SomamiR DB

SomamiR DB 2.0 Somatic mutations altering microRNA-ceRNA interactions
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Prediction criteria:	TargetScan sites only All 6mer or longer seed matches

PolymiRTS Database

RefSeq ID:	NM_005904
Gene Symbol:	SMAD7
Description:	Homo sapiens SMAD family member 7 (SMAD7), transcript variant 2, mRNA.
Gene Location:	chr18(-):46446222-46477081
Browse Associations
Browse Pathways

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.48919991A>C			COSN1745264		RK037_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-376a-5p	tgctttAATCTAaatgcaa	0	GUAGAUUC	m6b	Created	no TS	-0.073000	-0.210000
hsa-miR-4729	tgctttaatATAAATGcaa	19	UCAUUUAU	m7b	(m7b->m6b)	-0.081000	0.025000	0.060000
hsa-miR-4760-5p	tgctttAATCTAAAtgcaa	0	UUUAGAUU	m8a	Created	no TS	-0.246000	-3.500000
hsa-miR-656	tgcttTAATATaaatgcaa	20	AAUAUUAU	m6b	Disrupted	-0.004000	no TS	No effect
hsa-miR-376a-5p	tgctttAATCTAaatgcaa	0	GUAGAUUC	m6b	Created	no TS	-0.073	-0.21
hsa-miR-4729	tgctttaatATAAATGcaa	0	UCAUUUAU	m7b	(m7b->m6b)	-0.081	0.025	0.06
hsa-miR-4760-5p	tgctttAATCTAAAtgcaa	0	UUUAGAUU	m8a	Created	no TS	-0.246	-3.5
hsa-miR-656	tgcttTAATATaaatgcaa	0	AAUAUUAU	m6b	Disrupted	-0.004	no TS	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.48920372T>G			COSN1206701		HX17T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4442	tttgGTCCGGCataaccca	0	GCCGGACA	m7a	Created	NA	NA	-5.670000
hsa-miR-4633-5p	tttggtccGGCATAaccca	0	AUAUGCCU	m6b	Created	no TS	-0.078000	-11.160000
hsa-miR-4757-3p	tttggtcCGTCATaaccca	0	CAUGACGU	m6b	Disrupted	-0.141000	no TS	3.740000
hsa-miR-4442	tttgGTCCGGCataaccca	0	GCCGGACA	m7a	Created	NA	NA	-5.67
hsa-miR-4633-5p	tttggtccGGCATAaccca	0	AUAUGCCU	m6b	Created	no TS	-0.078	-11.16
hsa-miR-4757-3p	tttggtcCGTCATaaccca	0	CAUGACGU	m6b	Disrupted	-0.141	no TS	3.74

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.48920435C>T			COSN6416475		HX36T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4286	gccagcaAGTGGGGatgtc	7	ACCCCACU	m7b	Created	-0.084000	-0.373000	-12.760000

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.48920548C>G			COSN1206702		HCC42T		[liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1266	ctctcCCCTGAGcctctcc	12	CCUCAGGG	m7b	Created	-0.382000	-0.423000	0.130000
hsa-miR-1914-3p	ctctCCCCTCagcctctcc	0	GGAGGGGU	m6b	Disrupted	-0.176000	-0.077000	7.960000
hsa-miR-24-3p	ctctcccCTGAGCCtctcc	0	UGGCUCAG	m7b	Created	no TS	-0.032000	-10.270000
hsa-miR-2467-5p	ctctcccctGAGCCTCtcc	0	UGAGGCUC	m7b	(m6b->m7b)	no TS	-0.081000	1.530000
hsa-miR-3929	ctctccccTCAGCCTCtcc	5	GAGGCUGA	m8a	Disrupted	0.005000	no TS	10.870000
hsa-miR-4419b	ctctccccTCAGCCTCtcc	5	GAGGCUGA	m8a	Disrupted	-0.004000	no TS	8.140000
hsa-miR-4478	ctctccccTCAGCCTCtcc	5	GAGGCUGA	m8a	Disrupted	-0.013000	no TS	4.830000
hsa-miR-4518	ctctcCCCTGAGCctctcc	12	GCUCAGGG	m8a	Created	-0.372000	-0.422000	-1.560000
hsa-miR-485-5p	ctctcccctCAGCCTCTcc	5	AGAGGCUG	m8a	(m8a->m7a)	-0.048000	no TS	No effect
hsa-miR-1266	ctctcCCCTGAGcctctcc	0	CCUCAGGG	m7b	Created	-0.382	-0.423	0.13
hsa-miR-1914-3p	ctctCCCCTCagcctctcc	0	GGAGGGGU	m6b	Disrupted	-0.176	-0.077	7.96
hsa-miR-24-3p	ctctcccCTGAGCCtctcc	0	UGGCUCAG	m7b	Created	no TS	-0.032	-10.27
hsa-miR-2467-5p	ctctcccctGAGCCTCtcc	0	UGAGGCUC	m7b	(m6b->m7b)	no TS	-0.081	1.53
hsa-miR-3929	ctctccccTCAGCCTCtcc	0	GAGGCUGA	m8a	Disrupted	0.005	no TS	10.87
hsa-miR-4419b	ctctccccTCAGCCTCtcc	0	GAGGCUGA	m8a	Disrupted	-0.004	no TS	8.14
hsa-miR-4478	ctctccccTCAGCCTCtcc	0	GAGGCUGA	m8a	Disrupted	-0.013	no TS	4.83
hsa-miR-4518	ctctcCCCTGAGCctctcc	0	GCUCAGGG	m8a	Created	-0.372	-0.422	-1.56
hsa-miR-485-5p	ctctcccctCAGCCTCTcc	0	AGAGGCUG	m8a	(m8a->m7a)	-0.048	no TS	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr18:g.48920671G>T			COSN1206703		BN17T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-185-3p	ttcctgcCAGCCCCTgcca	6	AGGGGCUG	m8a	Disrupted	-0.148000	-0.047000	5.120000
hsa-miR-4492	ttcctgCCAGCCCCtgcca	0	GGGGCUGG	m8a	Disrupted	-0.084000	no TS	0.560000
hsa-miR-4498	ttcctgCCAGCCCctgcca	0	UGGGCUGG	m7b	Disrupted	-0.131000	no TS	0.160000
hsa-miR-5001-5p	ttcctgCCAGCCCctgcca	0	AGGGCUGG	m7b	Disrupted	-0.121000	no TS	0.590000
hsa-miR-762	ttcctgCCAGCCCCtgcca	0	GGGGCUGG	m8a	Disrupted	-0.140000	no TS	No effect
hsa-miR-185-3p	ttcctgcCAGCCCCTgcca	0	AGGGGCUG	m8a	Disrupted	-0.148	-0.047	5.12
hsa-miR-4492	ttcctgCCAGCCCCtgcca	0	GGGGCUGG	m8a	Disrupted	-0.084	no TS	0.56
hsa-miR-4498	ttcctgCCAGCCCctgcca	0	UGGGCUGG	m7b	Disrupted	-0.131	no TS	0.16
hsa-miR-5001-5p	ttcctgCCAGCCCctgcca	0	AGGGCUGG	m7b	Disrupted	-0.121	no TS	0.59
hsa-miR-762	ttcctgCCAGCCCCtgcca	0	GGGGCUGG	m8a	Disrupted	-0.14	no TS	No effect

