Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis

Table 1 Seeds and Confirmation status of the top 20 siRNAs

Transcript	Symbol	Score	Hexamer Seed	Heptamer Seed	Status	Enriched Seed
NM_003217	TEGT	3.51	CAAGGT	TCAAGGT	OTE	+
NM_016368	ISYNA1	3.43	TGTCCA	GTGTCCA	OTE	*
NM_001240	CCNT1	3.28	CAAGGT	TCAAGGT	OTE	+
NM_002197	ACO1	3.11	ACTTGA	CACTTGA	Unconfirmed	+
NM_003947	HAPIP	2.88	ACTTGA	TACTTGA	OTE	+
NM_002337	LRPAP1	2.8	TCACAA	ATCACAA	OTE	+
NM_005799	INADL	2.76	ACTTGA	AACTTGA	OTE	+
NM_003554	OR1E2	2.72	TTGTAA	TTTGTAA	Unconfirmed	-
NM_013345	GPR132	2.68	AGATCA	GAGATCA	Unconfirmed	+
NM_004584	RAD9A	2.65	TAAGGA	CTAAGGA	OTE	-
NM_003266	TLR4	2.64	AAAGTT	CAAAGTT	Unconfirmed	-
NM_000674	ADORA1	2.63	TAATAA	CTAATAA	OTE	+
NM_002382	MAX	2.57	AAGAAA	TAAGAAA	Hit	-
NM_006986	MAGED1	2.56	ACTTGA	AACTTGA	False +ve	+
NM_000875	IGF1R	2.55	CACTTA	ACACTTA	Hit	-
NM_016953	PDE11A	2.54	GTAAGA	GGTAAGA	Hit	-
NM_014379	KCNV1	2.54	TGTCCA	GTGTCCA	False +ve	*
NM_080674	C20orf86	2.52	CGTTGT	GCGTTGT	False +ve	-
NM_002467	MYC	2.51	TTACAC	GTTACAC	Hit	+
XM_497793	LOC402037	2.51	GCATTA	GGCATTA	False +ve	-

Table shows the top 20 siRNAs from the screen, their status: Hit, False pos (did not repeat), Unconfirmed (that is this siRNA reproducibly affected caspase-3/7 activation levels, but we could not confirm the involvement of the gene targeted), or OTE (off-target effect), the hexamer and heptamer seed sequences (sequences that appear more than once are shown in bold), and whether the seed is one which either appears more than once, or is in the set of enriched seed sequences (see Table 2). * The seed sequence TGTCCA appears once in the OTE siRNA ISYNA1 and once in the false positive siRNA targeting KCNV1.

ISSN: 1471-2164