Table 2. Summary of significant motifs found with each set of deletion mutant microarray data.
| Experiment | Motif | Best rank | Occurrence |
|---|---|---|---|
| gcn4 |
AAAAAAT, ATTTTTT |
2 |
all(1), neg(1) |
| significant genes: 108 (4+/104–) |
AAATTCC, GGAATTT |
2 |
all(1), neg(1) |
| biological_process unknown: 26 (0+/26–) |
AAGCCAC, GTGGCTT |
2 |
all(1), neg(1) |
| significant clusters: all(17), neg(16) |
AATTCCG, CGGAATT |
1 |
all(1), neg(1) |
| significant motifs: 10 |
ATATATA, TATATAT |
1 |
all(1), neg(1) |
| |
ATGACTC, GAGTCAT |
1 |
all(3), neg(3) |
| |
CACGTGA, TCACGTG |
1 |
all(4), neg(4) |
| |
GAGTCAC, GTGACTC |
1 |
all(1), neg(1) |
| |
GGAGTCA, TGACTCC |
2 |
all(1), neg(1) |
| |
TGACTCA, TGAGTCA |
1 |
all(12), neg(11) |
| gln3 |
AAATTCC, GGAATTT |
2 |
all(2), pos(2) |
| significant genes: 118 (83+/35–) |
AATTCCG, CGGAATT |
1 |
all(2), pos(3) |
| biological_process unknown: 29 (21+/8–) |
ACAGCGG, CCGCTGT |
2 |
all(1), pos(1) |
| significant clusters: all(13), pos(11), neg(3) |
ACTGTGG, CCACAGT |
1 |
all(1), neg(1) |
| significant motifs: 10 |
AGAAATA, TATTTCT |
2 |
all(1) |
| |
ATATATA, TATATAT |
1 |
all(2), neg(2) |
| |
ATGACTC, GAGTCATa |
1 |
all(4), pos(4) |
| |
CACGTGA, TCACGTG |
1 |
all(1), neg(3) |
| |
CTATGTC, GACATAG |
1 |
pos(1) |
| |
TGACTCA, TGAGTCAa |
1 |
all(5), pos(6) |
| mac1 |
ATAAGGG, CCCTTAT |
1 |
all(1), neg(1) |
| significant genes: 89 (46+/43–) |
ATGACTC, GAGTCATa |
1 |
all(2), neg(3) |
| biological_process unknown: 24 (17+/7–) |
CAGGTGC, GCACCTG |
2 |
pos(1) |
| significant clusters: all(11), pos(7), neg(5) |
GAGCAAA, TTTGCTC |
2 |
all(1), pos(1) |
| significant motifs: 8 |
GCAAAAA, TTTTTGC |
2 |
all(1) |
| |
GGGTGCA, TGCACCC |
1 |
all(7), pos(7) |
| |
GGTGCAA, TTGCACC |
2 |
all(1), pos(1) |
| |
TGACTCA, TGAGTCAa |
1 |
all(2), neg(2) |
| mbp1 |
AACGCGT, ACGCGTT |
1 |
all(2), pos(2) |
| significant genes: 11 (10+/1–) |
ACGCGTA, TACGCGT |
2 |
all(1), pos(1) |
| biological_process unknown: 1 (1+/0–) |
ACGCGTC, GACGCGT |
2 |
all(1), pos(1) |
| significant clusters: all(2), pos(2) |
|
|
|
| significant motifs: 3 |
|
|
|
| ste12 |
ATGAAAC, GTTTCAT |
2 |
all(3), neg(3) |
| significant genes: 79 (26+/53–) |
TGAAACA, TGTTTCA |
1 |
all(3), neg(3) |
| biological_process unknown: 38 (13+/25–) |
|
|
|
| significant clusters: all(3), neg(4) |
|
|
|
| significant motifs: 2 |
|
|
|
| swi4 |
AAATAGC, GCTATTT |
1 |
neg(1) |
| significant genes: 854 (573+/281–) |
AAATTCC, GGAATTT |
1 |
all(2), pos(2) |
| biological_process unknown: 341 (261+/80–) |
AAGCGAA, TTCGCTT |
2 |
neg(1) |
| significant clusters: all(15), pos(19), neg(5) |
AATTCCG, CGGAATT |
2 |
all(1), pos(1) |
| significant motifs: 11 |
ACCGGCT, AGCCGGT |
2 |
all(1) |
| |
ATATATA, TATATAT |
1 |
all(2), pos(3) |
| |
ATGACTC, GAGTCATa |
2 |
all(1), pos(6) |
| |
ATGCGAA, TTCGCAT |
2 |
neg(1) |
| |
CACGTGA, TCACGTG |
1 |
all(1), pos(3) |
| |
TATATAA, TTATATA |
1 |
neg(1) |
| |
TGACTCA, TGAGTCAa |
1 |
all(9), pos(12) |
| swi5 |
AAGCCAC, GTGGCTT |
2 |
all(2), pos(2) |
| significant genes: 103 (81+/22–) |
ATGACTC, GAGTCATa |
1 |
all(2), pos(2) |
| biological_process unknown: 45 (36+/9–) |
CACGTGA, TCACGTG |
1 |
all(4), pos(4) |
| significant clusters: all(7), pos(7) |
TGACTCA, TGAGTCAa |
1 |
all(3), pos(3) |
| significant motifs: 4 |
|
|
|
| yap1 |
AAGCCAC, GTGGCTT |
2 |
all(2), pos(2) |
| significant genes: 98 (72+/26–) |
AATGACT, AGTCATTa |
2 |
all(1), pos(1) |
| biological_process unknown: 30 (20+/10–) |
ATGACTC, GAGTCATa |
1 |
all(1), pos(2) |
| significant clusters: all(10), pos(9), neg(3) |
CACGTGA, TCACGTG |
1 |
all(4), pos(4) |
| significant motifs: 8 |
CAGGGTC, GACCCTG |
1 |
all(2), pos(2) |
| |
GTGAATA, TATTCAC |
1 |
all(1) |
| |
TGACTCA, TGAGTCAa |
1 |
all(2), pos(3) |
| TTACTAA, TTAGTAA | 1 | neg(1) |
In column one, the experiment name represents the TF being deleted in the mutant. +, up-regulated genes; –, down-regulated genes. In the first column, all(n) means that n significant clusters are obtained when we perform functional clustering using all significant genes from that array. Similarly, pos(n) and neg(n) mean that n significant clusters are obtained when we use only up-regulated genes or only down-regulated genes, respectively. In column two, motifs are presented as pairs of reverse complement sequences. Motifs in bold are those matching the known consensus. Motifs in italic are those similar to the known consensus. Column three shows the best rank of the motif found in the clusters. Column four shows the number of clusters in which the motif was detected. The meanings of ‘all’, ‘pos’ and ‘neg’ are the same as those in column one.
aMotifs matching the consensus Gcn4 binding site in experiments other than gcn4 deletion (see also Discussion).