Project 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.

2010-07-02 | E-GEOD-4654 | biostudies-arrayexpress

Unveiling protein functions through the dynamics of the interaction network.

Project description: Not available

| S-EPMC3052369 | biostudies-literature

Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network.

Project description: Not available

| S-EPMC6067004 | biostudies-literature

Genetic reconstruction of a functional transcriptional regulatory network

Project 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. Keywords: X scores and corresponding p-values derived using an error model

2007-04-01 | GSE4654 | GEO

Functional transcriptomic annotation and protein-protein interaction network analysis identify NEK2, BIRC5, and TOP2A as potential targets in obese patients with luminal A breast cancer.

Project description: Not available

| S-EPMC5842257 | biostudies-literature

Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets.

Project description: Not available

| S-EPMC2904735 | biostudies-literature