Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties

Ponsuksili, Siriluck; Du, Yang; Hadlich, Frieder; Siengdee, Puntita; Murani, Eduard; Schwerin, Manfred; Wimmers, Klaus

doi:10.1186/1471-2164-14-533

Table 5 Genes belonging to the modules dark-turquoise, red, black, and tan and their negatively-correlated miRNAs

Modules	miRNA family	Genes within modules negatively correlated with miRNA¹
Dark-turquoise	miR-153	CREM
Black	miR-1	NDUFB9, ATP5C1, DNAJC12, NDUFC2, TOMM6, *RRN3, PSTK, C1orf151*
	miR-103	GLRX3, LOC202051
	miR-130	*SLC22A23, LOC727762*
	miR-132	NDUFB9, ACBD6, GHITM, DNAJC12, GLRX3, *CBR1, ANAPC13, RRN3, HIBCH, MCEE, GYG1, UFC1, COPS4, GALK2, LOC665103, VTI1B*
	miR-133	*RRN3, COPS4, FLJ11506*
	miR-146	GLIS2
	miR-15	*KIF1B, TACC2, Wipf3, SLC22A23*
	miR-154	NDUFB9, *GHITM, GLRX3, LOC100132911, CHPT1, GYG1, UFC1, LANCL1, LOC728620, ATP6V1G1, MRPL35, VTI1B, CHCHD2*
	miR-17	SLC25A3, PRDX3, GHITM, *SAR1A, ATP5C1, COX17, BIN1, GLRX3, MYL2, TPM3, LOC647081, CNPY2, dJ196E23.2, LOC727762, MSRA*
	miR-181
	miR-19	SSBP3
	miR-205	SH3PXD2A, PEAR1
	miR-324	*CIC, UBAP1*
	miR-330	DNAJC12, *VTI1B*
	miR-339	*Ncor1*
	miR-375	*VTI1B*
	miR-379	C15orf24, GHITM, CIP29, TSPAN3, *GLRX3, PSMA2, ANAPC13, C8orf38, SRP14, CXorf26, LOC100132911, MRPS14, MCEE, GYG1, UFC1, LANCL1, LOC728620, COPS4, PSMA6, FLJ11506, VTI1B, TMEM126B*
	miR-425	BIN1, DBI, LAPTM4A
	miR-467	DNAJC12
	miR-503	SPCS2, GHITM, *BIN1, PARK7, DBI, LOC728620, H2AFY, dJ196E23.2, CHCHD2*
	miR-99	Ncor1
Red	miR-1	FDPS, GCHFR, C20orf24, STRA13
	miR-103	PPP1R7, *PSMC3*
	miR-124	*HSBP1, STRA13*
	miR-130	*STRA13*
	miR-132	*SNRNP25, PPP1R7, PSMC3, FDPS, N6AMT2, MRPS26, PSMB5, Snf8, DHDH, COPS6, HSD17B8, PQBP1, MRPS7, C7orf30, TFDP1, NHP2, LOC152217, PBXIP1, DNPEP, C12orf44, UROD, MRPL48*
	miR-133	FDPS, *TTC28*
	miR-146	CHCHD7
	miR-154	*PSMB2, WBSCR22, PPP1R7, PSMC3, LSM4, FDPS, PIH1D1, MRPS26. 5330431N19Rik, PSMB5, Snf8, JTB, DHDH, COPS6, PSMB7, LOC646330, MRPS34, PQBP1, SIVA1, MRPS7, STK24, RUVBL1, MRPL23, PFDN6, SSSCA1, PBXIP1, PRPS1, MRPL55, COMTD1, UROD, ROBLD3, C1orf144*
	miR-17	MYOZ1, CHCHD4, RUVBL1, PRPS1
	miR-196	MRPS7
	miR-202	STRA13
	miR-204	MRPS26, *STRA13*
	miR-214	*RUVBL1*
	miR-26	STRA13
	miR-330	*PPP1R7, FDPS, MRPS7*
	miR-335	PIH1D1
	miR-342	*MRPS7, RUVBL1*
	miR-375	*FDPS, LOC100039220, MRPS7, MRPL48*
	miR-379	MRPS7, MRPL48
	miR-467	WBSCR22, PSMC3, FDPS, MRPS7, STRA13, STRA13
	miR-503	MYOZ1
	miR-676	WIBG
tan	miR-132	*COL6A1*
	miR-133	COL6A1
	miR-145	*POSTN*
	miR-148	*DPYSL3*
	miR-154	COL6A1
	miR-181	COL12A1, FKBP10, *Aebp1, OGN*
	miR-204	COL6A1
	miR-205	*COL1A1, COL6A3, DPYSL3, MAGED1, DPYSL3, COPZ2, COL5A1*
	miR-320	*COL6A1*
	miR-330	*COL6A1*
	miR-342	COL6A1
	miR-375	*COL6A1*
	miR-423	*COL6A1*
	miR-425	DCN, COL3A1, *FBN1, COL6A3, LOC100129547, COL5A2, COL1A2, COL6A1, FSTL1, COL14A1*
	miR-455	COL6A1
	miR-488	CRISPLD2
	miR-9	*NID2, COL6A1, YWHAQ, CNN3, NID1, TSPAN6*

¹genes predicted as potential targets of the corresponding miRNAs are shown in bold.

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ISSN: 1471-2164

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