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_138557
Gene Symbol:	TLR4
Description:	Homo sapiens toll-like receptor 4 (TLR4), transcript variant 1, mRNA.
Browse Associations
Browse Pathways

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117714775C>G			COSN6377805		RK308_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-130a-3p	catggTGCACTagatatgc	0	CAGUGCAA	m6b	Disrupted	-0.125000	no TS	0.100000
hsa-miR-130b-3p	catggTGCACTagatatgc	0	CAGUGCAA	m6b	Disrupted	-0.132000	no TS	1.100000
hsa-miR-301a-3p	catggTGCACTagatatgc	0	CAGUGCAA	m6b	Disrupted	-0.132000	no TS	No effect
hsa-miR-301b	catggTGCACTagatatgc	0	CAGUGCAA	m6b	Disrupted	-0.132000	no TS	0.290000
hsa-miR-3130-3p	catGGTGCAGtagatatgc	0	GCUGCACC	m7b	(m6b->m7b)	-0.122000	-0.403000	-1.210000
hsa-miR-3666	catggTGCACTagatatgc	0	CAGUGCAA	m6b	Disrupted	-0.125000	no TS	0.010000
hsa-miR-4295	catggTGCACTagatatgc	0	CAGUGCAA	m6b	Disrupted	-0.122000	no TS	No effect
hsa-miR-4418	catggTGCAGTagatatgc	0	CACUGCAG	m6b	Created	-0.144000	-0.245000	-0.500000
hsa-miR-4473	catggtGCACTAGatatgc	0	CUAGUGCU	m7a	Disrupted	NA	NA	No effect
hsa-miR-4671-3p	catggTGCACTAgatatgc	0	UUAGUGCA	m7b	Disrupted	-0.164000	no TS	0.010000

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117715294C>T			COSN8294334		PCSI_0083_Pa_P_526		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3646	tccagttTTCATTTTttta	0	AAAAUGAA	m8a	Disrupted	0.064000	0.085000	No effect
hsa-miR-3662	tccagtttTCATTTTttta	0	GAAAAUGA	m7b	Disrupted	0.089000	0.101000	1.040000
hsa-miR-548ac	tccaGTTTTTattttttta	0	CAAAAACC	m6b	Created	no TS	0.060000	-1.770000
hsa-miR-548ae	tccAGTTTTTattttttta	0	CAAAAACU	m7b	(m6b->m7b)	no TS	0.023000	-0.280000
hsa-miR-548ah-3p	tccAGTTTTTattttttta	0	CAAAAACU	m7b	(m6b->m7b)	no TS	0.023000	-0.280000
hsa-miR-548aj-3p	tccAGTTTTTAttttttta	0	UAAAAACU	m8a	Created	no TS	0.023000	-0.250000
hsa-miR-548am-3p	tccAGTTTTTattttttta	0	CAAAAACU	m7b	(m6b->m7b)	no TS	0.023000	-0.240000
hsa-miR-548aq-3p	tccAGTTTTTattttttta	0	CAAAAACU	m7b	(m6b->m7b)	no TS	0.023000	-0.280000
hsa-miR-548d-3p	tccaGTTTTTattttttta	0	CAAAAACC	m6b	Created	no TS	0.074000	0.620000
hsa-miR-548e	tcCAGTTTTTattttttta	0	AAAAACUG	m8a	(m7a->m8a)	-0.129000	-0.156000	0.100000
hsa-miR-548f	tcCAGTTTTTattttttta	0	AAAAACUG	m8a	(m7a->m8a)	-0.129000	-0.156000	0.160000
hsa-miR-548h-3p	tccaGTTTTTattttttta	0	CAAAAACC	m6b	Created	no TS	0.060000	0.620000
hsa-miR-548x-3p	tccAGTTTTTAttttttta	0	UAAAAACU	m8a	Created	no TS	0.023000	-0.250000
hsa-miR-548z	tccaGTTTTTattttttta	0	CAAAAACC	m6b	Created	no TS	0.060000	0.620000
hsa-miR-570-3p	tccaGTTTTCattttttta	0	CGAAAACA	m6b	Disrupted	0.011000	no TS	0.390000

