Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

Dini, Pouya; Daels, Peter; Loux, Shavahn C.; Esteller-Vico, Alejandro; Carossino, Mariano; Scoggin, Kirsten E.; Ball, Barry A.

doi:10.1186/s12864-018-5341-2

Table 4 Correlation analysis between C24MC-associated miRNAs presenting a significantly higher expression level during early stage of pregnancy (45d), followed by a decline later in the gestation, and that of their putative mRNA targets (n = 130)

From: Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

MiRNA ID	Target mRNA	Correlation	P value	FDR
eca-miR-127-5p	MAF1	−0.5982	0.0144	0.049
	FBXL15	− 0.5917	0.0158	0.049
	ITK	− 0.5563	0.0252	0.049
	ZNF394	− 0.5381	0.0315	0.049
	PEF1	−0.5352	0.0326	0.049
	SNX10	−0.5212	0.0384	0.049
	YWHAQ	−0.5213	0.0384	0.049
	CDKN2AIP	−0.5065	0.0453	0.049
	ALDH1A3	−0.4986	0.0493	0.049
eca-miR-134-5p	PLD1	−0.7269	0.0014	0.003
eca-miR-134-5p	SLC14A1	−0.5934	0.0154	0.015
eca-miR-323-3p	CREBL2	−0.7515	0.0008	0.006
	AFTPH	−0.6925	0.0029	0.010
	DNAJC6	−0.6175	0.0108	0.017
	TMEFF2	−0.6123	0.0117	0.017
	PDE4B	−0.6045	0.0131	0.017
	TAF12	−0.5981	0.0144	0.017
	IGSF3	−0.501	0.048	0.048
eca-miR-370-5p	ZMAT3	−0.5327	0.0336	0.049
	DCDC2	−0.5266	0.0361	0.049
	PLEKHA3	−0.4989	0.0492	0.049
eca-miR-382-5p	JAM2	−0.7504	0.0008	0.002
eca-miR-382-5p	KLHL36	−0.5945	0.0152	0.015
eca-miR-409-3p	TM4SF18	−0.7353	0.0012	0.005
	MME	−0.6665	0.0048	0.010
	HBP1	− 0.6237	0.0098	0.012
	TNFSF14	−0.609	0.0123	0.012
eca-miR-411-3p	SEC24B	−0.8907	< 0.0001	0.001
	CXCL10	−0.7036	0.0024	0.011
	CC2D2A	−0.6435	0.0072	0.016
	MKS1	−0.6361	0.0081	0.016
	EXO5	− 0.6303	0.0089	0.016
	KRCC1	−0.6139	0.0114	0.017
	CADM1	−0.5907	0.016	0.019
	TSHZ1	−0.5881	0.0166	0.019
	DUSP10	−0.5092	0.044	0.044
eca-miR-412-3p	GABARAPL1	−0.6578	0.0056	0.017
	STARD3NL	−0.5598	0.0241	0.036
	MBTPS1	−0.5005	0.0483	0.048
eca-miR-412-5p	SRL	−0.6407	0.0075	0.008
eca-miR-432-5p	AXL	−0.5358	0.0324	0.035
eca-miR-432-5p	CYP46A1	−0.5283	0.0354	0.035
eca-miR-433-3p	PPP3R1	−0.6886	0.0032	0.022
	CTNNAL1	−0.6311	0.0088	0.031
	AXL	−0.5933	0.0154	0.036
	FAM107A	−0.5457	0.0288	0.044
	SH3BGRL	−0.5383	0.0315	0.044
	CYP46A1	−0.5234	0.0375	0.044
	MARK3	−0.5077	0.0447	0.045
eca-miR-485-3p	CHKA	−0.797	0.0002	0.003
	CCDC68	−0.7795	0.0004	0.003
	PLCL2	−0.7534	0.0008	0.004
	AKAP1	−0.6916	0.003	0.011
	CD36	−0.6645	0.005	0.011
	NR1D2	−0.6638	0.005	0.011
	RAB30	−0.6624	0.0052	0.011
	FAM26E	−0.6531	0.0061	0.011
	TTC39A	−0.629	0.009	0.015
	NTRK3	−0.6146	0.0113	0.017
	BRD3	−0.5751	0.0198	0.027
	GPAM	−0.5536	0.0261	0.033
	ZNF322	−0.533	0.0335	0.039
	PPP3R1	−0.5107	0.0432	0.046
	EDNRA	−0.4982	0.0495	0.049
