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Zhao Y, et al.  (2008) Development of a Novel Oligonucleotide Array-Based Transcription Factor Assay Platform for Genome-Wide Active Transcription Factor Profiling in Saccharomyces cerevisiae. J Proteome Res 7(3):1315-1325

Abstract: Transcription factors (TFs) play a central role in regulating gene expression and in providing interconnecting regulatory networks between related pathway elements. Although single TF assays provide some insights into pathway regulation, a method that allows the parallel investigation of all active TFs is highly desired to elucidate the complex inter-regulated cellular mechanisms. We have developed a novel oligonucleotide array-based transcription factor assay platform for genome-wide active TF profiling of Saccharomyces cerevisiae, which can simultaneously analyze the activities of 93 different TFs. The platform has been validated using 28 purified TFs produced in Escherichia coli, cell extracts from yeast strains overexpressing particular TFs, and by detailed control experiments. We then used the platform to examine the activity changes of all yeast TFs during diauxic shift, and results showed, in good agreement with previous studies, that the Sip4 was induced specifically. Other individual TFs required for growth in synthetic complete medium were also identified. Genome-wide analysis of TF activity is extremely useful in investigating complex gene regulatory networks and for the development of systematic understanding of the complexity of genomic functions. These results obtained in this report demonstrate the validity, and for the first time the utility, of this technology for genome-wide investigation of TF activities.

Status: Published Type: Journal Article PubMed ID: 18220337

Topics addressed in this paper

Number of different genes curated to this paper: 93

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
ABF1 ACE2 ADR1 AFT1 AFT2 ARG80 ARG81 ARR1 ASH1 AZF1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Omics yg ball
Other genomic analysis yg ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Techniques and Reagents yg ball

Topics Genes linked to topics (#11 - 20 )
BAS1 CAD1 CAT8 CBF1 CHA4 CIN5 CRZ1 CUP2 DAL82 ECM22
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#21 - 30 )
FKH1 FKH2 FZF1 GAL4 GAT1 GCN4 GCR1 GLN3 HAC1 HAP1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#31 - 40 )
HAP2 HAP3 HAP5 HCM1 HMRA1 HSF1 INO2 INO4 LEU3 LYS14
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#41 - 50 )
MBP1 MCM1 MET28 MET31 MET32 MET4 MIG1 MOT3 MSN2 MSN4
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#51 - 60 )
NDT80 NRG1 OAF1 PDR1 PDR3 PDR8 PHO2 PHO4 PIP2 PPR1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#61 - 70 )
PUT3 RAP1 REB1 RFX1 RGT1 RIM101 RLM1 RME1 ROX1 RPH1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#71 - 80 )
RTG1 RTG3 SIP4 SKN7 SKO1 SMP1 SOK2 STB5 STE12 STP2
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Function/Process blue ball
Mutants/Phenotypes blue ball
Primary Literature blue ball
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Strains/Constructs blue ball

Topics Genes linked to topics (#81 - 90 )
SUM1 SWI5 SWI6 TBF1 TEA1 TYE7 UGA3 UME6 WAR1 YAP1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#91 - 93 )
YAP3 YRR1 ZAP1
Additional Literature blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball
Regulatory Role blue ball blue ball blue ball

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