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117715798G>T			COSN6377806		RK308_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1304-3p	tcaaggCAGTGAGtataca	0	UCUCACUG	m7b	Created	no TS	-0.016000	No effect
hsa-miR-3680-5p	tcaaggcAGTGAGTataca	0	GACUCACU	m7b	Created	-0.140000	-0.198000	0.370000
hsa-miR-4798-3p	tcaaggcaGTGAGTataca	0	AACUCACG	m6b	Created	-0.180000	-0.246000	-0.080000

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117715997A>C			ICGC_A64AC6D0-2A78-11E2-8335-12FD496BB9B8		CPCG_0102_Pr_P_P2		ProstateCancer(OICR,CA)
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-335-3p	agggaaATGAAAAtaaaaa	0	UUUUUCAU	m7b	Disrupted	0.419	0.324	-1.05
hsa-miR-33a-5p	agggaAATGCAaataaaaa	0	GUGCAUUG	m6b	Created	no TS	0.047	-0.56
hsa-miR-33b-5p	agggaAATGCAaataaaaa	0	GUGCAUUG	m6b	Created	no TS	0.047	-0.03
hsa-miR-3680-3p	agggaaATGCAAAtaaaaa	0	UUUUGCAU	m7b	Created	no TS	-0.02	-3.56
hsa-miR-5696	agggAAATGAaaataaaaa	0	CUCAUUUA	m6b	Disrupted	0.26	0.13	0.01
hsa-miR-579	agggAAATGAAaataaaaa	0	UUCAUUUG	m7a	Disrupted	0.261	0.131	No effect
hsa-miR-644b-3p	agggAAATGAAaataaaaa	0	UUCAUUUG	m7a	Disrupted	0.26	0.127	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117716245A>C			COSN15189125		SM-4AX86		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117716353A>T			COSN8120405		8066491		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-501-3p	aaaatGTGCATatacgtac	0	AAUGCACC	m6b	Disrupted	-0.060000	no TS	0.030000
hsa-miR-502-3p	aaaatGTGCATatacgtac	0	AAUGCACC	m6b	Disrupted	-0.060000	no TS	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117716359G>A			COSN9697627		AOCS-105-1-9		[ovary][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-297	tgcatatACATACAatggg	0	AUGUAUGU	m7b	Created	no TS	-0.092000	-2.490000
hsa-miR-3149	tgcatataCATACAAtggg	0	UUUGUAUG	m7b	Created	no TS	-0.036000	-0.930000
hsa-miR-3924	tgcatATACATAcaatggg	0	AUAUGUAU	m7b	Created	-0.249000	-0.229000	-0.120000
hsa-miR-567	tgcatatACATACaatggg	0	AGUAUGUU	m6b	Created	no TS	-0.003000	-1.390000
hsa-miR-568	tgcaTATACATacaatggg	0	AUGUAUAA	m7a	Created	NA	NA	-0.040000
hsa-miR-675-3p	tgcatataCATACAatggg	0	CUGUAUGC	m6b	Created	no TS	-0.017000	-0.030000

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117716616C>T			ICGC_8171647C-2A78-11E2-96E7-04FD496BB9B8		CPCG_0102_Pr_P_P1		ProstateCancer(OICR,CA)
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-200a-5p	tatagtatGTAAGATGaat	0	CAUCUUAC	m8a	Created	-0.079	-0.17	-1.01
hsa-miR-200b-5p	tatagtatGTAAGATGaat	0	CAUCUUAC	m8a	Created	-0.072	-0.163	-0.8
hsa-miR-5689	tataGTATGCaagatgaat	0	AGCAUACA	m6b	Disrupted	-0.095	no TS	2.01
hsa-miR-600	tatagtaTGTAAGatgaat	0	ACUUACAG	m6b	Created	no TS	-0.015	-2.48