eca-miR-485-5p	ACACB	−0.7863	0.0003	0.005
	SNX27	−0.7736	0.0004	0.005
	SSH3	−0.7668	0.0005	0.005
	TYRO3	−0.7498	0.0008	0.005
	ITPRIP	−0.752	0.0008	0.005
	CDC42BPA	−0.7137	0.0019	0.008
	FADS3	−0.706	0.0022	0.008
	DFFA	−0.6948	0.0028	0.008
	KNOP1	−0.6954	0.0028	0.008
	MSI2	−0.6903	0.0031	0.008
	VDR	−0.6906	0.0031	0.008
	OLFML2A	−0.6713	0.0044	0.011
	NXN	−0.6692	0.0046	0.011
	IRAK4	−0.6638	0.005	0.011
	KDSR	−0.6498	0.0064	0.013
	INPP5B	−0.6389	0.0077	0.014
	C10orf76	−0.6302	0.0089	0.016
	PEX11B	−0.6178	0.0108	0.017
	TMUB2	−0.6162	0.011	0.017
	EFR3B	−0.5739	0.0201	0.030
	TMEM86A	−0.5483	0.0279	0.039
	G6PD	−0.5467	0.0284	0.039
	TMEM104	−0.5282	0.0355	0.045
	TMEM120B	−0.5276	0.0357	0.045
	ACVRL1	−0.5224	0.0379	0.045
	AP3S2	−0.5101	0.0435	0.048
	PPP1R13B	−0.5101	0.0435	0.048
	ZNF256	−0.5015	0.0478	0.049
	SEMA4D	−0.5011	0.048	0.049
	UAP1L1	−0.4978	0.0497	0.049
eca-miR-487a-5p	TSPAN3	−0.7604	0.0006	0.005
	KIF13A	−0.738	0.0011	0.005
	SEMA3D	−0.678	0.0039	0.009
	NSMF	−0.6753	0.0041	0.009
	CDKN2AIP	−0.5968	0.0147	0.026
	SORBS1	−0.5357	0.0325	0.042
	AKAP6	−0.5302	0.0346	0.042
	DACH1	−0.5236	0.0374	0.042
	AKTIP	−0.4985	0.0494	0.049
eca-miR-543-3p	NR3C1	−0.6944	0.0028	0.024
	RPAP2	−0.6608	0.0053	0.024
	NR1D2	−0.6509	0.0063	0.024
	GPCPD1	−0.6264	0.0094	0.024
	BTBD3	−0.6199	0.0104	0.024
	LRRC8D	−0.6084	0.0124	0.024
	MSL2	−0.5954	0.015	0.024
	TP53INP1	−0.5911	0.0159	0.024
	HSPA12A	−0.5872	0.0168	0.024
	ARMC8	−0.5759	0.0196	0.025
	PLEKHA8	−0.5341	0.0331	0.039
	BCL6B	−0.5266	0.0361	0.039
	API5	−0.5109	0.0431	0.043
hsa-miR-1247-3p	RHOBTB2	−0.7882	0.0003	0.003
	GRB7	−0.7564	0.0007	0.004
	KDSR	−0.6962	0.0027	0.008
	GLP1R	−0.6809	0.0037	0.008
	DVL1	−0.677	0.004	0.008
	AGFG2	−0.6728	0.0043	0.008
	EPN2	−0.6434	0.0072	0.011
	ACVRL1	−0.5895	0.0162	0.022
	WNT9B	−0.5606	0.0239	0.028
	NRP1	−0.5567	0.0251	0.028
	SEMA6D	−0.5216	0.0383	0.038
hsa-miR-154-5p	HECTD4	−0.6384	0.0078	0.018
	SALL1	−0.6115	0.0118	0.018
	C12orf29	−0.5164	0.0406	0.041

The miRNA expression was evaluated by RT-qPCR (− ΔC_T) and the respective mRNA expression was determined by RNA-sequencing (FPKM)
Since miRNAs down regulate their target mRNA/s expression, those target mRNAs in the RNA-seq dataset that exhibited the reverse pattern of expression compared to the miRNA expression pattern (negative correlation, r ≤ −0.5, P < 0.05) were selected. There was no significant correlation between the expression pattern of eca-miR-487b-3p and that of its predicted targets

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ISSN: 1471-2164

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