Table 2

Summary for most significant groups of conserved word pairs



Most significant word pair in consensus group




Conserved word pairs (compilation of overlapping words)
 Known transcription factors or motifs
 (χ2, p-value via Bonferroni)
 Median of min distance
Number of TCRs
 Expression conditions with significant gene subsets (FDR significance)
1
 G[AC]GATGAG, TGAAAATTTT
 PAC, RRPE
 240.6 (10-49)
 19±0.5
 162
 Repressed in multiple environmental stresses (10-6)
2
 ANTGAAA, GAAAAWT
 RRPE (Overlap)
 96.9 (2 × 10-16)
 43±11
 68
 Repressed in multiple environmental stresses (10-6)
3
 CTCCCC, CCCTTA
 Msn2/4p-like, (Overlap)
 53.8 (5 × 10-7)
 28±3.7
 15
 Induced in multiple environmental stresses (10-6)
4
 GGCGGGC, GTGGCA
 Ume6p, Rpn4p
 43.7 (9 × 10-5)
 48±16
 25
 Cadmium, diamide (10-4) MMS, heat shock (10-3)
5
 CCTTTT, GAGAAA
 Msn2/4p, Hsf1p
 56.2 (2 × 10-7)
 54±5.4
 69
 Heat shock (10-4)
6
 CCGCCG, ACCCCA
 Ume6p, Mig1p
 41.9 (2 × 10-4)
 17±1.5
 14
 Stationary phase (10-6)
7
 CCGCGG, CGGAAA
 Pdr1/3p, Unknown
 111 (2 × 10-19)
 44±12
 21
 Diamide (10-3)
8
 RACGCG, RCGAAA
 Swi6p/Mbp1p, Swi4/6p,
 83.0 (7 × 10-13)
 33±5.0
 33
 Cell cycle, G1 phase (10-6)
9
 GCACGTGC, ACTGTGGC
 Cbf1p | Pho4p, Met31/32p
 37.4 (2 × 10-3)
 22±2.5
 22
 Cadmium (10-6)
10
 T[AT]TTGTT, TGTTTAC
 Fkh1/2p (Overlap)
 51.1 (2 × 10-6)
 57±6.9
 48
 Cell cycle (10-3)
11
 TTTGTT, TTTTTY
 Fkh1/2p, TnC
 37.6 (2 × 10-3)
 49±4.4
 267
 Late nitrogen depletion (10-3)
12
 CCGATA, TCGTTT
 Hap1p, Ecm22p | Upc2p
 36.2 (4 × 10-3)
 41±5.9
 28
 Ergosterol inhibition (10-4) MMS (DNA damage) (10-3)
13
 TCGTTT, TATTGTT
 Rox1p, Ecm22p | Upc2p
 58.8 (4 × 10-8)
 55±0.5
 69
 Early menadione (10-3)
14
 TGACTC, TCTTTT
 Gcn4, TnC
 35.6
 59±9.1
 63
 Amino-acid starvation (10-5)

Statistics are listed for one representative word pair for each group of overlapping word pairs, numbered as in Figure 4. Multiple transcription factors that may bind the same sequence motif are separated by |. To summarize the close spacing () between conserved word pairs, we report the median of the distribution of minimum distances in S. cerevisiae ± standard deviation of the medians of the distribution of minimum distances in all four Saccharomyces genomes.

Chiang et al. Genome Biology 2003 4:R43   doi:10.1186/gb-2003-4-7-r43

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