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117716691A>G			COSN6377807		RK219_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-424-3p	gcacttaACGTTTTGttaa	0	CAAAACGU	m8a	Created	no TS	-0.097000	-1.340000
hsa-miR-4698	gcacttaaCATTTTGttaa	0	UCAAAAUG	m7b	Disrupted	0.082000	0.097000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117717019G>A			COSN14906473		LP6005409-DNA_F02		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1915-3p	catCCCTGGGtgtgtttcc	0	CCCCAGGG	m7b	(m7b->m6b)	-0.192000	no TS	3.620000
hsa-miR-329	catccctgGGTGTGTTtcc	0	AACACACC	m8a	Disrupted	-0.169000	-0.068000	0.920000
hsa-miR-362-3p	catccctgGGTGTGTTtcc	0	AACACACC	m8a	Disrupted	-0.193000	-0.074000	2.330000

Mutation			Mutation ID		Sample Name		Cancer Type
chr9:g.117717103G>A			COSN8120406		8030032		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-329	gggctGTGTGTatttgaaa	0	AACACACC	m6b	Disrupted	-0.169000	-0.101000	No effect
hsa-miR-362-3p	gggctGTGTGTatttgaaa	0	AACACACC	m6b	Disrupted	-0.193000	-0.119000	-0.100000
hsa-miR-3941	gggctGTGTGTAtttgaaa	0	UUACACAC	m7b	Disrupted	-0.141000	no TS	0.920000
hsa-miR-4672	gggCTGTGTAtatttgaaa	0	UUACACAG	m7b	(m6b->m7b)	no TS	-0.090000	-1.100000
hsa-miR-4789-5p	gggctGTGTATAtttgaaa	0	GUAUACAC	m7b	Created	no TS	-0.101000	-1.300000

