shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library

EURASIP Journal on Bioinformatics and Systems Biology

Table 2 Number of target candidate genes against shRNA constructed using random oligonucleotides

	Number of aligned genes with mismatches
Sequences of shRNA-coding DNA	0^a	1^a	2^a	3^a
GGTAGCTCGTTAATTTAAT	0	0	1	3
GAATTCCGCGGTACGGGGG	0	0	0	6
GAATGCAGCAGGAGGGAGG	0	1	8	278
GAACTGGACGCAGGCCTAT	0	0	2	53
GACTAGTCTACTTCCTTAG	0	0	0	31
GCGATCTCTACCACCTGGC	0	0	4	79
GCGTAATCGGGCGAATAAC	0	0	0	0
GATAGTGCACGTTGAAACA	0	0	1	38
GTAGGGGGACCTAGAACAT	0	0	2	20
GACAAACCCTGCCTAGTTA	0	0	0	17
GGATCCGAGTGCACCTAAA	0	0	0	28
GAAGTAATGCGCTCGATCC	0	0	1	13
GCCACGTATGGCCGTACTG	0	0	0	10
GCACAATGTAAAAAGAATA	0	2	5	131
GAGCCAGTAAAAGAATATC	0	1	4	55
GTGCACTACTCGCAGTGGG	0	0	2	34
GTTCCTAGACTTCAAATAA	0	0	2	53
GACCTACCCATGTAGCAAG	0	0	0	43
GAGAAGGCGTCTCCGGAGA	0	0	4	82
GAGGAATGATATGGCCTTG	0	0	1	54
GGGGCAGTGGCAGGTGATC	0	1	7	140
GACCAGGGACACATTAGAT	0	0	1	37
GATCTAAATATGGCAGGCA	0	0	0	44
GAAGACAGACACGGAGATC	0	0	7	112
GTCAGCCAGCAAAGAAGTG	0	0	7	115
GTGGACTAGTATCGATATA	0	0	1	10
GTGAACCAAGTTACTAGCT	0	0	0	39
GGCCCGGTTAGGAACACTT	0	0	0	7
GGCCAAGAAGATACACTAG	0	0	1	65
GGACAGGGCAACAATGTGG	0	0	1	44
GGAAGATATGCTCATTCGC	0	0	0	24
GGAAGTGGTAAGGACTCCA	0	0	3	65
GGAGTCAGTACAGATACGA	0	0	1	22
GCGTTAATTAATCAACATC	0	0	0	12
GGCGTGATCGTATGCACCA	0	0	0	13
GAGAAGTCCAGATCTTTCC	0	0	5	95
GGACCCTGTCCCTAGAAGT	0	0	2	72
GAAAACTGTCAGACCCGAG	0	0	1	46
GCATTCCAAAGAAAAGAAT	0	0	7	167
GTCACATATCCTGGACACG	0	0	1	36
GTGTATAGTGCAAGACAAT	0	0	0	48
GTGAGAACGTTGGAGAGCC	0	0	1	59
GTTTTGATCGGAGAATCCA	0	0	1	31
GCAAACATCCAGAAAGTAA	0	0	1	93
GTCCAGGGGTTGGGGATCG	0	0	1	34
GGGCGTAGGTCAAAGCATG	0	0	0	17
GGGCGGGGTAAAGAAACCA	0	0	0	17

Alignment between shRNA and human RefSeq was performed under conditions in which the indicated number of mismatches was allowed
^aRepresents number of mismatched nucleotides