Table 2. Transcription factors and the most significant DNA motif identified by REDUCER in the corresponding transcription factor perturbation experiment.
|
TF |
Motif (p-value) |
Known binding sitea |
Biological processb |
Activation conditionsc |
|
GCN4 |
tgactca (10-80) tgagtca (10-26) |
tga[c/g]tca |
transcriptional activator of amino acid biosynthetic genes |
AA, END |
|
MBP1 |
acgcgt (10-27) |
MCB site acgcg[t/a] |
DNA replication; cell cycle control |
CC, DS, LND, mHSdo |
|
MSN2 |
agggg (10-26) |
agggg |
Stress response |
ES, PHO |
|
MSN4 |
agggg (10-33) |
agggg |
Stress response |
ES |
|
PHO4 |
cacgtgg (10-30) |
cacgtg |
Phosphate metabolism |
PHO, HOO |
|
RTG1 |
ggtcacg (10-5) |
ggtcac |
interorganelle communication |
AA, END |
|
STE12 |
tgaaac (10-14) |
PRE site tgaaac[g/a] |
Invasive growth; pheromone induction; pseudohyphal growth |
LND |
|
YAP1 |
tgactca (10-8) |
tgactca |
Regulation of certain oxygen detoxification enzymes |
AA, END |
|
MAC1 |
tgcaccc (10-80) |
N/A |
Cu/Fe utilization, stress resistance |
CC, H2O2, SSC,
SST |
|
SIN3 |
cgcgcgc (10-24) |
N/A |
transcription |
None |
|
TUP1 |
aggcac (10-25) |
N/A |
Glucose repression |
LND, YPD |
a. Known binding site of each transcription factor is based on SwissProt database; b. Biological process for each transcription factor is taken from GO and SwissProt; c. Activation conditions: AA, amino acid starvation; CC, cell cycle; DS, diauxic shift; END, early nitrogen depletion (< 8 hour); ES, all environmental stresses; H2O2, constant 0.32 mM H2O2 exposure; HOO, hypo-osmotic shock; LND, late nitrogen depletion (³ 8 hour); mHSdo, mild heat shock from 29°C to 33°C at various osmolarity; PHO, phosphate metabolism; SSC, steady state growth on alternative carbon sources; SST, steady state growth at various temperatures; YPD, YPD stationary phase.