GEO DataSets

(Submitter supplied) Stress experiments repeating Gasch et al.,2000 conditions (Mol Biol Cell. 2000 Dec;11(12):4241-57). For each set of conditions I compared a deletion mutant for a predicted transcription regulator with a congenic wt strain. Groups of assays that are related as part of a time series. Keywords: time_series_design

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL2638 GPL3251 GPL2637

36 Samples

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(Submitter supplied) Wild type and ypl230w mutant under stationary phase. Cultures were grown to OD600 of 0.27 (Ypl230w mutants) and 0.4 (congenic wild-type; DBY8778), at which point time zero samples were collected. Samples were further collected at 2 (or 3), 5, 7, 9, and 24 hours. Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS283

Platform:

GPL289

12 Samples

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(Submitter supplied) Wild type and ppt1 mutant under hypo-osmotic shock. Cultures were grown with 1M sorbitol for ~20 hours, cells were collected by centrifugation and resuspended in YPD at time zero. Samples were collected at 0, 7, 15, 30 and 60 minutes after transfer to YPD. Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS282

Platform:

GPL288

10 Samples

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(Submitter supplied) Wild type and kin82 mutant under heat shock. Cells grown at 25°C were collected by centrifugation, resuspended in an equal volume of 37°C medium, and returned to 37°C for growth. Samples were collected at 0, 5, 15, 30 and 60 minutes after transfer to 37°C. Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS281

Platform:

GPL287

10 Samples

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Temporal analysis of wild type and ypl230w mutant strains in stationary phase. Cultures were grown to OD600 of 0.27 (ypl230w) and 0.4 (wild-type), then samples collected at various time points up to 24 hours.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain, 7 time sets

Platform:

GPL289

Series:

GSE408

12 Samples

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Temporal analysis of wild type and ppt1 mutant strains after hypo-osmotic shock. Cultures grown with 1M sorbitol for ~20 hours, then cells resuspended in YPD after which samples collected at several time points up to 1 hour.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain, 5 time sets

Platform:

GPL288

Series:

GSE407

10 Samples

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Temporal analysis of wild type and kin82 mutant strains after heat shock from 25°C to 37°C. Samples collected at several time points up to 1 hour.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain, 5 time sets

Platform:

GPL287

Series:

GSE406

10 Samples

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(Submitter supplied) Comparison of the transcriptomes of Saccharomyces cerevisiae wild type FY23 and a PDE2 deletion mutant DJ28. Keywords = PDE2 Keywords = Ras/cAMP pathway Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL422

10 Samples

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(Submitter supplied) Deciphering gene regulatory mechanisms through the analysis of high-throughput expression data is a challenging computational problem. Previous computational studies have used large expression datasets in order to resolve fine patterns of coexpression, producing clusters or modules of potentially coregulated genes. These methods typically examine promoter sequence information, such as DNA motifs or transcription factor occupancy data, in a separate step after clustering. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platforms:

GPL90 GPL2529

24 Samples

Download data: CEL, CHP, EXP, JPG

(Submitter supplied) The identification of gene regulatory modules is an important yet challenging problem in computational biology. While many computational methods have been proposed to identify regulatory modules, their initial success is largely compromised by a high rate of false positives, especially when applied to human cancer studies. New strategies are needed for reliable regulatory module identification. We present a new approach, namely multi-level support vector regression (ml-SVR), to systematically identify conditionspecific regulatory modules. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

6 Samples

Download data: CEL

(Submitter supplied) Genomewide characterization of YJR141W role in mRNA polyadenylation.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

16 Samples

Download data: BEDGRAPH

(Submitter supplied) In vitro experiment of stimulation of monocyte-derived dendritic cells with Saccaromyces cerevisiae in exponential growth phase. This experiment was performed to verify the comparability of microarray experiments using a pathway based logic (Beltrame et al., PLoS 2009) by comparing the analysis of this sample with other seven public data sets on monocyte-derived dendritic cells subjected to different stimuli retrieved from GEO Keywords: Case-control, transcriptional profiling, dendritic cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7763

6 Samples

Download data: CEL