Expression Data Set 8 details

Information Item Value
Dataset Name Rot: Glu/Gal/Mating type/Heat
Dataset Number 8
Short Description absolute and relative expression levels for yeast cells grown in 4 conditions
Source URL
Reference Roth, Hughes, Estep, Church, Nature Biotechnology 16, pp. 939-945 (1988)
Strains FY4(a) for Glu, Gal, Heat conditions; FY5(alpha) for Mating type. FY5 and FY4 are isogenic except for mating type.
Conditions Cells grown in yeast nitrogen base + ammonium sulfate without amino acids to mid log phase (2 to 4E7 cells/ml). Carbon: Glu, Mating type, Heat = glucose 2%; Gal = galactose 2%. Temperature: 30 deg. C.; "Heat" = 39 deg. water bath for 33 min.
Date Added to ExpressDB Feb 8 1999 8:14:29:516AM
Number of Measures on ExpressDB 28 (here to download dataset and view measure details)
Long Description Description of measures:

(1) Background levels. Estimated as the average intensity of 36 chip features that were found to have consistently low intensity values throughout the experiments.

(2) "Absolute" expression levels. Perfect Match probe intensities (PM) and Mismatch probe intensities for each ORF are background subtracted. PM and MM are normalized using the average background-subtracted PM for each chip. No normalization across chips was performed; this is not necessary for reported fold change measures. Absolute expression for an ORF is the median value of normalized PM-MM values for all ORF probe pairs. Normalized PM-MM values are known as "delta" values.

(3) Threshold detection levels. The threshold detection level for a delta value is taken to be sqrt(2)*background.

(4) Relative (fold change) expression levels. Ratios of corresponding delta values are computed for all probes for an ORF across two conditions. Where a probe delta value in one or both conditions is below detection threshold, the threshold value is used. Log10s are taken of the detla ratios. The median value of the log10s of the delta ratios is reported as the relative (fold change) intensity for the ORF. If the median value has involves threshold-adjusted deltas it is considered "below detection threshold" in the corresponding condition. In the reference work cited, Gal, Mating type, and Heat are all compared against Glu.

(5) Significance of relative expression levels. The median log10 delta value for an ORF is divided by the median deviation of all the log10 delta ratios from the median log10 delta ratio for the ORF. This value is reported as the "statistical significance" of the relative expression level value. If this value is > 1 and the median log10 delta is >= 0.2, the ORF is judged to have had a significant change in expression in the two conditions. This is reported as having a "significant fold change".

The foregoing information was extracted from "Regulons Revealed with Gene Expression Data and Studies on DNA Sequencing via Ion Conductance," Frederick Roth, Harvard University doctoral dissertation (1998). Additional information can be found in the reference cited in this record.

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