Molecular Vision: Zhao, Mol Vis 2013; 19:1815-1825. Table 1

Table 1. The results of the target gene and network analysis of selected miRNAs in the corneal endothelium of old mice compared to young mice.

miRNA_name	Gene symbol
mmu-mir-181a	2310067B10RIK, 5730419I09RIK, A930001N09RIK, ADHFE1, ARSJ, ATP6V1A, ATXN1, CBX4, CCAR1, CPD, CUL3, DDIT4, DDX3X, DHX57, DLGAP2, DOCK7, EED, EIF4A2, ELAVL4, ELP4, ESM1, EVI2A, HAND2, HSP90B1, IL1A, ILF3, INPP5E, KLHL5, LYRM1, MARK1, NNT, NPTN, NR6A1, OSBPL3, PAM, PDAP1, PHLDA1, PHOX2B, PLEKHJ1, PRKCD, RALA, RASSF8, RBBP7, RCBTB2, GMA, RNF145, SCHIP1, SEMA4C, SHOC2, SIN3B, SIX2, SLC4A10, SLC9A6, SYT3, TANC2, TXNDC12, ZBTB4, ZFAND6, ZMYND11
mmu-mir-181d	2610305D13RIK, 5730528L13RIK, AFG3L2, CPNE2, E2F5, FIGN, GDI1, HEY2, HMBS, IGF2BP2, LRRN1, MLF1, MOSPD1, MTAP1A, NDRG2, NPEPPS, PAK4, RASSF1, SEMA4G, TBC1D4, TOX, WDR20A,
mmu-mir-182	AADAT, AATK, ABHD2, ACVR1C, ADAM22, ADRA2C, AMPH, ANK3, ANXA11, ARF4, ARHGAP29, BDNF, CCDC41, CDO1, CDSN, CEP250, CHL1, CLPTM1L, COBL, CORO1C, CREB3L1, CTDSP1, CTTN, DAZAP2, DCUN1D4, DOS, EPAS1, EPHB1, ETL4, EVI5, EXOC4, FLOT1, FMR1, FOXF2, FOXO3, GNA13, HAND1, INPP5A, ISL1, JAZF1, KCMF1, KDELR1, KRT84, KTN1, L1CAM, LPHN2, LSM14A, MAGEL2, MARCKS, MGAT4C, MOBKL1A, MTCH2, MYO1B, NCOA4, NPM1, NRN1, OLFR976, PAIP2, PCDH8, PCX, PDIA4, PDZD4, PEX5, PLD1, PNPLA2, PPIL1, PPP1R13B, PPP1R2, PRDM1, RAB19, RAC1, RARG, RASA1, RGS17, RTN4, SH2D1A, SH3BP4, SLC1A2, SLITRK4, SLMO2, SNAP23, SP3, SPIN1, STK19, STK36, STOX2, TAF4A, TGFBI, TMEM115, TOB1, TOPBP1, TSNAX, WDR47, WHSC1L1, WWC2, XBP1, ZFP36, ZMPSTE24
mmu-mir-183	GMFB, GNB1, GNG5, HN1, IDH2, ITGB1, KCNK10, KCNK2, KIF2A, L3MBTL3, LRP6, MAPK8IP1, MTMR6, NPC2, PCDHGA8, PDCD4, PDCD6, PKP4, PLEKHA3, PPP2CB, PPP2R5C, PSEN2, PTDSS1, PTPN4, RCN2, RNF138, SEL1L, SLC35A1, SLITRK1, SLITRK3, 1810013L24RIK, AI314180, ARHGAP21, ASH2L, BC030476, BRD4, BTG1, CLCN3, CSMD1, DUSP10, FCHO2, SNX1, SOBP, SPCS2, SPRY2, STK38L, TMPO, TPM1, TTC14, UNC13B, ZDHHC6, ZEB2, ZFP592, ZFP609, ZFPM2, ZMYM2
mmu-mir-190	AHSA2, BC052040, BDNF, CEBPA, FGF14, GPHN, LMCD1, NKX6–1, SAMD4, SETBP1, SLC17A6
mmu-mir-31	1700066B19RIK, ACTG1, AF529169, AHSG, ATP8A1, COL5A1, COPS2, CTNND2, FNDC5, GLTSCR1, LYZL6, MAP4K5, MBOAT2, OSBP2, POU2F3, PPP3CA, PPP6C, SH2D1A, SLC35A2, SUPT16H, TACC2, TAF4A, TMPRSS11F, TRP53INP2, VPS39
mmu-mir-32	B3GALT2, ARHGAP29, BCL11B, CCNC, CCNL2, CHKA, COL27A1, DCBLD1, DKK3, DNAJB9, DPP10, FRY, GAP43, GFPT2, HAND2, HAS2, HERC2, HERPUD2, HIVEP1, HPS6, IBSP, ITGA6, ITPR1, KALRN, KIF5B, KLF2, LPIN1, LRRC4, LRRC8D, MORC3, MYO1B, PAX9, PCMTD1, PCOLCE2, PIK3CB, PPCS, PPP1R12C, PTPRK, RAB14, RSBN1, SLC25A32, SLC32A1, SMAD6, SMAD7, SUV420H1, SYNJ1, TFDP2, TSGA14, UGP2, USP28, ZFYVE21
mmu-mir-455	ABCF3, ANKS4B, ARMC8, BAX, BRPF1, D10WSU52E, DLG4, FBXL15, H13, H2AFX, HOXC4, HSF1, LHX2, MAGI1, MOSPD1, NDUFA2, NR2F2, PAX6, PCBP2, PCDH9, PLCD4, PNCK, PPP1R10, RMND5A, RTN4, RUSC1, SAP130, SCUBE2, SLC35F1, SMTN, SNX2, SSR1, TMEM62, TRAF1, TRIM3, VSNL1, ZFP238
mmu-mir-695	EIF2S1, EIF4E, SSBP3
mmu-mir-744	LRP3, NRGN, PPFIA3, RARA, SH3BGRL3, VPS37D
mmu-mir-706	ARHGEF17, ATF7IP2, ATP5G1, CEPT1, COPB1, CYC1, DACH2, H2AFV, HOXD13, MLH3, PABPC4, PBX1, PTGS1, STX8, TAF4A, TIA1, TNP1, TRIP12, WIPF2
mmu-mir-29c	ADAMTS18, COL4A1
mmu-mir-34c	NFE2L1, STK38L

