Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-4654 - Genetic reconstruction of a functional transcriptional regulatory network

Status
Submitted on 10 April 2006, released on 2 July 2010, last updated on 27 March 2012
Organism
Saccharomyces cerevisiae
Samples (538)
Array (1)
Protocols (2)
Description
Although global analyses of transcription factor binding provide one view of potential transcriptional regulatory networks, regulation also occurs at levels distinct from transcription factor binding. Here, we use a genetic approach to identify targets of transcription factors in yeast and reconstruct a functional regulatory network. First, we profiled transcriptional responses in S. cerevisiae strains with individual deletions of 263 transcription factors. Then we used directed-weighted graph modeling and regulatory epistasis analysis to identify indirect regulatory relationships between these transcription factors, and from this we reconstructed a functional transcriptional regulatory network. The enrichment of promoter motifs and Gene Ontology annotations provide insight into the biological functions of the transcription factors. Data values are X scores and corresponding p-values derived using an error model. We profiled transcriptional responses upon the individual deletion of more than 260 TFs. We used a directed-weighted graph modelling approach and regulatory epistasis analysis to identify indirect regulatory relationships, and thus constructed a refined, functional transcriptional regulatory network.
Experiment type
unknown experiment type 
Contacts
Vishy Iyer <iyerlab@gmail.com>, Patrick J Killion, Vishwanath R Iyer, Zhanzhi Hu
Citation
Genetic reconstruction of a functional transcriptional regulatory network. Zhanzhi Hu, Patrick J Killion and Vishwanath R Iyer.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-4654.idf.txt
Sample and data relationshipE-GEOD-4654.sdrf.txt
Processed data (1)E-GEOD-4654.processed.1.zip
Array designA-GEOD-3588.adf.txt
Links