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Table 1
Consensus sequences for the most significant groups of word pairs
	Hexamer list for word 1	Compiled sequence 1	TF for consensus 1	Hexamer list for word 2	Compiled sequence 2	TF for consensus 2	Number of word pairs

1	GAGATG GCGATG AGATGA CGATGA GATGAG ATGAGA ATGAGC TGAGAT TGAGCT GAGATG AGATGA AGCTCA	GMGATGAGMTSA	Unknown (PAC motif [38])	TGAAAA GAAAAA AAAAAT AAAATT AAATTT	TGAAAATTT	Unknown (RRPE motif [38])	75
2	AAGTGA AATGAA AGTGAA ATGAAA CTGAAA TGAAAA	ANTGAAAAA	Unknown (RRPE motif [38])	GAAAAA GAAAAT AAAATT AAATTT	GAAAAWTT	Unknown (RRPE motif [38])	40
3	GTTCCC CTCCCC ACCCCT TCCCCT	GYWCCCCT	(motif 38 [26])	CCCTTT CCTTTT CCTTAT	CCCTTWT	(motif 38 [26])	5
4*	GGCGGC GCGGCT	GGCGGCT	Ume6p	GTGGCA GGCAAA	GTGGCAAA	Rpn4p	2
5	CCCTTT CCTTTT	CCCTTTT	Msn2/4p-like	GGAGAA GGGAAA	GGRGAAA	Hsf1p	2
6	CGGCGG	CGGCGG	Ume6p	TACCCC ACCCCA CCCCAA	TACCCCAA	Mig1p	3
7*	CCGCGG	CCGCGG	Pdr1/3p	CGGAAA	CGGAAA	Unknown	1
8	AAACGC GACGCG AACGCG ACGCGT ACGCGA TCGCGT CGCGTC	ARWCGCGW	Mbp1p	CGCGAA ACGAAA GCGAAA CGAAAC CGAAAA	CRCGAAAM	Swi4/6p	9
9	TCACGT CACGTG ACGTGC	TCACGTGC	Cbf1p	ACTGTG CTGTGG TGTGGC GTGGCT	ACTGTGGCT	Met31/32p	6
10	TATTTT TTTTGT TTTGTT ATTGTT	TWTTGTT	Fkh1/2p	TGTTTA GTTTAC	TGTTTAC	Fkh1/2p	4
11	TTTGTT TTGTTT	TTTGTTT	Fkh1/2p	TTTTTC TTTTTT	TTTTTY	T_nC	4
12*	TCGTTT CGTTTA	TCGTTTA	Ecm22p \| Upc2p	CCGATA CGATAA	CCGATAA	Hap1p	4
13	TCGTTT CGTTTA	TCGTTTA	Ecm22p \| Upc2p	TATTGT ATTGTT	TATTGTT	Rox1p	2
14	CGTTTC GTTTCT	CGTTTCT	Ecm22p \| Upc2p	TTCTTT TCTTTT CTTTTT	TTCTTTTT	T_nC	5

The output P × C matrix of word pairs (P) that were significantly associated (p < 0.001) with at least five or more environmental conditions (C) was ordered using hierarchical clustering. Numbers correspond to groups of overlapping word pairs indicated in Figure 4. Asterisks denote sequence pairs whose involvement in multifactorial regulation has not been previously reported. Compiled sequences were assembled from groups of word pairs that were found in adjacent rows in the ordering of K-S p-values. As individual words must have passed all three statistical tests to be included in the output matrix, these consensus sequences may not reflect the actual biological specificities of conserved transcription factor binding sites (refer to [26,36] for a more complete list). Residues are shown in bold if they are invariant in at least two hexamers. Numbers denote the groups that are indicated in Figure 4. Multiple transcription factors that may bind the same sequence motif are separated by \|. IUPAC codes used: K (G or T); M (A or C); R (A or G); S (C or G); W (A or T).
Chiang et al. Genome Biology 2003 4:R43 doi:10.1186/gb-2003-4-7-r43

Table 1