Table 1A.

Selected mirBridge predictions with published evidence (see Table S1 for more details). “High-quality putative targets” are ones with either a conserved or high context-scoring site (see Experimental Procedures).

miRNA	Function	q value	High-quality putative targets	Evidence
146	IL1 receptor, NFKB, Toll Like Receptor signaling	0	TRAF6, IRAK1, TLR4	(Jones et al., 2009; Taganov et al., 2006)
15/16/195/424/497	Cell cycle; G1 to S	0	CCNE1, CCND1, CCND3, CCND2, CDC25A	(Linsley et al., 2007; Liu et al., 2008)
			CCNE1, WEE1, E2F3, CCND1, CCND3, CCND2, CDC25A
29	Collagen	0	COL4A1, COL4A5, COL4A4, COL4A6, COL4A2, COL4A3, FGA	(Li et al., 2009; van Rooij et al., 2008)
7	ErbB signaling; glioma	0	RAF1, EGFR, FRAP1, MAPK1, PIK3CD, PAK1, PIK3R3, RPS6KB1, CAMK2D, PAK2, TGFA, PTK2, CBL, ERBB4, CRKL, MAPK3	(Kefas et al., 2008; Webster et al., 2009)
			RAF1, RB1, CALM3, EGFR, FRAP1, MAPK1, PIK3CD, PIK3R3, CAMK2D, TGFA, IGF1R, MAPK3
7	insulin signaling	0.000208	IRS1, IRS2, RAF1, CALM3, FRAP1, MAPK1, PHKA2, PIK3CD, PIK3R3, RPS6KB1, MKNK1, CBL, FLOT2, PRKAG2, CRKL, SOCS2, PPARGC1A, MAPK3	(Bravo-Egana et al., 2008; Correa-Medina et al., 2009; Joglekar et al., 2009)
15/16/195/424/497	Wnt pathway	0.0356	FZD10, DVL1, CCND1, PAFAH1B1, PPP2R5C, FZD6, CCND3, DVL3, MAPK9, PRKCI, CCND2, WNT7A, FOSL1, WNT2B	(Bonci et al., 2008)
103/107	TNF pathway	0.0522	HRB, CASP3, TNF, MAP3K7, TNFAIP3, NR2C2	(Xie et al., 2009)
122	NO1 pathway	0.0546	SLC7A1, RYR2, CALM3, TNNI1	(Yang and Kaye, 2009)
15/16/195/424/497	prostate cancer	0.07345	CCNE1, AKT3, PIK3R1, MAP2K1, IKBKB, E2F3, RAF1, CCND1, PIK3R3, CHUK, CCNE1, FGFR1, FGFR2, GRB2, FOXO1, IGF1R, BCL2, CREB5, MAPK3	(Bonci et al., 2008)
135	TGF beta signaling	0.07389	SMAD5, ROCK2, SMURF2, THBS2, ROCK1, SMAD2, FKBP1A, NODAL, PPP2R1B, INHBA, TGFBR1, ACVR1B, BMPR1A, SP1, RPS6KB1, BMPR2, RUNX2, RBX1, SKI	(Li et al., 2008)
34a/449	Notch signaling	0.07389	NOTCH1, DLL1, NUMBL, HDAC1, JAG1, NOTCH2, NOTCH3	(Ji et al., 2008; Ji et al., 2009)
21	cytokine-cytokine receptor interaction	0.0865	IL12A, CCL20, CCL1, FASLG, TNFRSF11B, TNFRSF10B, IL1B, CCR7, LEPR, BMPR2, XCL1, LIFR, CNTFR, TGFBR2, CXCL5, ACVR2A	(Lu et al., 2009)
1/206	PIP3 signaling in cardiac myocytes	0.0977	IGF1, CREB5, YWHAZ, MET, CDC42, YWHAQ, PTPN1, PREX1	(Care et al., 2007; Sayed et al., 2007)
17-5p/20/93.mr/106/519.d	cell cycle; G1 to S	0.122	CCNE1, CCND1, CDC25A, SMAD3	(Cloonan et al., 2008; Pickering et al., 2009)
			CCNG2, RBL1, RPA2, WEE1, E2F1, CCND2, CDKN1A, MCM3, CDC25A, RB1, E2F3, CCND1, CCNE2
221/222	breast cancer estrogen signaling	0.1432	KIT, CDKN1B, NFYB, SERPINB5, ESR1, THBS1, THBS2	(Miller et al., 2008; Zhao et al., 2008)
34/449	BAD pathway (apoptosis)	0.1499	KIT, KITLG, BCL2, IGF1, PRKACB	(Chang et al., 2007; Cloonan et al., 2008; He et al., 2007)
let-7/98	breast cancer estrogen signaling	0.1595	CYP19A1, NGFB, CDH1, TP53, CDKN1A, FASLG, PPIA, THBS1, DLC1, PAPPA, IL6, DLC1, DST, PAPPA, CND1	(Schultz et al., 2007)
let-7/98	G1 to S	0.1871	E2F6, TP53, PRIM2, CDKN1A, CDC25A, RB1, CCND2, CCND1, CCND2, CCND2	(Schultz et al., 2008; Yu et al., 2007)