**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
117714755	rs200716692	G	G	hsa-miR-3620-3p hsa-miR-3680-5p hsa-miR-4798-3p hsa-miR-6784-3p hsa-miR-6862-3p hsa-miR-6865-3p	0	ctaAGGGTGAgta ctaaggGTGAGTA ctaaggGTGAGTA ctaaGGGTGAGta ctaaGGGTGAGta ctaAGGGTGAgta	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N	-0.16 -0.14 -0.18 -0.29 -0.299 -0.162
117714755	rs200716692	G	A	hsa-miR-4793-5p hsa-miR-5196-3p hsa-miR-6870-3p	0	ctaAGGATGAgta ctaAGGATGAgta ctaaGGATGAGta	Created Created Created	N N N	-0.114 -0.116 -0.239
117714816	rs199780461	A	A	hsa-miR-2276-5p hsa-miR-3130-3p hsa-miR-4793-3p hsa-miR-642a-5p hsa-miR-6892-3p	0	cagtgCAGAGGGA caGTGCAGAggga cAGTGCAGAggga cagtgcAGAGGGA cagtgcAGAGGGA	Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N	-0.391 -0.122 -0.284 -0.194 -0.153
117714816	rs199780461	A	C	hsa-miR-4655-3p hsa-miR-6803-3p	0	cagtgcCGAGGGA cagtgcCGAGGGA	Created Created	N N	-0.252 -0.249
117715051	rs11536886	C	C	hsa-miR-3609 hsa-miR-548ah-5p hsa-miR-548az-5p hsa-miR-548t-5p	0	tgtTCACTTTttc tgtTCACTTTttc tgttCACTTTTtc tgttCACTTTTtc	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.078 -0.124 -0.075 -0.075
117715051	rs11536886	C	T	hsa-miR-3646 hsa-miR-3662	0	tgTTCATTTtttc tgtTCATTTTttc	Created Created	N N	-0.018 -0.029
117715097	rs201521265	G	G	hsa-miR-17-3p hsa-miR-4418 hsa-miR-509-3-5p hsa-miR-509-5p	0	atgACTGCAGtcg atgaCTGCAGTcg atgaCTGCAGTcg atgaCTGCAGTcg	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.111 -0.144 -0.144 -0.125
117715097	rs201521265	G	A	hsa-miR-1183 hsa-miR-20b-3p	0	atgaCTACAGTcg atgACTACAGtcg	Created Created	N N	-0.108 -0.093
117715099	rs199501554	A	A	hsa-miR-17-3p hsa-miR-4418 hsa-miR-509-3-5p hsa-miR-509-5p	0	gACTGCAGtcgtc gaCTGCAGTcgtc gaCTGCAGTcgtc gaCTGCAGTcgtc	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.111 -0.144 -0.144 -0.125
117715099	rs199501554	A
117716304	rs190198965	G	G	hsa-miR-587	0	gtTATGGAAAcaa	Disrupted	N	0.029
117716304	rs190198965	G	A	hsa-miR-335-3p	0	gttATGAAAAcaa	Created	N	0.088
117716326	rs2853567	A	A	hsa-miR-1305 hsa-miR-335-3p	0	ccaTTGAAAAata ccatTGAAAAAta	Disrupted Disrupted	N N	0.093 0.112
117716326	rs2853567	A
117716359	rs199511657	G
117716359	rs199511657	G	A	hsa-miR-297 hsa-miR-3149 hsa-miR-3924 hsa-miR-567 hsa-miR-675-3p	0	atatACATACAAt atataCATACAAt atATACATAcaat atatACATACAat atataCATACAAt	Created Created Created Created Created	N N N N N	-0.092 -0.036 0.02 -0.003 -0.017
117716443	rs199673052	A	A	hsa-miR-376c-3p	0	tatgCTATGTAaa	Disrupted	N	-0.014
117716443	rs199673052	A	G	hsa-miR-3941 hsa-miR-466 hsa-miR-4672 hsa-miR-6768-5p	0	tatgcTGTGTAAa tatgcTGTGTAAa tatgCTGTGTAAa tatgCTGTGTAaa	Created Created Created Created	N N N N	0.019 0.023 -0.034 -0.023
117716492	rs199755109	A	A	hsa-miR-1252-3p hsa-miR-3646	0	TCATTTAtatgag TCATTTAtatgag	Disrupted Disrupted	N N	0.071 0.048
117716492	rs199755109	A	T	hsa-miR-3662 hsa-miR-548c-3p	0	TCATTTTtatgag tcATTTTTAtgag	Created Created	N N	0.033 0.172
117716646	rs202132427	A	A	hsa-let-7f-2-3p hsa-miR-1185-1-3p hsa-miR-1185-2-3p hsa-miR-1284	0	agCTGTATAgcag agCTGTATAgcag agCTGTATAgcag agcTGTATAGcag	Disrupted Disrupted Disrupted Disrupted	N N N N	0.019 0.038 0.038 -0.014
117716646	rs202132427	A	G	hsa-miR-187-5p hsa-miR-221-3p hsa-miR-222-3p hsa-miR-4672 hsa-miR-548v hsa-miR-6768-5p	0	agctgTGTAGCAg agctgTGTAGCAg agctgTGTAGCAg agCTGTGTAgcag agctgTGTAGCAg agCTGTGTAgcag	Created Created Created Created Created Created	N N N N N N	-0.062 -0.067 -0.067 -0.021 -0.062 -0.011
