Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs

Table 1 Comparison of motifs identified by different programs for the muscle genes ^1,2,3,4,5.

	Myf	SRF	Mef2	Tef	NVL	Combined
masking repeats ⁶	GGGACATG 14/2/68	TCAGCCCT 4/1/63	N	N	ATCAGCCC 4/2/60	34/5/191
1/7	AGGGGGCATG 14/1/19	N	N	N	N	34/1/19
2/7	GACAGCTG 14/9/41	ACAAGG 4/1/5	AAATAGCCCC 7/1/4	GACATCTGGC 4/1/14	N	34/12/64
3/7	CAGCTGTT 14/10/19	CCTTATTTGG 4/2/12	GCTAAAAATAGC 7/6/12	N	CATACAAGGC 4/1/2	34/19/45
4/7	GACAGCTG 14/9/19	CCCAAAATAGCC 4/1/5	CTATAAATAC 7/6/13	N	CCATACAAGGCC 4/1/3	34/17/40
2/7 W	GACAGCTG 14/6/43	TGCCCT 4/1/15	N	GACAGCTGAG 4/1/15	ACAAGGCC 4/1/31	34/9/104
3/7 W	ACAGCTGC 14/8/21	AGGGCA 4/1/12	GGGCTATAAA 7/2/9	AGGGCAGC 4/1/37	N	34/12/79
4/7 W	CAGCTGTT 14/9/15	CCAAATATGG 4/2/3	CCTAAGAATAGC 7/2/5	N	CATACAAGGC 4/1/2	34/14/25
Compare-Prospector	CTGTSA 14/1/4	KAGCYATA 4/1/1	GYTATW 7/5/7	CAGCTGTS 4/1/4	N	34/8/16
Toucan ⁷	GGGrmAGG 14/1/5	N	N	N	CCTGCT 4/2/12	34/3/17

¹ x/y/z in the table denotes: experimentally determined binding sites/overlap between experimental sites and predicted sites/predicted sites by a discovered motif.
² Refer to Figure 1 for the description of 't/7' as well as 't/7 W'.
³ 'N' in a table cell indicates that the corresponding motif was not detected.
⁴ Representation of degenerated nucleotides: M = (AC), S = (GC), V = (AGC), R = (AG), Y = (CT), H = (ACT), W = (AT), K = (GT), D = (AGT), B = (GCT), N = (AGCT)
⁵ None of the motifs reported by our approach, CompareProspector or Toucan predicted the experimentally determined Sp1 binding site.
⁶ Masking repeats represents the 5000-bp upstream sequences (no gap), for which only the repeat regions were masked, were used.
⁷ Motifs identified by Toucan were taken from their report [7].

ISSN: 1471-2105