group; ^flog₂FC: log₂ transformed fold change in gene expression between the two groups; ^gFDR: False discovery rate correction according to Benjaminin and Hockberg; ^hindicates repeat elements

ISSN: 2049-1891