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
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

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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Copyright (c) 2006 by Wayne Rindone and the President and Fellows of Harvard University