117716657	rs188281650	C	C	hsa-let-7d-3p hsa-let-7e-3p hsa-miR-4680-5p	0	agagtTCGTATAA agagttCGTATAA AGAGTTCgtataa	Disrupted Disrupted Disrupted	N N N	-0.308 -0.114 -0.057
117716657	rs188281650	C	T	hsa-let-7a-3p hsa-let-7b-3p hsa-let-7f-1-3p hsa-let-7f-2-3p hsa-miR-1185-1-3p hsa-miR-1185-2-3p hsa-miR-300 hsa-miR-381-3p hsa-miR-4666a-3p hsa-miR-4789-5p hsa-miR-98-3p	0	agagtTTGTATAA agagtTTGTATAA agagtTTGTATAA agagttTGTATAA agagttTGTATAA agagttTGTATAA agagtTTGTATAa agagtTTGTATAa agagtTTGTATAa agagttTGTATAA agagtTTGTATAA	Created Created Created Created Created Created Created Created Created Created Created	N N N N N N N N N N N	-0.02 -0.041 -0.02 0.017 0.027 0.027 0.049 0.042 0.055 0.028 -0.02
117716690	rs200301435	C	C	hsa-miR-4698	0	acttaaCATTTTG	Disrupted	N	-0.015
117716690	rs200301435	C	T	hsa-miR-4477a	0	aCTTAATAttttg	Created	N	-0.002
117716733	rs200901388	T	T	hsa-miR-5579-5p hsa-miR-8076	0	tTACCATAtacat ttaCCATATAcat	Disrupted Disrupted	N N	-0.069 -0.034
117716733	rs200901388	T	C	hsa-miR-297 hsa-miR-299-3p hsa-miR-4491 hsa-miR-4536-5p hsa-miR-4657 hsa-miR-567	0	ttaccACATACAt ttaCCACATAcat ttaCCACATAcat tTACCACAtacat ttaCCACATAcat ttaccACATACAt	Created Created Created Created Created Created	N N N N N N	-0.027 -0.073 -0.065 -0.086 -0.072 -0.029
117716734	rs202038980	A	A	hsa-miR-3924 hsa-miR-5579-5p hsa-miR-8076	0	taccatATACATA TACCATAtacata taCCATATAcata	Disrupted Disrupted Disrupted	N N N	-0.02 -0.069 -0.034
117716734	rs202038980	A	G	hsa-miR-4802-3p hsa-miR-493-5p hsa-miR-942-3p	0	taCCATGTAcata taccATGTACAta taCCATGTAcata	Created Created Created	N N N	-0.07 -0.031 -0.075
117716735	rs199611415	T	T	hsa-miR-3924 hsa-miR-8076	0	accatATACATAt aCCATATAcatat	Disrupted Disrupted	N N	-0.02 -0.034
117716735	rs199611415	T	A	hsa-miR-4307 hsa-miR-584-5p	0	accatAAACATAt ACCATAAacatat	Created Created	N N	0.065 -0.052
117716835	rs201725806	T	T	hsa-let-7a-3p hsa-let-7b-3p hsa-let-7f-1-3p hsa-miR-300 hsa-miR-381-3p hsa-miR-4666a-3p hsa-miR-7849-3p hsa-miR-98-3p	0	atcaaaTTGTATA atcaaaTTGTATA atcaaaTTGTATA atcaaaTTGTATA atcaaaTTGTATA atcaaATTGTATA atcaAATTGTAta atcaaaTTGTATA	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N N N	-0.072 -0.072 -0.082 0.007 0.007 -0.089 0.007 -0.063
117716835	rs201725806	T	G	hsa-miR-4789-5p	0	atcaaaGTGTATA	Created	N	-0.136
117717101	rs201586210	G	G	hsa-miR-329-3p hsa-miR-362-3p hsa-miR-3941 hsa-miR-603	0	ggctGTGTGTAtt ggctGTGTGTAtt ggctGTGTGTAtt ggctGTGTGTAtt	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.068 -0.074 -0.141 -0.062
117717101	rs201586210	G	A	hsa-miR-6856-3p	0	GGCTGTAtgtatt	Created	N	-0.198
117717119	rs201308639	G
117717119	rs201308639	G	A	hsa-miR-329-3p hsa-miR-362-3p hsa-miR-3941 hsa-miR-603	0	GTGTGTAtgtccg GTGTGTAtgtccg GTGTGTAtgtccg GTGTGTAtgtccg	Created Created Created Created	N N N N	-0.095 -0.109 -0.13 -0.135
117717348	rs11536894	C	C	hsa-miR-3924	0	cctATACATAAat	Disrupted	N	-0.229
117717348	rs11536894	C	T	hsa-miR-190a-3p hsa-miR-5011-5p hsa-miR-6083	0	cctATATATAAat ccTATATATAaat cctatATATAAAt	Created Created Created	N N N	-0.141 -0.075 -0.002
117717351	rs201462763	A	A	hsa-miR-3924	0	ATACATAAatacc	Disrupted	N	-0.229
117717351	rs201462763	A	G	hsa-miR-6516-3p hsa-miR-664a-3p	0	aTACATGAAtacc atacATGAATAcc	Created Created	N N	-0.317 -0.031
117717360	rs199639022	A	A	hsa-miR-200a-5p hsa-miR-200b-5p hsa-miR-331-5p hsa-miR-6509-5p	0	taccTAAGATAaa taccTAAGATAaa TACCTAAgataaa TACCTAAgataaa	Disrupted Disrupted Disrupted Disrupted	N N N N	-0.079 -0.072 -0.161 -0.233
117717360	rs199639022	A	G	hsa-miR-5571-3p	0	taCCTAGGAtaaa	Created	N	-0.304

**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