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Table 2 Summary for most significant groups of conserved word pairs

From: Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts

   

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, T n C

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, T n C

35.6

59±9.1

63

Amino-acid starvation (10-5)

  1. 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.