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

RefSeq ID:	NM_006769
Gene Symbol:	LMO4
Description:	Homo sapiens LIM domain only 4 (LMO4), mRNA.
Gene Location:	chr1(+):87794150-87814607
Browse Associations

Somatic mutations that impact miRNA target sites

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.87345178C>T			COSN5745069		HX20T		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4457	gtttgtaCCTTGTGtttta	0	UCACAAGG	m7b	Created	no TS	-0.239000	-6.700000
hsa-miR-4731-3p	gtttgtacCTTGTGTttta	0	CACACAAG	m7b	Created	no TS	-0.099000	-5.300000
hsa-miR-4801	gtttgtacCTTGTGTttta	0	UACACAAG	m7b	Created	no TS	-0.136000	-1.970000
hsa-miR-624-3p	gtttgtACCTTGTGtttta	0	CACAAGGU	m8a	Created	no TS	-0.148000	-4.460000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.87348307C>G			COSN7285986		8033691		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1273c	ggtgcTGTCGCacctatga	0	GGCGACAA	m6b	Created	-0.265000	-0.434000	-0.160000
hsa-miR-1302	ggtgcTGTCCCAcctatga	2	UUGGGACA	m7b	Disrupted	-0.051000	no TS	No effect
hsa-miR-196b-3p	ggtGCTGTCGcacctatga	0	UCGACAGC	m7b	(m6b->m7b)	no TS	-0.201000	No effect
hsa-miR-4298	ggtgcTGTCCCAcctatga	2	CUGGGACA	m7b	Disrupted	-0.097000	no TS	1.410000
hsa-miR-4648	ggtgctGTCCCACctatga	2	UGUGGGAC	m7b	Disrupted	-0.149000	no TS	4.470000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.87348564A>G			COSN8638835		J63_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-639	actaGCAGCGAagtgtagc	2	AUCGCUGC	m7b	Created	-0.151000	-0.656000	-4.340000

*By default, only target sites identified by TargetScan are displayed. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.

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
87347808	rs113207922	G
			A	hsa-miR-1233-5p hsa-miR-4265 hsa-miR-4296 hsa-miR-4312 hsa-miR-4322 hsa-miR-4648 hsa-miR-4654 hsa-miR-4769-5p hsa-miR-5187-5p hsa-miR-6728-5p hsa-miR-6759-5p hsa-miR-6778-5p hsa-miR-6796-5p	3 3 3 5 3 3 3 3 5 5 3 3 3	caTCCCACAaggc catCCCACAAggc catCCCACAAggc catcccACAAGGC catCCCACAAggc caTCCCACAaggc cATCCCACAaggc cATCCCACAaggc CATCCCAcaaggc CATCCCAcaaggc catCCCACAAggc caTCCCACAaggc catCCCACAAggc	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	-0.023 -0.044 -0.041 -0.05 -0.031 -0.066 -0.11 -0.11 -0.04 -0.072 -0.042 -0.023 -0.026

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