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_002445
Gene Symbol:	MSR1
Description:	Homo sapiens macrophage scavenger receptor 1 (MSR1), transcript variant SR-AII, mRNA.
Gene Location:	chr8(-):15996825-16050300
Browse Associations

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16139589A>T			COSN6918071		RK187_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-3143	tgggattacATGTTATatt	5	AUAACAUU	m7a	(m7a->m6a)	-0.013000	-0.013000	No effect
hsa-miR-380-3p	tgggATTACATgttatatt	1	UAUGUAAU	m7b	Disrupted	-0.051000	no TS	0.020000

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16139881T>A			COSN6918072		RK200_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1277-5p	ttagaATATATTTtaaaaa	0	AAAUAUAU	m8a	Created	-0.195000	-0.232000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140091A>T			COSN6518221		HX18T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140093C>A			COSN6518222		HX18T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140150A>T			COSN5234005		SS6003323		[oesophagus][NS][carcinoma][adenocarcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-340-5p	gttCTTTATAttcaaacat	4	UUAUAAAG	m7b	(m7b->m6c)	0.014000	no TS	0.010000
hsa-miR-5585-3p	gttctttaTATTCAaacat	3	CUGAAUAG	m6b	Disrupted	-0.003000	no TS	2.100000

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140390A>T			COSN8575846		tumor_4166706		[haematopoietic_and_lymphoid_tissue][NS][lymphoid_neoplasm][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-548c-3p	tttcatttGATTTTTactg	2	CAAAAAUC	m7b	Disrupted	0.155000	0.097000	1.490000
hsa-miR-551b-5p	tttcatTTGATTTttactg	3	GAAAUCAA	m7b	Disrupted	-0.036000	no TS	1.720000
hsa-miR-7-1-3p	tttcATTTGTTttttactg	1	CAACAAAU	m7b	Created	0.014000	0.027000	No effect
hsa-miR-7-2-3p	tttcATTTGTTttttactg	1	CAACAAAU	m7b	Created	0.014000	0.036000	0.370000

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140583A>C			COSN4878373		tumor_4135350		[haematopoietic_and_lymphoid_tissue][NS][lymphoid_neoplasm][Burkitt_lymphoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4315	gtcaagcAAAGCGattcct	1	CCGCUUUC	m6b	Disrupted	-0.149000	no TS	8.340000
hsa-miR-4790-5p	gtcaagcAAAGCGATtcct	1	AUCGCUUU	m8a	Disrupted	-0.175000	no TS	2.790000

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140807A>C			COSN8518620		227_T		[lung][NS][carcinoma][squamous_cell_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1909-3p	tctgctCCCCTGCtcatac	0	CGCAGGGG	m7b	Created	no TS	-0.237000	-2.980000
hsa-miR-4468	tctgctcccCTGCTCatac	8	AGAGCAGA	m6b	Created	-0.080000	-0.181000	-2.090000
hsa-miR-4690-5p	tctgctccCCTGCTCatac	0	GAGCAGGC	m7a	Created	NA	NA	-11.240000
hsa-miR-939	tctGCTCCCCtgctcatac	0	UGGGGAGC	m7b	(m6c->m7b)	no TS	-0.259000	-0.120000

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140874C>A			COSN8518621		J15_T		[lung][NS][carcinoma][squamous_cell_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-141-3p	tttggttcCAGTGTTgtac	0	UAACACUG	m7b	Created	no TS	-0.122000	-0.030000
hsa-miR-200a-3p	tttggttcCAGTGTTgtac	0	UAACACUG	m7b	Created	no TS	-0.103000	-0.010000
hsa-miR-4681	tttggTTCCCGTgttgtac	1	AACGGGAA	m7b	Disrupted	-0.228000	no TS	8.010000
hsa-miR-602	tttggttCCCGTGTtgtac	0	GACACGGG	m7b	Disrupted	-0.311000	no TS	5.610000

Mutation			Mutation ID		Sample Name		Cancer Type
chr8:g.16140985C>T			9_132720		CRC-1-Tumor		Colorectal adenocarcinoma
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1224-3p	tgggttgGGTGGGacatcc	8	CCCCACCU	m6b	Created	0	-0.166	No effect
hsa-miR-1260a	tgggttgGGTGGGAcatcc	7	AUCCCACC	m7b	Created	no TS	-0.25	No effect
hsa-miR-1260b	tgggttgGGTGGGAcatcc	7	AUCCCACC	m7b	Created	no TS	-0.25	No effect
hsa-miR-1280	tgggttgGGTGGGAcatcc	7	UCCCACCG	m7a	Created	no TS	-0.202	No effect
hsa-miR-4258	tgggttgGGCGGGacatcc	8	CCCCGCCA	m6b	Disrupted	-0.261	no TS	No effect
hsa-miR-4433-5p	tgggttggGTGGGACatcc	7	CGUCCCAC	m7b	Created	no TS	-0.446	-5.38

