TABLE 3.
Consensus motifs whose associated genes were found to be upregulated or downregulated by T-profiler analysisa
| Time point | Upregulated motifs enriched in:
|
Downregulated motifs enriched in:
|
||
|---|---|---|---|---|
| CO | N2 | CO | N2 | |
| 15 min | CWTCC (GCR1, 0.0039), CCCCT (MSN2-4, 0.0060), CGCNNNNNNNNNNNNN NBCGB (unknown, 0.030) | AGGGG (MSN2-4, 6.8 × 10−5), TCTCC (ADR1, 0.016), TCCGYGGA (PDR3, 0.033), TCCGYGGR (unknown, 0.049) | CGATGAG (PAC, 0.0012) | AAAATTT (rRPE, 3.0 × 10−9), CGATGAG (PAC, 3.7 × 10−7), GCGATGAGMTGARAW (rRNA?, 0.0046) |
| 30 min | CCCCT (MSN2-4, 2.0 × 10−6), AGGGG (MSN2-4, 9.2 × 10−6) | AGGGG (MSN2-4, 2.8 × 10−9), CCCCT (MSN2-4, 1.4 × 10−6), TATAWAW (TBP, 2.7 × 10−4), TCCGYGGR (unknown, 3.1 × 10−4), TCCGYGGA (PDR3, 5.1 × 10−4), TGCACCC (RCS1, 0.0085) | CGATGAG (PAC, 8.2 × 10−6), AAAATTT (rRPE, 2.6 × 10−4) | AAAATTT (rRPE, 3.4 × 10−11), CGATGAG (PAC, 2.0 × 10−7), CCRTACA (RAP1, 2.0 × 10−5), GCGATGAGMTGARAW (rRNA?, 0.0019), YCGTNNNNMRYGAY (ABF1, 0.0055) |
| 45 min | AGGGG (MSN2-4, 1.6 × 10−7), CCCCT (MSN2-4, 0.001), TCCGYGGA (PDR3, 0.012), HRCCCYTWDT (MSN2-4, 0.025), TCCGYGGR (unknown, 0.031) | AGGGG (MSN2-4, < 10−15), CCCCT (MSN2-4, < 10−15), TATAWAW (TBP, 2.8 × 10−6), TCCGYGGA (PDR3, 5.5 × 10−6), TCCGYGGR (unknown, 6.1 × 10−5), HRCCCYTWDT (MSN2/4, 2.3 × 10−4), CCNNNWWRGG (MCM1, 0.018), TCTCC (ADR1, 0.029), TCCGCGG (unknown, 0.030) | AAAATTT (rRPE, 2.1 × 10−10), CGATGAG (PAC, 2.0 × 10−8), GCGATGAGMTGARA W (rRNA?, 0.0030), CCRTACA (RAP1, 0.0055) | AAAATTT (rRPE, 3.9 × 10−11), CGATGAG (PAC, 1.2 × 10−9), CCRTACA (RAP1, 2.5 × 10−9), GCGATGAGMTGARAW (rRNA?, 0.0060) |
| 60 min | AGGGG (MSN2-4, < 10−15), CCCCT (MSN2-4, < 10−15), TATAWAW (TBP, 0.0015), HRCCCYTWDT (MSN2/4, 0.0092), TCCGYGGA (PDR3, 0.041), CCNNNWWRGG (MCM1, 0.044) | AGGGG (MSN2-4, < 10−15), CCCCT (MSN2-4, < 10−15), TATAWAW (TBP, 1.8 × 10−5), TCCGYGGA (PDR3, 0.0022), HRCCCYTWDT (MSN2/4, 0.020) | AAAATTT (rRPE, < 10−15), CGATGAG (PAC, 1.1 × 10−13), CCRTACA (RAP1, 7.2 × 10−5), GCGATGAGMTGARA W (rRNA?, 7.8 × 10−4), TGACTCA (GCN4, 0.025) | AAAATTT (rRPE, 8.2 × 10−8), CGATGAG (PAC, 3.5 × 10−7), CCRTACA (RAP1, 0.0022) |
| 120 min | AGGGG (MSN2-4, 2.4 × 10−8), TCCGYGGA (PDR3, 1.2 × 10−6), CCCCT (MSN2-4, 1.4 × 10−5), TCCGYGGR (unknown, 1.2 × 10−4), TATAWAW (TBP, 0.0046), HRCCCYTWDT (MSN2/4, 0.018) | CCCCT (MSN2-4, 2.9 × 10−8), AGGGG (MSN2-4, 4.2 × 10−7), TCCGYGGA (PDR3, 7.0 × 10−6), TCCGYGGR (unknown, 1.3 × 10−4), TATAWAW (TBP, 0.0021), HRCCCYTWDT (MSN2/4, 0.027), TCCGCGG (unknown, 0.049) | CCRTACA (RAP1, < 10−15), AAAATTT (rRPE, 6.6 × 10−10), CGATGAG (PAC, 1.2 × 10−4) | CCRTACA (RAP1, < 10−15), AAAATTT (rRPE, 9.4 × 10−10), CGATGAG (PAC, 2.8 × 10−4) |
| 24 h | CCCCT (MSN2-4, 2.9 × 10−8), AGGGG (MSN2-4, 8.2 × 10−6), TCCGYGGA (PDR3, 3.8 × 10−4), TCCGYGGR (unknown, 0.0011), CGGNNNNNNNNNNNCCG (GAL4, 0.0036), CGGNNNNNNNNNNCCG (PUT3, 0.0060), TGCACCC (RCS1, 0.010), GCAYGTG (INO4, 0.019), ATGYGRAWW (NBF, 0.025), TCCGCGG (unknown, 0.039) | TCCGYGGA (PDR3, 3.1 × 10−4), AGGGG (MSN2-4, 7.8 × 10−4), CGGNNNNNNNNNNCCG (PUT3, 0.0010), TCCGYGGR (unknown, 0.0018), CGGNNNNNNNNNNNCCG (GAL4, 0.016), ATGYGRAWW (NBF, 0.035), TCCGCGG (unknown, 0.039), CCCCT (MSN2-4, 0.041), CGGGGTA (MIG1, 0.044) | AAAATTT (rRPE, 4.9 × 10−11), CGATGAG (PAC, 2.3 × 10−7), CCRTACA (RAP1, 0.0092) | AAAATTT (rRPE, 2.1 × 10−7), CCRTACA (RAP1, 4.2 × 10−5), TGACTCA (GCN4, 5.5 × 10−5), CGATGAG (PAC, 8.6 × 10−4) |
a
Motifs that were enriched by treatment with either gas at each time point are listed, along with the cognate transcription factor (if known) and the E value in parentheses. Besides A, C, G, and T, the other one-letter codes represent different nucleotides as follows: R for purines, Y for pyrimidines, N for any nucleotide, W for weak (A or T), S for strong (C or G), M for amino (A or C), K for keto (G or T), B for any nucleotide that is not A, H for any not G, D for any not C, and V for any not T.