The selected miRNAs were mmu-miR-181a, mmu-miR-181d, mmu-miR-182, mmu-miR-183, mmu-miR-190, mmu-miR-31, mmu-miR-32, mmu-miR-455, mmu-miR-695, mmu-miR-744, mmu-miR-706, mmu-miR-29c, and mmu-miR-34c. Prediction of miRNA target genes can be performed by a computational approach. First, the potential binding sites in the mRNA 3′ according to specific base-pairing rules were identified and second, implementation of cross-species conservation requirements was performed. The prediction of miRNA target genes was performed with the following three different miRNA target prediction algorithms: PicTar, miRanda v5 and TargetScan v5.1. Each algorithm has a definite rate of both false positive and false negative predictions. Based on these database searches, the genes with target sites for all of three co-expressed miRNAs were identified as a potential cooperative target gene set. Then, these results were integrated into the gene network analysis using the software Medusa. The common target gene between mmu-miR-181d and mmu-miR-455 was motile sperm domain containing 1 (MOSPD1), that between mmu-miR-31 and mmu-miR-182 was RNA polymerase II, TATA box binding protein (TBP)-associated factor (TAF4A), that between mmu-miR-455 and mmu-miR-182 was reticulon 4 (RTN4), that between mmu-miR-182 and mmu-miR-190 was brain-derived neurotrophic factor (BDNF), that between mmu-miR-142–3p and mmu-miR-34c was protein phosphatase 1, regulatory subunit 10 (PPP1R10), and that between mmu-miR-142–3p and mmu-miR-124 was leucine rich repeat containing 1 (LRRC1).