**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
16139437	rs1480143	A	A	hsa-miR-548c-3p hsa-miR-6716-5p	1 1	ATTTTTAttccca atttttATTCCCA	Disrupted Disrupted	N N	0.097 -0.135
16139437	rs1480143	A	G	hsa-miR-1292-5p hsa-miR-4471 hsa-miR-8059	1 1 1	atttttGTTCCCA atttttGTTCCCA atttttGTTCCCA	Created Created Created	N N N	-0.192 -0.187 -0.191
16139774	rs10585203	-	TATATATT	hsa-miR-1277-5p	0	tatatatATATATTttttttttttttt	Unknown	N	No Change
16139774	rs10585203	-	-
16139778	rs56355714	-	A	hsa-miR-190a-3p hsa-miR-5011-5p	0	ATATATAtatttt aTATATATAtttt	Unknown Unknown	N N	-0.311 -0.276
16139778	rs56355714	-	-	hsa-miR-1277-5p hsa-miR-5692a hsa-miR-5692b hsa-miR-5692c	0	ATATATTAtttt atatATTATTTt atATATTATttt atATATTATttt	Unknown Unknown Unknown Unknown	N N N N	-0.017 -0.05 -0.136 -0.136
16139780	rs56156153	-	A	hsa-miR-190a-3p hsa-miR-5011-5p	0	ATATATAtatatt aTATATATAtatt	Unknown Unknown	N N	-0.467 -0.416
16139780	rs56156153	-	-	hsa-miR-1277-5p hsa-miR-369-3p hsa-miR-374a-5p hsa-miR-374b-5p hsa-miR-5692b hsa-miR-5692c	0	ATATATTAtatt ataTATTATAtt ataTATTATAtt ataTATTATAtt atATATTATAtt atATATTATAtt	Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N	-0.017 -0.028 -0.144 -0.126 -0.154 -0.154
16139782	rs56158010	-	A	hsa-miR-190a-3p hsa-miR-5011-5p	0	ATATATAtatata aTATATATAtata	Unknown Unknown	N N	-0.623 -0.427
16139782	rs56158010	-	-	hsa-miR-1277-5p hsa-miR-369-3p hsa-miR-374a-5p hsa-miR-374b-5p hsa-miR-410-3p hsa-miR-5692b hsa-miR-5692c	0	ATATATTAtata ataTATTATAta ataTATTATAta ataTATTATAta atataTTATATA atATATTATAta atATATTATAta	Unknown Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N N	-0.211 -0.028 -0.143 -0.125 -0.025 -0.154 -0.154
16139784	rs56053018	-	A	hsa-miR-190a-3p hsa-miR-5011-5p	0	ATATATAtatata aTATATATAtata	Unknown Unknown	N N	-0.622 -0.425
16139784	rs56053018	-	-	hsa-miR-1277-5p hsa-miR-369-3p hsa-miR-374a-5p hsa-miR-374b-5p hsa-miR-410-3p hsa-miR-5692b hsa-miR-5692c	0	ATATATTAtata ataTATTATAta ataTATTATAta ataTATTATAta atataTTATATA atATATTATAta atATATTATAta	Unknown Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N N	-0.201 -0.027 -0.143 -0.125 -0.025 -0.153 -0.153
16139794	rs67548047	A	A	hsa-miR-190a-3p hsa-miR-5011-5p	1 1	ATATATAtatata aTATATATAtata	Disrupted Disrupted	N N	-0.611 -0.406
16139794	rs67548047	A	T	hsa-miR-1277-5p hsa-miR-410-3p	1 0	ATATATTtatata atatatTTATATA	Created Created	N N	-0.188 -0.022
16139812	rs200856617	A	A	hsa-miR-190a-3p hsa-miR-5011-5p	1 1	ATATATAtatata aTATATATAtata	Disrupted Disrupted	N N	-0.516 -0.408
16139812	rs200856617	A	T	hsa-miR-1277-5p hsa-miR-410-3p	1 1	ATATATTtatata atatatTTATATA	Created Created	N N	-0.152 -0.01
16140580	rs115232574	G	G	hsa-miR-4315 hsa-miR-4790-5p	1 1	cAAAGCGAttcct cAAAGCGAttcct	Disrupted Disrupted	N N	-0.149 -0.175
16140580	rs115232574	G	C	hsa-miR-135a-5p hsa-miR-135b-5p hsa-miR-3119	1 1 1	caAAGCCATtcct caAAGCCATtcct cAAAGCCAttcct	Created Created Created	N N N	-0.137 -0.137 -0.085
16140985	rs201315825	C	C	hsa-miR-4258 hsa-miR-4449 hsa-miR-7108-3p	4 4 4	gttgGGCGGGAca gttgggCGGGACA gttGGGCGGGAca	Disrupted Disrupted Disrupted	N N N	-0.261 -0.217 No Change
16140985	rs201315825	C	T	hsa-miR-1224-3p hsa-miR-1260a hsa-miR-1260b hsa-miR-4433-5p hsa-miR-4433b-5p	4 4 4 4 4	gttgGGTGGGAca gttgGGTGGGAca gttgGGTGGGAca gttggGTGGGACA gttgggTGGGACA	Created Created Created Created Created	N N N N N	-0.166 -0.25 -0.25 -0.446 -0.182

**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