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

Table 1 Candidate biomarkers distinguishing S. uberis positive cows from control (healthy) cows: six DE genes and five dMHBs

DE genes^a	Chr^b	log₂FC^c	FDR^d	Importance^e	dMHBs^f	MHL-diff^g	FDR	Importance	Overlapping elements
LOC104972351	Chr5	5.76	3.45E-08	− 0.02	chr2:27911955:27911972	0.21	1.08E-02	−0.39	STK39
LOC107131803	Scaffold	3.09	2.78E-07	−0.15	chr8:112623075:112623120	0.22	1.37E-02	−0.25	Intergenic
SLC40A1	Chr2	−2.28	9.82E-07	0.97	chr5:32984279:32984330	0.26	1.37E-02	−0.80	ALTR2C_BT^h
SMPD3	Chr18	−2.75	1.15E-06	0.16	chr19:7781358:7781427	0.22	2.02E-02	−0.20	COIL
TCF7L2	Chr26	2.49	2.74E-06	−0.04	chr24:7353387:7353442	0.35	2.09E-02	−0.32	CD226
LOC112447173	Chr1	6.84	6.34E-06	−0.11

^aDE gene: differentially expressed genes between S. uberis-positive and negative groups; ^bchr: chromosome, ^clog₂FC: log₂ transformed fold change in gene expression between the two groups; ^dFDR: False discovery rate correction according to Benjaminin and Hockberg; ^eImportance: loading weights 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; ^fdMHB: differential methylation haplotype block; ^gMHL-diff: the difference of MHL (methylation haplotype load) between two groups; ^hrepeat element

ISSN: 2049-1891