Expression Data Set 46 details

Information Item	Value
Dataset Name	Butow study of genome wide responses to mitochondrial dysfunction
Dataset Number	46
Short Description	Signed geometric means of log base 10 ratios of replicated microarray hybridizations
Source URL	http://hamon.swmed.edu/butow_array/petite.html
Reference	Epstein, C.B.; Waddle, J.A.; Hale, W. IV; Dave, V.; Thornton, J.; Macatee, T.L.; Garner, H.R.; Butow, R.A.; Genome-Wide Responses to Mitochondrial Dysfunction; Mol. Biol. Cell (2001) 12: 297-308;
Strains	PSY142 (Matalpha leu2 lys2 ura3p+) and isogenic derivatives
Conditions	NONE
Date Added to ExpressDB	Oct 31 2000 4:18:12:803PM
Number of Measures on ExpressDB	11 (here to download dataset and view measure details)
Long Description	Numbers represent the signed geometric means of log (base 10) ratios of replicated microarray hybridizations. Positive numbers represent genes induced by the mutation or chemical treatment, and negative numbers indicate repression. The number 0 indicates a discrepant response between the two replicates (that is, the gene was induced once and repressed once). Graphical images of the array scans are found at the URL under the unique slide names, given in the measure desriptions, two slide names for each measure. Abstract from this citation: Mitochondrial dysfunction can lead to diverse cellular and organismal responses. We used DNA microarrays to characterize the transcriptional responses to different mitochondrial perturbations in Saccharomyces cerevisiae. We examined respiratory-deficient petite cells and respiratory-competent wild-type cells treated with the inhibitors of oxidative phosphorylation antimycin, carbonyl cyanide m-chlorophenylhydrazone, or oligomycin. We show that respiratory deficiency, but not inhibition of mitochondrial ATP synthesis per se, induces a suite of genes associated with both peroxisomal activities and metabolite-restoration (anaplerotic) pathways that would mitigate the loss of a complete tricarboxylic acid cycle. The array data suggested, and direct microscopic observation of cells expressing a derivative of green fluorescent protein with a peroxisomal matrix-targeting signal confirmed, that respiratory deficiency dramatically induces peroxisome biogenesis. Transcript profiling of cells harboring null alleles of RTG1, RTG2, or RTG3, genes known to control signaling from mitochondria to the nucleus, suggests that there are multiple pathways of cross-talk between these organelles in yeast. Abstract from the companion methods paper Epstein, C.B.; Hale, W. IV; Butow, R.A.; Numerical Methods for Handling Uncertainty in Microarray Data -- an Example Analyzing Perturbed Mitochondrial Function in Yeast; Methods in Call Biology 66 (December 2000): Microarray technology is in an explosive growth phase, and several recent reviews have described the essentials of the method. Here, we discuss methodological issues related to the processing and evaluation of numerical results from microarray experiments, which have not been thoroughly treated elsewhere in the literature. We review our procedures for selecting the optimal scanner sensitivity, for computation of expression ratios, for handling low values and blank subtraction, and for normalization of data. We present a method for analysis of the naturally occurring internal redundancy of the yeast genome, enabling estimation of spot to spot reproducibility within a single array hybridization. Our method may be used to compute an index of reproducibility of replicate measurements, which can be applied both to comparisons between experiments done within a laboratory, as well as to comparisons between the array efforts of different laboratories using different methods and different array platforms. Finally, we illustrate the application of microarray technology to the study of how perturbations of mitochondrial function affect gene expression in yeast.

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