**Germline mutations in target sites of miRNAs in somatic mutation table**
Location	SNP ID	Ancestral Allele	Allele	miR ID	Conservation	miRSite	FuncClass	Validation	context+ score change
48920145	rs16950112	A	A	hsa-miR-329-5p	3	aaaAAAACCTgag	Disrupted	N	-0.155
48920145	rs16950112	A	C	hsa-miR-1266-5p hsa-miR-4518 hsa-miR-6823-5p	14 14 3	aaaaaaCCCTGAG aaaaaaCCCTGAG aaaaAACCCTGAg	Created Created Created	N N N	-0.306 -0.285 -0.407
48920219	rs16950113	A	A	hsa-miR-1206 hsa-miR-4729 hsa-miR-5696 hsa-miR-579-3p hsa-miR-664b-3p hsa-miR-6853-3p	18 17 16 17 17 17	gtttaaATGAACA gttTAAATGAaca gttTAAATGAAca gtttAAATGAAca gtttAAATGAAca gtttaAATGAACA	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N	-0.083 0.025 -0.067 0.015 0.022 -0.249
48920219	rs16950113	A	G	hsa-miR-302a-5p	18	GTTTAAGtgaaca	Created	N	-0.081
48920435	rs190053734	C
48920435	rs190053734	C	T	hsa-miR-4286	1	agcaAGTGGGGAt	Created	N	-0.289
48920778	rs138939641	T	T	hsa-miR-3126-5p hsa-miR-4419a hsa-miR-4510 hsa-miR-6127 hsa-miR-6129 hsa-miR-6130 hsa-miR-6133 hsa-miR-6731-5p hsa-miR-6760-5p hsa-miR-6834-5p hsa-miR-6875-5p hsa-miR-8085	2 2 2 2 2 2 2 6 2 2 2 6	ctcctcTCCCTCA ctcctCTCCCTCA ctcctCTCCCTCA ctcctCTCCCTCA ctcctCTCCCTCA ctcctCTCCCTCA ctcctCTCCCTCA ctcCTCTCCCtca ctccTCTCCCTca ctcctcTCCCTCA ctcctcTCCCTCA ctcCTCTCCCtca	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N N N N N N N	-0.087 -0.236 -0.236 -0.246 -0.225 -0.215 -0.236 -0.072 -0.034 -0.077 -0.091 -0.053
48920778	rs138939641	T	C	hsa-miR-1914-3p hsa-miR-3184-5p hsa-miR-423-5p hsa-miR-4716-3p hsa-miR-4723-5p hsa-miR-5194 hsa-miR-5698 hsa-miR-6734-5p hsa-miR-6738-5p hsa-miR-6794-5p hsa-miR-6825-5p hsa-miR-6870-5p hsa-miR-7106-5p hsa-miR-7111-5p hsa-miR-765	2 2 2 2 6 2 6 2 2 2 5 6 4 6 2	ctcctcCCCCTCA ctcctcCCCCTCA ctcctcCCCCTCA ctccTCCCCCTca ctcCTCCCCCtca ctcctcCCCCTCA ctcCTCCCCCtca ctcctcCCCCTCA ctcctcCCCCTCA ctccTCCCCCTca ctCCTCCCCctca ctcCTCCCCCtca cTCCTCCCcctca ctcCTCCCCCtca CTCCTCCccctca	Created Created Created Created Created Created Created Created Created Created Created Created Created Created Created	N N N N N N N N N N N N N N N	-0.108 -0.089 -0.092 -0.1 -0.116 -0.111 -0.107 -0.123 -0.118 -0.128 -0.115 -0.144 -0.01 -0.135 -0.028

**Genome Browser**
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Somatic mutations that impact miRNA target sites

Germline mutations in target sites of miRNAs in somatic mutation table

Genome Browser