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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 2, 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.