Hog1 ChIP Chip
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE4862 | GEO | 2006/05/26
SECONDARY ACCESSION(S): PRJNA95747
REPOSITORIES: GEO
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Project description:mRNA amount (RA) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: Time course
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Project description:Cells regulate gene expression using a complex network of signaling pathways, transcription factors and promoters. To gain insight into the structure and function of these networks we analyzed gene expression in single and multiple mutant strains to build a quantitative model of the Hog1 MAPK-dependent osmotic stress response in budding yeast. Our model reveals that the Hog1 and general stress (Msn2/4) pathways interact, at both the signaling and promoter level, to integrate information and create a context-dependent response. Keywords: Stress response network analysis using genetically modified cells 85 samples were used to dissect the structure and function of the Hog1 network (Critical Samples measured in triplicate). The overall strategy was to double mutant or epistasis analysis to break down the influence that genes in the Hog1 network have on each other and the genome-wide stress response. This was done by comparing the expression in strains with different combinations of genes deleted and fitting the data to quantitative models. See Capaldi et. al. Nature Genetics 2008 for details.
2008-07-29 | E-GEOD-12270 | biostudies-arrayexpress
Project description:In budding yeast, this signaling pathway— the high-osmolarity glycerol (HOG) response —culminates in dual phosphorylation and nuclear translocation of the MAPK, Hog1 (ortholog of mammalian p38/SAPK). Induction of at least 50 genes requires nuclear Hog1, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we found that cells lacking the karyopherin (Nmd5) required for Hog1 nuclear import or in which Hog1 was permanently anchored at the plasma membrane(HOG1-CCAAX) (or both) withstood hyperosmotic challenge by three different solutes (1 M sorbitol, KCl or NaCl). In cells where activated Hog1 is excluded from the nucleus, there was little change in transcriptional program after exposure to hyperosmotic shock (comparable to hog1∆ cells), as judged by examining several diagnostic mRNAs and by global transcript measurements using microarrays. Systematic genetic analysis ruled out the need for any transcription factor known to be influenced by Hog1 (Hot1, Msn2, Msn4, Sko1 and Smp1). Keywords: Time course of stress response gene expression array
2008-06-01 | GSE8703 | GEO
Project description:Cells regulate gene expression using a complex network of signaling pathways, transcription factors and promoters. To gain insight into the structure and function of these networks we analyzed gene expression in single and multiple mutant strains to build a quantitative model of the Hog1 MAPK-dependent osmotic stress response in budding yeast. Our model reveals that the Hog1 and general stress (Msn2/4) pathways interact, at both the signaling and promoter level, to integrate information and create a context-dependent response. Keywords: Stress response network analysis using genetically modified cells
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Project description:Yeast Hmo1 ChIP-chip in triplicate with single untagged control Keywords: ChIP-chip
2006-01-19 | GSE4046 | GEO
Project description:In budding yeast, this signaling pathway— the high-osmolarity glycerol (HOG) response —culminates in dual phosphorylation and nuclear translocation of the MAPK, Hog1 (ortholog of mammalian p38/SAPK). Induction of at least 50 genes requires nuclear Hog1, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we found that cells lacking the karyopherin (Nmd5) required for Hog1 nuclear import or in which Hog1 was permanently anchored at the plasma membrane(HOG1-CCAAX) (or both) withstood hyperosmotic challenge by three different solutes (1 M sorbitol, KCl or NaCl). In cells where activated Hog1 is excluded from the nucleus, there was little change in transcriptional program after exposure to hyperosmotic shock (comparable to hog1∆ cells), as judged by examining several diagnostic mRNAs and by global transcript measurements using microarrays. Systematic genetic analysis ruled out the need for any transcription factor known to be influenced by Hog1 (Hot1, Msn2, Msn4, Sko1 and Smp1). Keywords: Time course of stress response gene expression array The transcriptomes' of HOG1-GFP, hog1del, and HOG1-CCAAX strains before and after 60 min hyperosmotic shock with 1M sorbitol at 25C were compared. Three biological replicates were done, with the first biological replicate done in technical triplicate, and the final two biological replicates beind done in technical duplicate by in slide duplication of features. Several supplementary files attached to the Series are summarized below: GSE8703 B1, B2, B3 Tscombined_matrix files show the averages of the technical replicates for each biological replicate. GSE8703 B1, B2, B3 norm_to_0_matrix files show the fold change over the time course (log2 time 60 - log2 time 0) for each of the three strains in each biological replicate. GSE8703 Figure_S6 shows the 30 genes with the most significant difference between the HOG1-GFP strain and the hog1del strain as determined by SAM. Genes were identified as: >3 fold induction in HOG1-GFP over 60 minute hyperosmotic shock and <3 fold induction in hog1del over 60 minute hyperosmotic shock.
2008-06-01 | E-GEOD-8703 | biostudies-arrayexpress
Project description:mRNA amount (RA) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: Time course Transcriptomic analysis of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F18-F24).
2010-06-19 | E-GEOD-13099 | biostudies-arrayexpress
Project description:Transcription rate (TR) analysis of W303 hog1 mutant yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: Time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F18-F24).
2010-06-19 | E-GEOD-13098 | biostudies-arrayexpress