Assessing Computational Steps for CLIP-Seq Data Analysis

Table 2

Top 10 tetramers in Caco-2 CLIP peaks (FDR < 0.001).

(a)

Caco2-1
Background from INPUT			Raw	Background from genome
4mers	Percent (%)	value	Rank	value
GGAG^a	19.6^a		10	1.00
AGGA^b	18.4^b		17	1.00
CAGG^c	18.3^c		19	1.00
TGGC^d	18.3^d		20	0.18
GTGG^e	18.3^e		21	0.65
TGGG^f	17.8^f		23	1.00
AAGA	17.0		28	0.05
GCAG^g	17.0^g		29	1.00
GGTG	16.8		30	1.00
GGCT	16.8		32	1.00

(b)

Caco2-2
Background from INPUT			Raw	Background from genome
4mers	Percent (%)	value	Rank	value
GGAG^a	20.1^a		9	1.00
TGGC^d	19.1^d		13	0.05
GTGG^e	18.8^e		16	0.41
TGGG^f	18.4^f		19	1.00
GGTG	17.9		23	1.00
AGGA^b	17.7^b		24	1.00
GCAG^g	17.6^g		26	1.00
CAGG^c	17.3^c		27	1.00
CAGA	17.0		30	1.00
AAGA	16.1		39	1.00

(c)

Caco2-3
Background from INPUT			Raw	Background from genome
4mers	Percent (%)	value	Rank	value
GGAG^a	21.2^a		7	1.00
GAAG	19.5		12
TGGC^d	19.4^d		13
CAGG^c	18.3^c		18	1.00
AGGA^b	17.9^b		21	1.00
TGGG^f	17.9^f		22	1.00
GTGG^e	17.8^e		24	1.00
GCAG^g	17.7^g		26	1.00
AGAA	17.4		27	1.00
GGAA	17.1		28	1.00

Tetramers common in all three samples have the same letters.