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.

Sudbery et al. BMC Genomics 2010 11:175   doi:10.1186/1471-2164-11-175

Open Data